tznurmin/tea_curated · Datasets at Hugging Face

attribution_text stringclasses 398 values	hash stringclasses 398 values	license stringclasses 1 value	license_url stringclasses 1 value	license_version stringclasses 1 value	ner_tags sequencelengths 28 417	tokens sequencelengths 28 417
Original work titled: 'Binding and Flip as Initial Steps for BP-100 Antimicrobial Actions' (Scientific Reports/Nature Publishing Group UK) by the following authors: Peter Park; Leandro R. Franco; Hernan Chaimovich; Kaline Coutinho; Iolanda M. Cuccovia; Filipe S. Lima DOI: 10.1038/s41598-019-45075-5	5388809896c7b2a9adf5d708f6ea4b08	CC-BY	http://creativecommons.org/licenses/by/4.0/	4.0	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]	[ "Introduction", "Cationic", "antimicrobial", "peptides", "(CAMPs)", "are", "short-length,", "amphiphilic,", "rich", "in", "basic", "residues", "of", "the", "innate", "immune", "system", "of", "complex", "organisms,", "serving", "as", "the", "first", "defense", "line", "against", "pathogens.", "CAMPs", "can", "potentially", "give", "rise", "to", "a", "new", "generation", "of", "drugs", "due", "to", "their", "broad", "spectrum", "of", "antimicrobial", "activity", "against", "bacteria,", "rare", "cases", "of", "the", "appearance", "of", "AMP-resistant", "bacteria,", "selectivity,", "and", "rapid", "effects.", "Due", "to", "their", "potential", "advantage", "as", "antimicrobials,", "new", "AMPs", "are", "increasingly", "being", "isolated", "or", "synthesized", "and", "their", "properties", "investigated.", "Although", "increasing", "evidence", "shows", "that", "some", "AMPs", "may", "also", "act", "intracellularly,", "inhibiting", "proteins", "1", ",", "nucleic", "acids", "1", "–", "4", "and", "cell-wall", "synthesis", "1", "–", "5", "and", "inducing", "cell", "apoptosis", "1", ",", "3", ",", "5", ",", "most", "of", "them", "kill", "cells", "by", "disturbing", "the", "membrane’s", "integrity", "1", ",", "2", ",", "6", ",", "7", ".", "Several", "CAMPs", "seem", "to", "disturb", "the", "membrane", "of", "cells", "by", "self-aggregation", "on", "the", "membrane", "and", "forming", "pores", "beyond", "a", "peptide/lipid", "(P/L)", "ratio", "threshold", "1", ",", "2", ".", "BP100", "(H-KKLFKKILKYL-NH", "2", "),", "is", "a", "hybrid", "CAMP", "synthesized", "by", "combinatorial", "chemistry", "involving", "parts", "of", "two", "natural", "AMPs,", "melittin,", "and", "cecropin", "A", "8", ".", "BP100", "shows", "high", "antimicrobial", "activity", "and", "selectivity", "against", "some", "Gram-negative", "bacteria,", "with", "a", "promising", "minimal", "inhibitory", "concentration", "ranging", "from", "2.5", "to", "5", "µM", "and", "low", "cytotoxicity", "against", "mammalian", "cells", "making", "this", "peptide", "an", "exciting", "candidate", "for", "therapeutic", "use", "8", ".", "BP100", "conformation", "and", "activity", "on", "model", "membranes", "have", "been", "extensively", "analyzed", "with", "experimental", "techniques", "9", "–", "13", ".", "BP100", "has", "a", "random", "coil", "conformation", "in", "solution", "and", "zwitterionic", "bilayers", "but", "acquires", "predominantly", "alpha-helical", "and", "amphipathic", "conformation", "in", "the", "presence", "of", "negatively", "charged", "membranes.", "BP100", "is", "highly", "mobile", "on", "the", "membrane", "surface", "and", "orients", "parallel", "in", "predominantly", "negatively", "charged", "vesicles", "9", ",", "10", "." ]
Original work titled: 'Binding and Flip as Initial Steps for BP-100 Antimicrobial Actions' (Scientific Reports/Nature Publishing Group UK) by the following authors: Peter Park; Leandro R. Franco; Hernan Chaimovich; Kaline Coutinho; Iolanda M. Cuccovia; Filipe S. Lima DOI: 10.1038/s41598-019-45075-5	5388809896c7b2a9adf5d708f6ea4b08	CC-BY	http://creativecommons.org/licenses/by/4.0/	4.0	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]	[ "CAMPs", "can", "potentially", "give", "rise", "to", "a", "new", "generation", "of", "drugs", "due", "to", "their", "broad", "spectrum", "of", "antimicrobial", "activity", "against", "bacteria,", "rare", "cases", "of", "the", "appearance", "of", "AMP-resistant", "bacteria,", "selectivity,", "and", "rapid", "effects.", "Due", "to", "their", "potential", "advantage", "as", "antimicrobials,", "new", "AMPs", "are", "increasingly", "being", "isolated", "or", "synthesized", "and", "their", "properties", "investigated.", "Although", "increasing", "evidence", "shows", "that", "some", "AMPs", "may", "also", "act", "intracellularly,", "inhibiting", "proteins", "1", ",", "nucleic", "acids", "1", "–", "4", "and", "cell-wall", "synthesis", "1", "–", "5", "and", "inducing", "cell", "apoptosis", "1", ",", "3", ",", "5", ",", "most", "of", "them", "kill", "cells", "by", "disturbing", "the", "membrane’s", "integrity", "1", ",", "2", ",", "6", ",", "7", ".", "Several", "CAMPs", "seem", "to", "disturb", "the", "membrane", "of", "cells", "by", "self-aggregation", "on", "the", "membrane", "and", "forming", "pores", "beyond", "a", "peptide/lipid", "(P/L)", "ratio", "threshold", "1", ",", "2", ".", "BP100", "(H-KKLFKKILKYL-NH", "2", "),", "is", "a", "hybrid", "CAMP", "synthesized", "by", "combinatorial", "chemistry", "involving", "parts", "of", "two", "natural", "AMPs,", "melittin,", "and", "cecropin", "A", "8", ".", "BP100", "shows", "high", "antimicrobial", "activity", "and", "selectivity", "against", "some", "Gram-negative", "bacteria,", "with", "a", "promising", "minimal", "inhibitory", "concentration", "ranging", "from", "2.5", "to", "5", "µM", "and", "low", "cytotoxicity", "against", "mammalian", "cells", "making", "this", "peptide", "an", "exciting", "candidate", "for", "therapeutic", "use", "8", ".", "BP100", "conformation", "and", "activity", "on", "model", "membranes", "have", "been", "extensively", "analyzed", "with", "experimental", "techniques", "9", "–", "13", ".", "BP100", "has", "a", "random", "coil", "conformation", "in", "solution", "and", "zwitterionic", "bilayers", "but", "acquires", "predominantly", "alpha-helical", "and", "amphipathic", "conformation", "in", "the", "presence", "of", "negatively", "charged", "membranes.", "BP100", "is", "highly", "mobile", "on", "the", "membrane", "surface", "and", "orients", "parallel", "in", "predominantly", "negatively", "charged", "vesicles", "9", ",", "10", ".", "BP100", "secondary", "structure", "formation", "and", "bacteria", "killing", "performance", "seem", "to", "be", "directly", "related", "to", "negative", "charge", "content", "in", "membranes,", "thus", "explaining", "its", "high", "selectivity", "towards", "negative", "bacterial", "membrane", "and", "low", "cytotoxicity", "against", "predominantly", "less", "negatively", "charged", "mammalian", "cell", "membranes", "11", ",", "14", ".", "Experimental", "approaches", "to", "investigate", "peptide/membrane", "interactions", "mainly", "focus", "macroscopic-averaged", "insight", "on", "a", "mesoscopic", "scale." ]
Original work titled: 'Binding and Flip as Initial Steps for BP-100 Antimicrobial Actions' (Scientific Reports/Nature Publishing Group UK) by the following authors: Peter Park; Leandro R. Franco; Hernan Chaimovich; Kaline Coutinho; Iolanda M. Cuccovia; Filipe S. Lima DOI: 10.1038/s41598-019-45075-5	5388809896c7b2a9adf5d708f6ea4b08	CC-BY	http://creativecommons.org/licenses/by/4.0/	4.0	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]	[ "BP100", "secondary", "structure", "formation", "and", "bacteria", "killing", "performance", "seem", "to", "be", "directly", "related", "to", "negative", "charge", "content", "in", "membranes,", "thus", "explaining", "its", "high", "selectivity", "towards", "negative", "bacterial", "membrane", "and", "low", "cytotoxicity", "against", "predominantly", "less", "negatively", "charged", "mammalian", "cell", "membranes", "11", ",", "14", ".", "Experimental", "approaches", "to", "investigate", "peptide/membrane", "interactions", "mainly", "focus", "macroscopic-averaged", "insight", "on", "a", "mesoscopic", "scale.", "A", "detailed", "description", "of", "peptide/membrane", "interactions", "at", "the", "atomic", "scale", "may", "help", "to", "gain", "information", "on", "CAMPs", "disruption", "mechanisms,", "permitting", "the", "rational", "design", "of", "new", "derivatives", "and,", "therefore,", "the", "better", "therapeutic", "use", "of", "these", "novel", "antimicrobials.", "Molecular", "Dynamics", "(MD)", "simulations", "provide", "atomic-level", "insights", "and", "have", "been", "widely", "used", "to", "study", "the", "interaction", "of", "AMPs", "with", "membranes", "15", "–", "18", ".", "MD", "simulations", "were", "also", "utilized", "to", "study", "BP100’s", "structure", "and", "activity:", "Wang", "Y.", "et", "al.", "17", "performed", "an", "8", "µs-long", "MD", "simulation", "of", "BP100", "in", "DMPC", "bilayer", "and", "found", "that", "BP100", "remained", "in", "the", "surface-bound-state", "inserting", "through", "its", "C-terminus.", "They", "also", "reported", "the", "unfolding", "of", "BP100", "N-terminus", "(Lys1", "and", "Lys2)", "after", "1.5", "µs,", "resulting", "in", "a", "tilt", "angle", "of", "97°", "and", "81%", "helicity", "10", ",", "17", ".", "In", "a", "study", "with", "Brownian", "Dynamics", "simulations", "with", "a", "coarse-grained", "peptide", "model,", "Alves", "et", "al.", "18", "simulated", "BP100", "confined", "in", "model", "membranes", "at", "293", "K", "for", "1", "µs", "each", "and", "reported", "the", "high", "stability", "of", "BP100", "pre-folded", "alpha", "helix", "and", "a", "threefold", "decrease", "in", "its", "lateral", "diffusion", "in", "POPC:", "POPG", "membranes", "relative", "to", "that", "in", "POPC", "membrane", "18", ".", "In", "this", "work", "we", "report", "simulations,", "in", "solution", "and", "membranes,", "extending", "for", "more", "than", "25", "µs", "of", "BP100", "and", "membranes", "of", "1,2-dipalmitoyl-sn-glycerol-3-phosphocholine", "(DPPC),", "1,2-dipalmitoyl-sn-glycerol-3-phosphoglycerol", "(DPPG),", "and", "DPPC:", "DPPG", "mixtures", "(1:1)." ]
Original work titled: 'Binding and Flip as Initial Steps for BP-100 Antimicrobial Actions' (Scientific Reports/Nature Publishing Group UK) by the following authors: Peter Park; Leandro R. Franco; Hernan Chaimovich; Kaline Coutinho; Iolanda M. Cuccovia; Filipe S. Lima DOI: 10.1038/s41598-019-45075-5	5388809896c7b2a9adf5d708f6ea4b08	CC-BY	http://creativecommons.org/licenses/by/4.0/	4.0	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]	[ "In", "this", "work", "we", "report", "simulations,", "in", "solution", "and", "membranes,", "extending", "for", "more", "than", "25", "µs", "of", "BP100", "and", "membranes", "of", "1,2-dipalmitoyl-sn-glycerol-3-phosphocholine", "(DPPC),", "1,2-dipalmitoyl-sn-glycerol-3-phosphoglycerol", "(DPPG),", "and", "DPPC:", "DPPG", "mixtures", "(1:1).", "We", "systematically", "investigated", "the", "dependence", "of", "BP100", "secondary", "structure", "on", "DPPG", "lipids", "which", "agrees", "with", "experimental", "findings", "11", ".", "We", "also", "analyzed", "the", "contribution", "of", "PG-containing", "lipid", "rafts", "on", "BP100", "conformation", "and", "behavior.", "In", "most", "simulations", "containing", "DPPG", "lipids,", "we", "observed", "the", "occurrence", "of", "a", "dynamic", "transition", "of", "the", "peptide", "adsorbed", "at", "the", "membrane", "interface,", "where", "the", "apolar", "facet", "of", "the", "BP100", "(Fig.", "1c", "),", "initially", "exposed", "to", "water,", "rotates", "toward", "the", "membrane", "interior,", "leaving", "the", "polar", "facet", "of", "the", "peptide", "exposed", "to", "water.", "This", "process,", "defined", "here", "as", "peptide", "flip,", "could", "be", "part", "of", "CAMPs", "primary", "antimicrobial", "mechanism.", "Constraining", "four", "residues", "of", "the", "peptide", "into", "an", "alpha", "helix", "turn,", "we", "observed", "that", "the", "unconstrained", "regions", "of", "the", "peptide", "rapidly", "acquired", "an", "alpha-helix", "conformation", "in", "DPPG-containing", "membranes,", "suggesting", "that", "the", "formation", "of", "these", "small", "alpha-helical", "nuclei", "in", "peptide/membrane", "interactions", "may", "be", "the", "initial", "step", "for", "the", "peptide", "insertion", "into", "the", "hydrophobic", "core", "of", "the", "membranes.", "Figure", "1", "BP100", "initial", "structures:", "random", "coil", "L", "-BP100", "(", "a", ")", "and", "alpha-helical", "α", "-BP100", "(", "b", ").", "Helical", "wheel", "projection", "(", "c", "),", "Lys5", "and", "Ile7", "were", "used", "as", "representative", "residues", "of", "polar", "and", "apolar", "moieties,", "respectively.", "In", "(", "d", ")", "DPPC", "(in", "blue)", "and", "DPPG", "(in", "yellow).", "Atom", "names", "are", "shown", "for", "peptide", "and", "lipids;", "they", "were", "used", "in", "our", "peptide-lipid", "pair", "analysis.", "Methods", "All", "simulations", "sets", "were", "assembled,", "carried", "out", "and", "analyzed", "using", "GROMACS", "5.0.2", "software", "package." ]
Original work titled: 'Binding and Flip as Initial Steps for BP-100 Antimicrobial Actions' (Scientific Reports/Nature Publishing Group UK) by the following authors: Peter Park; Leandro R. Franco; Hernan Chaimovich; Kaline Coutinho; Iolanda M. Cuccovia; Filipe S. Lima DOI: 10.1038/s41598-019-45075-5	5388809896c7b2a9adf5d708f6ea4b08	CC-BY	http://creativecommons.org/licenses/by/4.0/	4.0	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]	[ "Simulation", "sets", "Simulations", "Peptide/Lipid", "Waters/Lipid", "Time", "(ns)", "Bilayers", "DPPC", "0/128", "54", "860", "DPPG", "53", "1100", "PCPG-R", "0/[64/64]", "54", "1200", "PCPG-NR", "52", "1200", "Peptide", "in", "water", "L", "-BP100", "in", "water", "1/0", "—", "2000", "α", "-BP100", "in", "water", "—", "2850", "Peptide", "with", "bilayers", "L", "-BP100", "in", "DPPC", "1/128", "54", "1700", "α", "-BP100", "in", "DPPC", "54", "2000", "L", "-BP100", "in", "DPPG", "1/128", "53", "1700", "α", "-BP100", "in", "DPPG", "53", "2000", "L", "-BP100", "in", "PCPG-R", "1/[64/64]", "54", "1600", "α", "-BP100", "in", "PCPG-R", "54", "2000", "L", "-BP100", "in", "PCPG-NR", "1/[64/64]", "52", "1700", "α", "-BP100", "in", "PCPG-NR", "52", "2000", "Partially", "constrained", "peptide", "in", "DPPG", "α-", "BP100", "(res1–5)", "in", "DPPG", "1/128", "54", "600", "α-", "BP100", "(res4–8)", "in", "DPPG", "54", "600", "α-", "BP100", "(res7–11)", "in", "DPPG", "54", "600", "Lipid", "bilayers", "We", "used", "Slipids", "forcefield", "19", "parameters", "were", "chosen", "to", "simulate", "DPPC,", "DPPG,", "and", "DPPC/DPPG", "mixed", "bilayers.", "64-lipids-per-monolayer", "DPPC", "and", "DPPG", "pure", "membrane", "topologies", "were", "taken", "from", "the", "Slipids", "developer", "group", "website", "(http://www.fos.su.se/~sasha/Slipids/Downloads.html).", "Mixed", "bilayers", "of", "DPPC", "and", "DPPG", "containing", "32", "DPPCs", "and", "32", "DPPGs", "in", "each", "leaflet", "were", "constructed", "using", "the", "PACKMOL", "20", "software.", "One", "membrane", "was", "composed", "of", "randomly", "distributed", "lipids", "(PCPG-NR)", "on", "both", "leaflets", "and", "the", "other,", "a", "4", "×", "4", "DPPG", "raft", "was", "placed", "in", "the", "center", "of", "both", "monolayers", "(PCPG-R)", "and", "the", "remaining", "48", "lipids", "were", "randomly", "distributed", "(Fig.", "2", ")." ]
Original work titled: 'Binding and Flip as Initial Steps for BP-100 Antimicrobial Actions' (Scientific Reports/Nature Publishing Group UK) by the following authors: Peter Park; Leandro R. Franco; Hernan Chaimovich; Kaline Coutinho; Iolanda M. Cuccovia; Filipe S. Lima DOI: 10.1038/s41598-019-45075-5	5388809896c7b2a9adf5d708f6ea4b08	CC-BY	http://creativecommons.org/licenses/by/4.0/	4.0	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]	[ "The", "area", "per", "lipid", "and", "membrane", "thickness", "were", "calculated", "for", "all", "membranes", "and", "thNen", "compared", "with", "experimental", "data", "and", "those", "obtained", "by", "Slipids", "authors", "(Tables", "S1", "and", "S2", ").", "The", "last", "trajectory", "frames", "of", "the", "membrane", "simulations", "were", "used", "to", "build", "our", "peptide-lipid", "systems.", "Peptide-in-solution", "and", "peptide-lipid", "systems", "Following", "a", "study", "by", "Beauchamp", "et", "al.", "22", ",", "ff99sb-ildn-NMR", "force", "field", "was", "chosen", "to", "characterize", "BP100", "in", "our", "modeling", "due", "to", "its", "good", "performance", "in", "simulating", "peptides", "and", "proteins", "structures", "in", "TIP3P", "water", "when", "compared", "with", "NMR", "measurements.", "BP100", "(H-Lys-Lys-Leu-Phe-Lys-Lys-Ile-Leu-Lys-Tyr-Leu-NH", "2", ")", "has", "an", "amidated", "C-terminal", "and", "a", "+6", "charge", "at", "physiological", "pH,", "with", "all", "its", "Lysines", "and", "N-terminal", "amine", "protonated.", "To", "study", "secondary", "structure", "behavior", "of", "BP100", "both", "in", "solution", "and", "in", "bilayers,", "two", "initial", "BP100", "conformations", "were", "used:", "linear", "BP100", "(", "L", "-BP100)", "and", "alpha-helical", "BP100", "(", "α", "-BP100)", "(Fig.", "1", "a,b", ").", "In", "the", "peptide/water", "system,", "one", "peptide", "(", "α", "-BP100", "or", "L-BP100", "initial", "conformation)", "were", "simulated", "in", "a", "cubic", "box", "with", "3975", "TIP3P", "water", "molecules", "for", "more", "than", "1", "microsecond", "with", "its", "+6", "charges", "neutralized", "with", "6", "Cl", "−", "ions", "(Dang", "23", ").", "Simulations", "containing", "peptides", "with", "membranes", "had", "a", "peptide/lipid", "ratio", "of", "1/128", "and", "the", "peptide", "was", "initially", "positioned", "in", "parallel", "orientation", "with", "the", "membrane", "surface", "approximately", "2", "nm", "away.", "For", "the", "α", "-BP100,", "additionally,", "we", "tested", "two", "parallel", "orientations,", "where", "the", "polar", "amino", "acids", "were", "facing", "the", "membrane", "and", "a", "random", "orientation.", "For", "the", "perpendicular", "orientation", "we", "tested", "two", "ways", "with", "either", "the", "C-terminal", "or", "N-terminal", "facing", "the", "interface.", "For", "all", "these", "initial", "conditions,", "we", "obtained", "the", "same", "final", "location", "and", "orientation", "of", "the", "peptide", "that", "will", "be", "discussed", "in", "the", "results", "section." ]
Original work titled: 'Binding and Flip as Initial Steps for BP-100 Antimicrobial Actions' (Scientific Reports/Nature Publishing Group UK) by the following authors: Peter Park; Leandro R. Franco; Hernan Chaimovich; Kaline Coutinho; Iolanda M. Cuccovia; Filipe S. Lima DOI: 10.1038/s41598-019-45075-5	5388809896c7b2a9adf5d708f6ea4b08	CC-BY	http://creativecommons.org/licenses/by/4.0/	4.0	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]	[ "Atmospheric", "pressure", "of", "1", "bar", "was", "kept", "with", "the", "Berendsen", "barostat", "26", "and", "semi-isotropic", "pressure", "coupling", "was", "used", "for", "all", "systems.", "All", "bonds", "were", "constrained", "with", "LINCS", "27", "algorithm.", "Long-range", "electrostatic", "correction", "was", "treated", "by", "a", "Particle-mesh-Ewald", "method", "28", "with", "a", "real-space", "cut-off", "of", "1.5", "nm.", "van", "der", "Waals", "interactions", "were", "truncated", "at", "1.5", "nm", "distance", "with", "a", "switch", "function", "from", "1.4", "nm.", "Simulation", "analyses", "Lipid/peptide", "contacts", "For", "the", "computation", "of", "lipid", "contacts", "with", "BP100", "and", "pair", "frequency,", "we", "labeled", "some", "lipid(s)", "and", "BP100", "atoms", "as", "“polar”", "or", "“apolar”,", "based", "on", "charges.", "Then,", "the", "radial", "distribution", "function", "(RDF)", "between", "each", "pair", "of", "apolar", "(or", "polar)", "atoms", "of", "the", "lipids/BP100", "system", "were", "computed.", "The", "time", "window", "selected", "for", "computing", "these", "RDFs", "includes", "that", "of", "the", "membrane", "bound", "peptide", "250", "ns-before", "and", "250", "ns-after", "the", "peptide", "flip.", "The", "pairs", "with", "distinguishable", "RDF", "peaks", "and", "following", "minimum", "were", "used", "to", "analyze", "the", "number", "of", "polar", "and", "apolar", "contacts", "between", "lipids", "and", "peptide.", "A", "cutoff", "distance", "for", "each", "pair", "was", "defined", "from", "the", "position", "of", "the", "first", "minimum", "in", "the", "RDF", "curve,", "and", "a", "contact", "was", "defined", "as", "a", "pair", "of", "atoms", "at", "smaller", "distance", "than", "their", "corresponding", "cutoff", "distance.", "The", "simulations", "were", "analyzed", "and", "the", "total", "number", "of", "polar", "and", "apolar", "contacts", "as", "a", "function", "of", "time", "was", "obtained.", "Additionally,", "some", "polar", "and", "apolar", "pairs", "were", "analyzed", "individually.", "Peptide", "hydration", "The", "time", "evolution", "of", "the", "solvent", "shell", "surrounding", "the", "peptide", "in", "its", "α", "and", "L", "conformations", "in", "all", "simulated", "membranes", "was", "analyzed", "using", "the", "minimum", "distance", "distribution", "function", "(MDDF)", "29", "between", "the", "peptide", "and", "the", "water", "molecules,", "as", "well", "as", "the", "average", "number", "of", "water", "molecules", "N(r),", "within", "a", "distance", "r", "=", "0.5", "nm,", "named", "here", "as", "N(0.5).", "For", "comparison", "the", "MDDF", "of", "BP100", "in", "water", "was", "used", "to", "define", "the", "bulk", "water", "hydration", "shell", "at", "the", "same", "distance." ]
Original work titled: 'Binding and Flip as Initial Steps for BP-100 Antimicrobial Actions' (Scientific Reports/Nature Publishing Group UK) by the following authors: Peter Park; Leandro R. Franco; Hernan Chaimovich; Kaline Coutinho; Iolanda M. Cuccovia; Filipe S. Lima DOI: 10.1038/s41598-019-45075-5	5388809896c7b2a9adf5d708f6ea4b08	CC-BY	http://creativecommons.org/licenses/by/4.0/	4.0	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]	[ "A", "cutoff", "distance", "for", "each", "pair", "was", "defined", "from", "the", "position", "of", "the", "first", "minimum", "in", "the", "RDF", "curve,", "and", "a", "contact", "was", "defined", "as", "a", "pair", "of", "atoms", "at", "smaller", "distance", "than", "their", "corresponding", "cutoff", "distance.", "The", "simulations", "were", "analyzed", "and", "the", "total", "number", "of", "polar", "and", "apolar", "contacts", "as", "a", "function", "of", "time", "was", "obtained.", "Additionally,", "some", "polar", "and", "apolar", "pairs", "were", "analyzed", "individually.", "Peptide", "hydration", "The", "time", "evolution", "of", "the", "solvent", "shell", "surrounding", "the", "peptide", "in", "its", "α", "and", "L", "conformations", "in", "all", "simulated", "membranes", "was", "analyzed", "using", "the", "minimum", "distance", "distribution", "function", "(MDDF)", "29", "between", "the", "peptide", "and", "the", "water", "molecules,", "as", "well", "as", "the", "average", "number", "of", "water", "molecules", "N(r),", "within", "a", "distance", "r", "=", "0.5", "nm,", "named", "here", "as", "N(0.5).", "For", "comparison", "the", "MDDF", "of", "BP100", "in", "water", "was", "used", "to", "define", "the", "bulk", "water", "hydration", "shell", "at", "the", "same", "distance.", "Results", "The", "17", "sets", "of", "simulations", "(Table", "1", ")", "were", "run", "for", "more", "than", "25", "µs", "of", "simulation", "time,", "and", "each", "unconstrained", "peptide/membrane", "simulation", "had", "at", "least", "1.6", "µs", "of", "simulation.", "After", "comparing", "the", "simulated", "membrane", "properties", "with", "experimental", "and", "other", "computational", "studies", "(Tables", "S1", "and", "S2", "),", "we", "systematically", "analyzed", "the", "peptide", "conformation", "in", "solution", "and", "on", "bilayers,", "peptide", "trajectory,", "and", "dynamics", "on", "membranes", "and", "the", "effect", "of", "BP100", "on", "model", "bilayers.", "In", "the", "following", "sections,", "we", "describe", "our", "results.", "Secondary", "structure", "Peptide", "in", "solution", "To", "study", "BP100", "secondary", "structure", "in", "water,", "we", "did", "simulations", "for", "more", "than", "2", "µs", "with", "both", "α-BP100", "and", "L-BP100", "initial", "conformations.", "Figure", "4", "shows", "that", "BP100", "conformation", "in", "solution", "was,", "predominantly,", "random", "coil.", "The", "peptide", "lost", "the", "initial", "alpha", "helix", "conformation", "in", "approximately", "40", "ns", "when", "starting", "with", "an", "alpha-helix", "configuration", "and", "occasionally", "formed", "an", "alpha-helix", "turn", "in", "the", "5–9", "residue", "region", "(Fig.", "4a", ").", "For", "L-BP100", "in", "solution,", "we", "observed", "a", "similar", "pattern", "(Fig.", "4b", ").", "Circular", "Dichroism", "(CD)", "shows", "that", "BP100", "is", "random", "in", "solution", "10", ",", "11", ",", "30", ",", "and", "our", "simulations", "reproduced", "these", "data." ]
Original work titled: 'Binding and Flip as Initial Steps for BP-100 Antimicrobial Actions' (Scientific Reports/Nature Publishing Group UK) by the following authors: Peter Park; Leandro R. Franco; Hernan Chaimovich; Kaline Coutinho; Iolanda M. Cuccovia; Filipe S. Lima DOI: 10.1038/s41598-019-45075-5	5388809896c7b2a9adf5d708f6ea4b08	CC-BY	http://creativecommons.org/licenses/by/4.0/	4.0	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]	[ "4a", ").", "For", "L-BP100", "in", "solution,", "we", "observed", "a", "similar", "pattern", "(Fig.", "4b", ").", "Circular", "Dichroism", "(CD)", "shows", "that", "BP100", "is", "random", "in", "solution", "10", ",", "11", ",", "30", ",", "and", "our", "simulations", "reproduced", "these", "data.", "Figure", "4", "Secondary", "structure", "analyses", "graphs", "of", "α", "-BP100", "(", "a", ")", "and", "L", "-BP100", "(", "b", ")", "in", "solution.", "In", "both", "cases,", "the", "peptide", "shows", "predominance", "in", "random", "coil", "structure", "(orange)", "with", "occasional", "formation", "of", "1", "alpha", "helix", "turn", "(blue)", "in", "residues", "5", "to", "9.", "Peptide", "in", "bilayers", "BP100", "conformation,", "antimicrobial", "activity,", "and", "PG", "content", "are", "related", "11", ".", "We", "simulated", "α-BP100", "and", "L-BP100", "on", "DPPC,", "DPPG,", "PCPG-R,", "and", "PCPG-NR", "at", "323", "K,", "above", "DPPG", "and", "DPPC", "transition", "temperatures.", "In", "all", "cases,", "the", "peptide", "was", "rapidly", "adsorbed", "on", "the", "membranes", "and", "diffused", "laterally.", "Figure", "5", "shows", "that", "the", "BP100", "alpha-helical", "conformation", "was", "proportional", "to", "PG", "content,", "as", "the", "alpha-helix", "percentage", "in", "DPPC", "is", "considerably", "smaller", "than", "that", "observed", "in", "DPPG-containing", "membranes.", "Alpha-helix", "formed", "in", "the", "5", "to", "9", "residues", "region", "(Lys-Lys-Ile-Leu-Lys)", "was", "highly", "stable", "in", "all", "simulations.", "Figure", "5", "Secondary", "structure", "analyses", "of", "α", "-BP100", "in", "DPPC", "(", "a", "),", "DPPG", "(", "b", "),", "PCPG-R", "(", "c", ")", "and", "PCPG-NR", "(", "d", ").", "In", "DPPC,", "α-BP100", "alpha-helix", "conformation", "reached", "a", "plateau", "at", "38%", "helicity", "throughout", "the", "simulation,", "being", "relatively", "less", "stable", "than", "α-BP100", "in", "bilayers", "containing", "DPPG,", "where", "a", "higher", "propensity", "of", "maintaining", "its", "conformation", "was", "observed.", "For", "pure", "DPPG", "(Fig.", "5b", ")", "we", "found", "73%", "(8", "out", "of", "11", "residues),", "and", "for", "both", "PCPG", "(1:1)", "membranes", "we", "report", "54%", "(6", "out", "of", "11)", "of", "helicity", "(Fig.", "5c,d", ")." ]
Original work titled: 'Binding and Flip as Initial Steps for BP-100 Antimicrobial Actions' (Scientific Reports/Nature Publishing Group UK) by the following authors: Peter Park; Leandro R. Franco; Hernan Chaimovich; Kaline Coutinho; Iolanda M. Cuccovia; Filipe S. Lima DOI: 10.1038/s41598-019-45075-5	5388809896c7b2a9adf5d708f6ea4b08	CC-BY	http://creativecommons.org/licenses/by/4.0/	4.0	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]	[ "5", ").", "This", "secondary", "structure", "pattern", "led", "us", "to", "suggest", "that", "the", "residues", "5", "to", "9", "are", "related", "to", "helix", "nucleation,", "in", "which", "the", "formation", "of", "this", "helix", "core", "could", "be", "the", "first", "step", "in", "the", "AMP", "actions.", "Following", "this", "assumption,", "we", "tested", "three", "conformations", "with", "α-BP100", "torsionally", "constrained", "in", "three", "regions:", "res1–5,", "res4–8,", "res7–11", "(Fig.", "3", ")", "and", "simulated", "with", "pure", "DPPG", "membranes.", "Figure", "6", "shows", "the", "evolution", "of", "the", "secondary", "structure", "in", "each", "simulation.", "Figure", "6", "Secondary", "structure", "analyses", "graphs", "of", "BP100", "in", "DPPG", "with", "one", "turn", "constraints", "on", "res1–5", "(", "a", "),", "res", "4–8", "(", "b", ")", "and", "res7–11", "(", "c", ").", "α-BP100", "with", "constraints", "on", "residues", "1–5", "(Lys-Lys-Leu-Phe-Lys)", "acquired", "identical", "helicity", "(73%)", "to", "α-BP100", "with", "no", "constraints", "at", "the", "same", "conditions", "(Fig.", "5b", "),", "after", "50", "ns", "of", "simulation", "(Fig.", "6a", "),", "with", "a", "helix", "spanning", "from", "Lys2", "to", "Lys9", "(Fig.", "6a", ").", "Constraints", "on", "residues", "4–8", "(Phe-Lys-Lys-Ile-Leu)", "showed", "an", "overall", "52%", "of", "helicity", "(Fig.", "6b", "),", "with", "a", "helix", "spanning", "from", "Phe4", "to", "Lys9", "(Fig.", "6b", ").", "Constraints", "on", "residues", "7–11", "(Ile-Leu-Lys-Tyr-Leu)", "did", "not", "affect", "the", "rest", "of", "the", "peptide", "conformation", "(Fig.", "6c", ")", "in", "600", "ns", "of", "simulation.", "Peptide", "flip", "Simulation", "trajectories", "analyses", "(Fig.", "7", ")", "revealed", "that", "the", "peptide", "in", "alpha-helix", "conformation", "initially", "adsorbed", "at", "the", "DPPG-containing", "membranes", "interface", "with", "its", "hydrophilic", "facet", "in", "contact", "with", "the", "membrane,", "leaving", "the", "hydrophobic", "facet", "exposed", "to", "water.", "We", "observed", "that", "the", "alpha-helix", "rotated,", "inserting", "the", "hydrophobic", "facet", "into", "the", "hydrophobic", "region", "of", "the", "membrane.", "We", "define", "this", "dynamic", "phenomenon,", "observed", "in", "our", "simulations,", "as", "peptide", "flip." ]
Original work titled: 'Binding and Flip as Initial Steps for BP-100 Antimicrobial Actions' (Scientific Reports/Nature Publishing Group UK) by the following authors: Peter Park; Leandro R. Franco; Hernan Chaimovich; Kaline Coutinho; Iolanda M. Cuccovia; Filipe S. Lima DOI: 10.1038/s41598-019-45075-5	5388809896c7b2a9adf5d708f6ea4b08	CC-BY	http://creativecommons.org/licenses/by/4.0/	4.0	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]	[ "Peptide", "flip", "was", "also", "observed", "in", "α", "-BP100", "in", "DPPC,", "α", "-BP100", "in", "PCPG-R,", "and", "α", "-BP100", "res(1–5)", "in", "DPPG", "simulations.", "The", "peptide", "flip", "caused", "dehydration", "(Fig.", "8", ").", "When", "in", "contact", "with", "membranes,", "depending", "on", "the", "secondary", "structure", "of", "the", "peptide", "and", "the", "lipid", "nature,", "the", "hydration", "of", "the", "peptide", "was", "slightly", "different.", "However,", "when", "the", "peptide", "flip", "took", "place,", "its", "hydration", "was", "drastically", "altered.", "Figure", "8", "Average", "number", "of", "water", "molecules", "up", "to", "a", "distance", "of", "0.5", "nm,", "N(0.5),", "obtained", "from", "the", "minimum-distance", "distribution", "function", "(MDDF),", "between", "L-BP100", "(", "a", ")", "and", "α", "-BP100", "(", "b", ")", "and", "water", "molecules.", "Vertical", "lines", "indicate", "when", "peptide", "flip", "occurred.", "In", "the", "peptide/membrane", "simulations", "with", "L-BP100", "as", "a", "starting", "configuration", "(Fig.", "8a", "),", "no", "significant", "change", "in", "the", "number", "of", "water", "molecules", "surrounding", "the", "peptide", "was", "observed", "in", "comparison", "the", "150", "obtained", "in", "the", "bulk", "aqueous", "solution.", "In", "the", "last", "500", "ns", "of", "simulation,", "N(0.5)", "was", "approximately", "178", "±", "11", "in", "DPPC,", "145", "±", "7", "in", "DPPG,", "145", "±", "13", "in", "PCPG-NR,", "and", "148", "±", "3", "in", "PCPG-R.", "No", "peptide", "flip", "was", "detected", "in", "the", "trajectories", "for", "those", "simulations.", "However,", "in", "the", "peptide/membrane", "simulations", "with", "α-BP100", "as", "a", "starting", "configuration", "(Fig.", "8b", "),", "N", "(0.5)", "lowered", "in", "DPPC", "(starting", "at", "~700", "ns),", "DPPG", "(~1500", "ns)", "and", "PCPG-R", "(~390", "ns).", "Alongside", "with", "dehydration,", "a", "peptide-flip", "was", "observed", "in", "DPPG", "and", "PCPG-R.", "For", "the", "α-", "BP100", "in", "DPPC", "simulation,", "we", "observed", "a", "semi-flip,", "as", "the", "peptide", "alpha-helical", "conformation", "was", "only", "38%", "(Fig.", "5a", "),", "suggesting", "that", "the", "peptide", "overall", "polar/apolar", "segregation", "(Fig.", "2c", ")", "was", "lost.", "The", "peptide", "flip", "transition", "time", "varied", "from", "100", "to", "400", "ns." ]
Original work titled: 'Binding and Flip as Initial Steps for BP-100 Antimicrobial Actions' (Scientific Reports/Nature Publishing Group UK) by the following authors: Peter Park; Leandro R. Franco; Hernan Chaimovich; Kaline Coutinho; Iolanda M. Cuccovia; Filipe S. Lima DOI: 10.1038/s41598-019-45075-5	5388809896c7b2a9adf5d708f6ea4b08	CC-BY	http://creativecommons.org/licenses/by/4.0/	4.0	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]	[ "Alongside", "with", "dehydration,", "a", "peptide-flip", "was", "observed", "in", "DPPG", "and", "PCPG-R.", "For", "the", "α-", "BP100", "in", "DPPC", "simulation,", "we", "observed", "a", "semi-flip,", "as", "the", "peptide", "alpha-helical", "conformation", "was", "only", "38%", "(Fig.", "5a", "),", "suggesting", "that", "the", "peptide", "overall", "polar/apolar", "segregation", "(Fig.", "2c", ")", "was", "lost.", "The", "peptide", "flip", "transition", "time", "varied", "from", "100", "to", "400", "ns.", "During", "the", "peptide-flip,", "in", "the", "simulations", "of", "α-BP100", "in", "DPPG", "and", "PCPG-R,", "the", "mean", "number", "N(0.5)", "was", "reduced", "from", "147", "±", "5", "and", "142", "±", "7", "to", "76", "±", "4", "and", "75", "±", "4,", "respectively.", "These", "represent", "on", "average", "a", "reduction", "of", "approximately", "48%", "in", "the", "number", "of", "water", "molecules", "in", "the", "hydration", "shell", "of", "α-BP100.", "In", "DPPC,", "we", "detected", "a", "smaller", "decrease", "in", "the", "hydration", "of", "α-BP100,", "around", "45%", "(from", "172", "±", "8", "to", "94", "±", "2),", "having", "around", "20", "water", "molecules", "more", "after", "the", "semi-flip.", "Figure", "9", "shows", "the", "density", "profile", "before", "and", "after", "peptide", "flip", "for", "α-BP100", "in", "DPPG", "and", "PCPG-R.", "We", "chose", "residues", "Lys5", "and", "Ile7", "to", "illustrate", "the", "changes", "in", "the", "mean", "position", "of", "hydrophobic", "and", "hydrophilic", "residues", "with", "respect", "to", "the", "membrane", "due", "to", "the", "peptide", "flip.", "These", "residues", "are", "polar", "and", "apolar,", "respectively,", "and", "located", "opposite", "to", "each", "other", "when", "in", "an", "alpha-helix", "conformation", "(Fig.", "2c", ").", "Trajectory", "visualization", "and", "density", "profile", "(Figs", "7", "and", "9", ")", "clearly", "show", "the", "distinct", "orientation", "in", "BP100", "hydrophobic", "facet", "before", "and", "after", "peptide", "flip.", "During", "the", "initial", "phase", "of", "approaching", "towards", "the", "membrane,", "BP100", "polar", "side", "faces", "the", "membrane", "with", "its", "N-terminal", "residues", "(Lys1", "and", "Lys2)", "interacting", "with", "the", "bilayer", "headgroups.", "After", "the", "flip,", "the", "apolar", "residues", "facet", "turns", "to", "the", "membrane,", "and", "simultaneously", "inserts", "into", "the", "bilayer,", "below", "the", "carbonyl", "carbons", "(C31)", "of", "the", "lipids", "(Fig.", "9", ").", "Figure", "9", "Peptide", "flip", "observed", "through", "number", "density", "analysis." ]
Original work titled: 'Binding and Flip as Initial Steps for BP-100 Antimicrobial Actions' (Scientific Reports/Nature Publishing Group UK) by the following authors: Peter Park; Leandro R. Franco; Hernan Chaimovich; Kaline Coutinho; Iolanda M. Cuccovia; Filipe S. Lima DOI: 10.1038/s41598-019-45075-5	5388809896c7b2a9adf5d708f6ea4b08	CC-BY	http://creativecommons.org/licenses/by/4.0/	4.0	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]	[ "After", "the", "flip,", "the", "apolar", "residues", "facet", "turns", "to", "the", "membrane,", "and", "simultaneously", "inserts", "into", "the", "bilayer,", "below", "the", "carbonyl", "carbons", "(C31)", "of", "the", "lipids", "(Fig.", "9", ").", "Figure", "9", "Peptide", "flip", "observed", "through", "number", "density", "analysis.", "(", "a", "and", "b", ")", "show", "respectively", "before", "and", "after", "the", "flip", "in", "α", "-BP100", "in", "DPPG", "simulation;", "c)", "and", "d)", "demonstrate", "the", "flip", "for", "α", "-BP100", "in", "PCPG-R", "simulation.", "Lys5", "represents", "the", "polar", "side", "of", "BP100", "and", "Ile7,", "the", "apolar", "facet", "(Fig.", "2c", ").", "OC3", "(DPPG", "head", "group", "further", "out", "glycerol", "Oxygen),", "N", "chol", "(DPPC", "head", "group", "choline", "Nitrogen),", "P", "(Phosphorus)", "and", "C31", "(first", "carbon", "from", "sn-1", "acyl", "chain)", "are", "shown", "to", "display", "BP100", "insertion", "into", "the", "bilayer", "after", "the", "flip.", "Peptide", "flip", "was", "not", "observed", "in", "α-BP100", "in", "PCPG-NR,", "where", "DPPG", "lipids", "were", "initially", "scattered", "randomly.", "PG", "content", "might", "be", "related", "to", "the", "occurrence", "of", "the", "flip,", "but", "also,", "the", "PG", "content", "in", "the", "vicinity", "of", "BP100.", "Several", "studies", "suggest", "membrane-active", "peptides", "cause", "anionic", "lipid", "clustering,", "or", "subdomain", "formation,", "upon", "binding", "to", "bilayers", "containing", "neutral", "and", "charged", "phospholipids", "35", "–", "37", ".", "The", "same", "mechanism", "could", "be", "involved", "in", "BP100/bilayers", "interactions.", "Lipid", "clustering", "The", "distribution", "of", "the", "lipids", "in", "the", "vicinity", "of", "BP100", "was", "evaluated", "by", "computing", "the", "total", "number", "of", "lipids", "in", "contact", "with", "α-BP100", "as", "a", "function", "of", "time", "(Fig.", "S5", "),", "the", "time-averaged", "values", "(Table", "2", ",", "Fig.", "10", "),", "and", "the", "lipid", "raft", "size", "distribution", "(Fig.", "S6", ").", "Table", "2", "Average", "number", "of", "lipids", "in", "contact", "with", "BP100", "in", "simulations", "using", "α", "-BP100", "as", "the", "peptide", "starting", "configuration,", "except", "α", "-BP100", "(1–5),", "which", "had", "permanent", "constraints", "on", "residues", "1", "to", "5.", "Standard", "deviations", "are", "shown", "in", "parenthesis." ]
Original work titled: 'Binding and Flip as Initial Steps for BP-100 Antimicrobial Actions' (Scientific Reports/Nature Publishing Group UK) by the following authors: Peter Park; Leandro R. Franco; Hernan Chaimovich; Kaline Coutinho; Iolanda M. Cuccovia; Filipe S. Lima DOI: 10.1038/s41598-019-45075-5	5388809896c7b2a9adf5d708f6ea4b08	CC-BY	http://creativecommons.org/licenses/by/4.0/	4.0	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]	[ "Average", "Number", "of", "Lipids", "in", "Contact", "with", "BP100", "Simulation", "Lipid", "in", "Contact", "Average", "α", "-BP100", "in", "DPPC", "DPPC", "10.7", "(±2.6)", "α", "-BP100", "in", "DPPG", "DPPG", "13.1", "(±1.4)", "α", "-BP100", "(1–5)", "in", "DPPG", "DPPG", "13.5", "(±1.9)", "α", "-BP100", "in", "PCPG-R", "Total", "12.3", "(±1.7)", "DPPC", "3.6", "(±1.5)", "DPPG", "8.7", "(±1.2)", "α", "-BP100", "in", "PCPG-NR", "Total", "11.0", "(±1.7)", "DPPC", "2.7", "(±1.3)", "DPPG", "8.3", "(±1.6)", "Figure", "10", "Average", "Number", "of", "DPPCs", "(", "a", ")", "and", "DPPGs", "(", "b", ")", "in", "contact", "with", "BP100", "analyzed", "for", "all", "constraint-free", "simulations", "containing", "BP100", "in", "an", "initially", "alpha", "helical", "conformation", "in", "DPPC,", "DPPG,", "PCPG-R", "and", "PCPG-NR", "membranes.", "Vertical", "lines", "represent", "the", "average", "time", "where", "peptide", "flip", "was", "observed.", "Standard", "deviation", "error", "bars", "are", "represented", "as", "fillings.", "α-BP100", "in", "DPPC", "simulation", "had", "on", "average", "10.7", "peptide/lipid", "contacts", "(Table", "2", ")", "and", "a", "steady", "increase", "in", "the", "number", "of", "contact", "lipids", "(Figs", "10b", "and", "S5a", ").", "This", "increase", "is", "due", "to", "the", "peptide", "losing", "its", "alpha-helical", "conformation", "(Fig.", "5a", "),", "expanding", "the", "available", "peptide", "interaction", "area", "with", "the", "membrane.", "Lipid", "raft", "size", "distribution", "also", "shows", "a", "broader", "distribution", "of", "DPPC", "raft", "size,", "supporting", "this", "observation", "(Fig.", "S6a", ").", "A", "semi-peptide", "flip", "was", "observed", "at", "~700", "ns", "of", "simulation", "and,", "concomitantly,", "while", "BP100", "inserts", "into", "the", "bilayer", "as", "the", "density", "profile", "shows", "(Fig.", "S4a,b", "),", "the", "number", "of", "DPPCs", "in", "contact", "with", "BP100", "increased", "(Fig.", "S5a", ")." ]
Original work titled: 'Binding and Flip as Initial Steps for BP-100 Antimicrobial Actions' (Scientific Reports/Nature Publishing Group UK) by the following authors: Peter Park; Leandro R. Franco; Hernan Chaimovich; Kaline Coutinho; Iolanda M. Cuccovia; Filipe S. Lima DOI: 10.1038/s41598-019-45075-5	5388809896c7b2a9adf5d708f6ea4b08	CC-BY	http://creativecommons.org/licenses/by/4.0/	4.0	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]	[ "S5a", ").", "α-BP100", "in", "DPPG", "simulation", "shows", "on", "average", "13.1", "DPPGs", "in", "close", "contact", "with", "the", "peptide", "(Table", "2", ").", "The", "number", "of", "DPPGs", "in", "contact", "rose", "after", "the", "flip,", "approximately", "in", "1500", "ns", "of", "simulation", "(Figs", "10a", "and", "S5b", ")", "and", "concurrently,", "BP100", "inserted", "deeply", "into", "the", "membrane", "(Fig.", "7a,b", ").", "Constrained", "α-BP100", "(res1–5)", "in", "DPPG,", "which", "showed", "identical", "alpha-helix", "content", "with", "α-BP100", "in", "DPPG", "(73%,", "Figs", "5b", "and", "6a", "),", "not", "only", "exhibits", "peptide", "flip", "in", "approximately", "300", "ns", "of", "simulation", "but", "also", "has,", "on", "average,", "13.5", "DPPGs", "in", "contact", "with", "BP100", "(Table", "2", ").", "In", "the", "simulation", "with", "α-BP100", "in", "PCPG-NR,", "the", "number", "of", "DPPG", "in", "contact", "with", "the", "peptide", "showed", "a", "slight", "increase", "(Fig.", "10b", "),", "reaching", "the", "average", "value", "observed", "in", "the", "simulation", "with", "PCPG-R", "(Table", "2", ").", "Also,", "lipid", "raft", "size", "probability", "analysis", "(Fig.", "S6d", ")", "showed", "a", "narrower", "peak", "distribution", "for", "DPPGs", "in", "contact", "with", "BP100", "in", "PCPG-R", "system,", "compared", "to", "PCPG-NR", "(Fig.", "S6e", "),", "indicating", "that", "DPPG", "lipid", "raft", "size", "was", "stable.", "Peptide", "flip", "was", "observed", "in", "the", "PCPG-R", "set", "after", "~390", "ns", "of", "simulation", "and", "no", "significant", "variation", "of", "the", "number", "of", "DPPG", "in", "contact", "with", "peptide", "was", "observed.", "Polar", "and", "apolar", "interaction", "analysis", "Peptide", "contact", "analysis", "revealed", "the", "increase", "of", "lipid/peptide", "contacts", "after", "peptide", "flip", "and", "DPPG", "clustering", "on", "PCPG", "membranes.", "We", "analyzed", "the", "nature", "of", "the", "intermolecular", "interactions", "that", "determine", "peptide-membrane", "interactions", "throughout", "the", "simulations.", "We", "calculated", "the", "number", "of", "polar", "and", "apolar", "pair", "contacts", "between", "peptide", "atoms", "and", "membrane", "atoms", "(Figs", "S7", "–", "S13", ").", "Using", "α-BP100", "in", "PCPG-R", "system", "as", "an", "example,", "Fig.", "11", "shows", "the", "sum", "of", "the", "10", "most", "frequent", "apolar/polar", "pairs", "between", "BP100", "with", "DPPC", "and", "DPPG." ]
Original work titled: 'Binding and Flip as Initial Steps for BP-100 Antimicrobial Actions' (Scientific Reports/Nature Publishing Group UK) by the following authors: Peter Park; Leandro R. Franco; Hernan Chaimovich; Kaline Coutinho; Iolanda M. Cuccovia; Filipe S. Lima DOI: 10.1038/s41598-019-45075-5	5388809896c7b2a9adf5d708f6ea4b08	CC-BY	http://creativecommons.org/licenses/by/4.0/	4.0	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]	[ "Figure", "11", "BP100", "pair", "occurrence", "with", "DPPC", "(", "a", ")", "and", "DPPG", "(", "b", ")", "for", "α", "-BP100", "in", "PCPG-R", "simulation.", "Graphs", "show", "the", "sum", "of", "the", "ten", "most", "frequent", "apolar/polar", "pairs", "during", "the", "simulation.", "Pairs", "were", "calculated", "using", "the", "monolayer", "facing", "the", "peptide.", "Green", "vertical", "lines", "indicate", "when", "peptide", "flip", "occurred", "(circa", "390", "ns).", "The", "total", "number", "of", "pairs,", "regardless", "if", "it", "is", "polar", "or", "apolar,", "between", "BP100", "and", "DPPG", "is", "higher", "than", "that", "with", "DPPC", "(Fig.", "11", "),", "which", "directly", "reflects", "on", "the", "number", "of", "lipids", "in", "contact", "with", "BP100", "(Fig.", "10", ").", "During", "the", "initial", "approach", "of", "the", "peptide", "towards", "the", "bilayer,", "polar", "interactions", "between", "charged", "Lysines", "and", "DPPG", "headgroup", "dominate", "the", "interaction", "(Figs", "11", "b,", "S9", ",", "S10", ",", "S12", "and", "S13", ").", "The", "primary", "interaction", "was", "between", "positively", "charged", "(+1)", "Lysine", "side", "chain", "amino", "group", "(NZ)", "and", "DPPG", "head", "phosphoglycerol", "group", "oxygens", "(OC2,", "OC3),", "even", "after", "peptide", "flip", "(Figs", "S9", ",", "S10", ",", "S12", "and", "S13", ").", "Before", "the", "peptide", "flip,", "the", "number", "of", "polar", "contacts", "is", "higher", "than", "the", "apolar", "contacts", "for", "DPPG/BP100.", "As", "the", "peptide", "starts", "to", "flip,", "the", "number", "of", "apolar", "contacts", "increase,", "while", "the", "polar", "contacts", "decrease.", "After", "the", "peptide", "flip", "is", "completed,", "apolar", "contacts", "are", "as", "numerous", "as", "the", "polar", "contacts", "(Fig.", "11a,b", "and", "S7–10,13", ").", "Also,", "after", "the", "flip,", "apolar", "contacts", "between", "BP100", "and", "DPPG", "were", "more", "frequent", "than", "with", "DPPC", "(Fig.", "11b", ").", "The", "higher", "peptide/DPPG", "apolar", "contact", "frequency", "after", "the", "flip", "is", "also", "observed", "for", "other", "simulations", "with", "peptide", "flip", "(Figs", "S7", "–", "10", ",", "13).", "Discussion", "Peptide", "secondary", "structure", "CD", "spectra", "of", "BP100", "in", "solution", "and", "POPC", "LUVs", "show", "no", "secondary", "structure", "10", ",", "11", ",", "30", "Our", "simulations", "with", "BP100", "in", "solution,", "and", "DPPC", "membrane", "exhibited", "the", "same", "pattern." ]
Original work titled: 'Binding and Flip as Initial Steps for BP-100 Antimicrobial Actions' (Scientific Reports/Nature Publishing Group UK) by the following authors: Peter Park; Leandro R. Franco; Hernan Chaimovich; Kaline Coutinho; Iolanda M. Cuccovia; Filipe S. Lima DOI: 10.1038/s41598-019-45075-5	5388809896c7b2a9adf5d708f6ea4b08	CC-BY	http://creativecommons.org/licenses/by/4.0/	4.0	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]	[ "The", "primary", "interaction", "was", "between", "positively", "charged", "(+1)", "Lysine", "side", "chain", "amino", "group", "(NZ)", "and", "DPPG", "head", "phosphoglycerol", "group", "oxygens", "(OC2,", "OC3),", "even", "after", "peptide", "flip", "(Figs", "S9", ",", "S10", ",", "S12", "and", "S13", ").", "Before", "the", "peptide", "flip,", "the", "number", "of", "polar", "contacts", "is", "higher", "than", "the", "apolar", "contacts", "for", "DPPG/BP100.", "As", "the", "peptide", "starts", "to", "flip,", "the", "number", "of", "apolar", "contacts", "increase,", "while", "the", "polar", "contacts", "decrease.", "After", "the", "peptide", "flip", "is", "completed,", "apolar", "contacts", "are", "as", "numerous", "as", "the", "polar", "contacts", "(Fig.", "11a,b", "and", "S7–10,13", ").", "Also,", "after", "the", "flip,", "apolar", "contacts", "between", "BP100", "and", "DPPG", "were", "more", "frequent", "than", "with", "DPPC", "(Fig.", "11b", ").", "The", "higher", "peptide/DPPG", "apolar", "contact", "frequency", "after", "the", "flip", "is", "also", "observed", "for", "other", "simulations", "with", "peptide", "flip", "(Figs", "S7", "–", "10", ",", "13).", "Discussion", "Peptide", "secondary", "structure", "CD", "spectra", "of", "BP100", "in", "solution", "and", "POPC", "LUVs", "show", "no", "secondary", "structure", "10", ",", "11", ",", "30", "Our", "simulations", "with", "BP100", "in", "solution,", "and", "DPPC", "membrane", "exhibited", "the", "same", "pattern.", "α-BP100", "and", "L-BP100", "in", "solution", "showed", "similar", "behavior,", "with", "a", "prevalence", "of", "random", "conformation", "(Fig.", "4", ").", "In", "a", "related", "MD", "study", "of", "AMPs", "interacting", "with", "membranes", "17", ",", "an", "8", "µs-long", "all-atom", "MD", "simulation", "of", "BP100", "in", "DMPC", "at", "35◽", "the", "authors", "reported", "a", "full", "helix", "length", "during", "1.5", "µs", "and", "a", "subsequent", "unfolding", "event", "of", "Lysines", "at", "positions", "1", "and", "2,", "resulting", "in", "81%", "of", "helicity", "on", "a", "pure", "zwitterionic", "bilayer.", "However,", "as", "reported", "for", "other", "simulated", "peptides", "in", "the", "same", "work,", "the", "forcefield", "used", "could", "result", "in", "an", "over-helical", "artifact", "17", ".", "A", "Brownian", "Dynamics", "simulation", "study", "of", "BP100", "confined", "inside", "an", "implicit", "POPC", "membrane", "reports", "a", "stable", "alpha-helix", "18", "." ]
Original work titled: 'Binding and Flip as Initial Steps for BP-100 Antimicrobial Actions' (Scientific Reports/Nature Publishing Group UK) by the following authors: Peter Park; Leandro R. Franco; Hernan Chaimovich; Kaline Coutinho; Iolanda M. Cuccovia; Filipe S. Lima DOI: 10.1038/s41598-019-45075-5	5388809896c7b2a9adf5d708f6ea4b08	CC-BY	http://creativecommons.org/licenses/by/4.0/	4.0	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]	[ "Peptide-lipid", "pair", "analysis", "(Fig.", "S7", ")", "showed", "that", "cationic", "Lysine", "residues", "interacted", "mainly", "with", "phosphate", "groups", "of", "the", "DPPC", "bilayer,", "evidencing", "that", "electrostatic", "interactions", "were", "present.", "In", "the", "case", "of", "L-BP100", "in", "DPPC,", "no", "alpha-helical", "structure", "formation", "was", "observed", "(Fig.", "S3", "),", "and", "for", "α-BP100,", "the", "peptide", "alpha-helix", "conformation", "was", "mostly", "lost,", "although", "one", "helix", "turn", "from", "residues", "5", "to", "9", "remained", "(Fig.", "5A", ").", "The", "minimum", "alpha-helix", "length", "detected", "by", "CD", "spectroscopy", "is", "proposed", "to", "encompass", "seven", "to", "eleven", "residues", "38", ",", "hence", "the", "alpha-helix", "turn", "in", "residues", "5–9", "might", "not", "be", "detected", "by", "CD.", "Alternatively,", "this", "could", "be", "an", "over-helical", "forcefield", "artifact", "22", ",", "but", "it", "also", "indicates", "the", "high", "stability", "of", "the", "alpha-helix", "formed", "by", "the", "(5–9)", "Lys-Lys-Ile-Leu-Lys", "sequence.", "This", "stability", "leads", "us", "to", "conjecture", "that", "BP100", "alpha-helix", "formation", "could", "be", "initiated", "through", "a", "core", "sequence,", "a", "nascent", "helix", "39", ".", "The", "negatively", "charged", "membrane", "interface", "could", "promote", "the", "initial", "peptide", "folding.", "To", "support", "this,", "we", "performed", "three", "600", "ns-long", "simulations", "with", "constrained", "alpha", "helices", "of", "BP100", "on", "three", "regions:", "residues", "1", "to", "5", "(Lys-Lys-Leu-Phe-Lys),", "4", "to", "8", "(Phe-Lys-Lys-Ile-Leu)", "and", "7", "to", "11", "(Ile-Leu-Lys-Tyr-Leu)", "in", "pure", "DPPG", "bilayers.", "The", "secondary", "structure", "analysis", "of", "the", "constrained", "BP100", "simulations", "yielded", "different", "outcomes.", "Constraint", "on", "residues", "1", "to", "5", "rapidly", "induced", "almost", "full", "alpha-helix", "content", "from", "Lys2", "to", "Lys9", "(Fig.", "6A", "),", "reaching", "73%", "of", "helicity,", "similar", "to", "α-BP100", "in", "DPPG", "without", "constraints", "(Fig.", "5B", ").", "Constraint", "on", "residues", "4", "to", "8", "also", "showed", "a", "helix", "formation", "tendency", "(overall", "63%", "helicity,", "5", "out", "of", "11", "residues,", "from", "Phe4", "to", "Lys9)." ]
Original work titled: 'Binding and Flip as Initial Steps for BP-100 Antimicrobial Actions' (Scientific Reports/Nature Publishing Group UK) by the following authors: Peter Park; Leandro R. Franco; Hernan Chaimovich; Kaline Coutinho; Iolanda M. Cuccovia; Filipe S. Lima DOI: 10.1038/s41598-019-45075-5	5388809896c7b2a9adf5d708f6ea4b08	CC-BY	http://creativecommons.org/licenses/by/4.0/	4.0	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]	[ "We", "find", "1.53", "kcal/mol", "for", "residues", "1", "to", "5", "(Lys-Lys-Leu-Phe-Lys),", "1.68", "kcal/mol", "for", "residues", "4", "to", "8", "(Phe-Lys-Lys-Ile-Leu),", "and", "1.62", "kcal/mol", "for", "residues", "7–11", "(Ile-Leu-Lys-Tyr-Leu).", "Our", "secondary", "structure", "data", "indicates", "that", "BP100", "nascent", "helix", "could", "be", "formed", "either", "in", "the", "region", "between", "residues", "1", "to", "5", "or", "between", "residues", "5", "to", "9.", "We", "favor", "the", "latter", "due", "to", "the", "presence", "of", "positively", "charged", "Lysine", "residues", "in", "the", "N-terminal", "side", "(Lys1", "and", "Lys2)", "which", "could", "produce", "an", "energetically", "unfavorable", "barrier", "to", "initial", "peptide", "folding.", "The", "5–9", "region", "shows", "high", "stability", "in", "all", "constraint-free", "α-BP100/membranes", "simulations", "and", "has", "the", "overall", "lowest", "energy", "barrier", "in", "the", "helix", "propensity", "scale", "40", ".", "DPPG", "seems", "to", "have", "a", "helix-stabilizing", "effect", "on", "BP100.", "All", "the", "simulations", "with", "α-BP100", "in", "DPPG-containing-membranes", "showed", "high", "alpha-helical", "content,", "including", "the", "region", "of", "residues", "5", "to", "9.", "Our", "helicity", "results", "from", "the", "simulations", "with", "α-BP100", "in", "pure", "DPPG", "(73%)", "and", "in", "PCPG", "(50:50)", "mixed", "bilayers", "(54%)", "are", "remarkably", "close", "to", "those", "reported", "in", "experimental", "studies:", "54%", "in", "POPC:POPG", "(50:50)", "11", "and", "61%", "in", "DMPC/DMPG", "(75:25)", "LUVs", "10", ",", "and", "maximum", "observable", "alpha-helix", "spectrum", "for", "BP100", "in", "pure", "POPG", "vesicles", "11", "proving", "that", "BP100", "alpha-helical", "structure", "is", "dependent", "on", "PG", "content", "11", ".", "For", "L-BP100", "simulations", "with", "DPPG,", "PCPG-R,", "and", "PCPG-NR,", "no", "secondary", "structure", "formation", "was", "detected", "(Fig.", "S3", "),", "with", "the", "peptide", "being", "in", "a", "random", "conformation.", "Non-biased", "random", "peptide", "simulations", "require", "much", "longer", "simulation", "time", "to", "sample", "the", "peptide", "conformational", "potential", "landscape", "or", "might", "dwell", "in", "several", "local", "minimum-energy", "states." ]
Original work titled: 'Binding and Flip as Initial Steps for BP-100 Antimicrobial Actions' (Scientific Reports/Nature Publishing Group UK) by the following authors: Peter Park; Leandro R. Franco; Hernan Chaimovich; Kaline Coutinho; Iolanda M. Cuccovia; Filipe S. Lima DOI: 10.1038/s41598-019-45075-5	5388809896c7b2a9adf5d708f6ea4b08	CC-BY	http://creativecommons.org/licenses/by/4.0/	4.0	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]	[ "For", "L-BP100", "simulations", "with", "DPPG,", "PCPG-R,", "and", "PCPG-NR,", "no", "secondary", "structure", "formation", "was", "detected", "(Fig.", "S3", "),", "with", "the", "peptide", "being", "in", "a", "random", "conformation.", "Non-biased", "random", "peptide", "simulations", "require", "much", "longer", "simulation", "time", "to", "sample", "the", "peptide", "conformational", "potential", "landscape", "or", "might", "dwell", "in", "several", "local", "minimum-energy", "states.", "Peptide", "flip", "BP100", "is", "too", "short", "to", "span", "the", "bilayer", "thickness,", "especially", "in", "the", "alpha-helical", "conformation,", "and", "thus", "single", "molecule", "pore", "formation", "is", "an", "unlikely", "scenario.", "NMR", "data", "of", "BP100", "in", "DMPC:", "DMPG", "(3:1)", "10", "shows", "that", "upon", "binding", "to", "negatively", "charged", "membranes,", "alpha-helical", "BP100", "positions", "parallel", "to", "the", "membrane", "as", "in", "a", "surface-bound", "orientation,", "and", "has", "an", "azimuthal", "rotation", "angle", "close", "to", "160°,", "with", "Lysine", "residues", "facing", "the", "solvent.", "This", "last", "arrangement", "is", "commonly", "observed", "with", "other", "CAMPs", "30", "–", "33", ".", "Peptide/membrane", "simulations", "with", "initially", "alpha-helical", "BP100", "had", "its", "polar", "moiety", "facing", "the", "membrane,", "for", "being", "the", "most", "probable", "scenario", "in", "a", "physical", "environment.", "In", "the", "α-BP100", "in", "DPPG", "(Fig.", "7", "),", "α-BP100", "in", "DPPC,", "α-BP100", "in", "PCPG-R", "and", "α-BP100", "(res1–5)", "in", "DPPG", "simulations", "trajectories,", "we", "observed", "the", "binding", "of", "BP100", "from", "bulk", "solution", "to", "the", "membranes", "with", "its", "Lysines", "residues", "pointing", "towards", "the", "bilayer,", "and", "then,", "the", "peptide", "rotated,", "leaving", "its", "apolar", "facet", "facing", "the", "interior", "of", "the", "bilayer.", "We", "termed", "this", "transition", "peptide", "flip.", "Although", "BP100", "surface-bound", "state", "is", "reported", "12", ",", "17", ",", "no", "previous", "peptide/membrane", "MD", "simulation", "work", "has", "reported", "a", "peptide", "flip", "transition.", "Peptide", "flip", "brings", "significant", "outcomes", "regarding", "BP100", "localization", "in", "the", "membrane,", "in", "peptide/membrane", "interaction", "and", "the", "peptide", "hydration,", "possibly", "being", "a", "crucial", "step", "of", "carpet", "mechanism", "for", "BP100", "and", "other", "CAMPs.", "Through", "the", "density", "profile,", "we", "observed", "deep", "penetration", "of", "the", "peptide", "into", "the", "membrane", "through", "its", "apolar", "residues", "with", "larger", "side-chains,", "after", "the", "flip", "(Fig.", "7", ")." ]
Original work titled: 'Binding and Flip as Initial Steps for BP-100 Antimicrobial Actions' (Scientific Reports/Nature Publishing Group UK) by the following authors: Peter Park; Leandro R. Franco; Hernan Chaimovich; Kaline Coutinho; Iolanda M. Cuccovia; Filipe S. Lima DOI: 10.1038/s41598-019-45075-5	5388809896c7b2a9adf5d708f6ea4b08	CC-BY	http://creativecommons.org/licenses/by/4.0/	4.0	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]	[ "Through", "the", "density", "profile,", "we", "observed", "deep", "penetration", "of", "the", "peptide", "into", "the", "membrane", "through", "its", "apolar", "residues", "with", "larger", "side-chains,", "after", "the", "flip", "(Fig.", "7", ").", "BP100", "hydration", "analysis", "also", "shows", "a", "decrease", "in", "the", "overall", "peptide", "hydration", "after", "the", "flip", "(Fig.", "8", ").", "Apolar/polar", "pair", "interaction", "analysis", "(Fig.", "11", ")", "revealed", "that", "after", "the", "flip,", "the", "number", "of", "contacts", "between", "apolar", "residues", "from", "the", "lipids", "and", "the", "peptide", "increases", "significantly,", "while", "the", "number", "of", "contacts", "between", "polar", "groups", "of", "the", "lipids", "and", "the", "peptides", "slightly", "decreases.", "In", "other", "words,", "peptide", "flip", "intensifies", "peptide", "binding", "to", "membranes", "burying", "the", "apolar", "residues", "of", "the", "peptide", "deeper", "into", "the", "membrane", "core.", "We", "investigated", "what", "factors", "could", "lead", "to", "the", "occurrence", "of", "BP100", "peptide", "flip.", "Membrane", "composition", "appears", "to", "have", "a", "significant", "role.", "For", "BP100", "alpha-helical", "structure", "formation", "is", "favored", "in", "negatively", "charged", "membranes", "8", ".", "In", "our", "simulations,", "BP100", "entirely", "flipped", "in", "DPPG", "enriched", "regions", "of", "the", "membrane.", "Peptide", "flip", "was", "detected", "in", "α-BP100", "in", "DPPG,", "α-BP100", "(res1–5)", "in", "DPPG", "and", "α-BP100", "in", "PCPG-R", "systems.", "No", "peptide", "flip", "was", "detected", "in", "the", "other", "constrained", "BP100", "simulations", "(α-BP100", "(res4–8)", "in", "DPPG", "and", "α-BP100", "(res7–11)", "in", "DPPG).", "However,", "it", "is", "hasty", "to", "affirm", "that", "it", "is", "unlikely", "to", "expect", "peptide", "flip", "to", "happen", "in", "those", "systems", "with", "600", "ns", "of", "simulation", "time.", "For", "instance,", "peptide", "flip", "was", "observed", "after", "1.4", "µs", "of", "simulation", "in", "α-BP100", "in", "DPPG.", "Hydration", "analysis", "(Fig.", "8b", ")", "and", "density", "profile", "(Fig.", "S4A,B", ")", "for", "α-BP100", "in", "DPPC", "show", "also", "that", "BP100", "flipped.", "However,", "the", "alpha-helix", "secondary", "structure", "is", "mostly", "lost", "(Fig.", "5a", ").", "For", "this", "reason,", "BP100", "amphiphilic", "apolar-polar", "facet", "separation", "(Fig.", "2c", ")", "is", "lost." ]
Original work titled: 'Binding and Flip as Initial Steps for BP-100 Antimicrobial Actions' (Scientific Reports/Nature Publishing Group UK) by the following authors: Peter Park; Leandro R. Franco; Hernan Chaimovich; Kaline Coutinho; Iolanda M. Cuccovia; Filipe S. Lima DOI: 10.1038/s41598-019-45075-5	5388809896c7b2a9adf5d708f6ea4b08	CC-BY	http://creativecommons.org/licenses/by/4.0/	4.0	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]	[ "For", "instance,", "peptide", "flip", "was", "observed", "after", "1.4", "µs", "of", "simulation", "in", "α-BP100", "in", "DPPG.", "Hydration", "analysis", "(Fig.", "8b", ")", "and", "density", "profile", "(Fig.", "S4A,B", ")", "for", "α-BP100", "in", "DPPC", "show", "also", "that", "BP100", "flipped.", "However,", "the", "alpha-helix", "secondary", "structure", "is", "mostly", "lost", "(Fig.", "5a", ").", "For", "this", "reason,", "BP100", "amphiphilic", "apolar-polar", "facet", "separation", "(Fig.", "2c", ")", "is", "lost.", "Additionally,", "the", "apolar", "moiety", "of", "the", "peptide", "could", "have", "a", "crucial", "role", "in", "peptide", "flip.", "Hydration", "analysis", "(Fig.", "8", ")", "suggests", "peptide", "flip", "results", "in", "peptide", "dehydration", "and", "concomitantly", "enhances", "peptide/lipid", "interaction", "(Fig.", "11", "),", "increasing", "specially", "apolar", "contacts", "(Fig.", "11", ").", "Similar", "behavior", "was", "observed", "in", "a", "study", "of", "the", "interaction", "of", "micelles", "with", "polyatomic", "counterions", "with", "apolar", "and", "polar", "moieties.", "Experimental", "results", "and", "MD", "simulations", "showed", "that", "counterions", "with", "the", "same", "apolar", "groups", "but", "different", "polar", "groups", "resulted", "in", "similar", "ionic", "affinities", "for", "dodecyltrimethylammonium", "micelles,", "and", "the", "simulations", "showed", "that", "counterion", "adsorption", "to", "the", "micelles", "was", "related", "with", "the", "dehydration", "of", "the", "apolar", "group", "of", "the", "counterions", "rather", "than", "by", "the", "polar", "group", "41", ".", "These", "factors", "could", "help", "to", "explain", "BP100", "selectivity", "towards", "negatively", "charged", "bacterial", "membranes", "and", "low", "cytotoxicity.", "Results", "of", "leakage", "from", "the", "inner", "compartment", "of", "LUVs", "upon", "addition", "of", "BP100", "showed", "that", "BP100", "leakage", "ability", "is", "proportional", "to", "PG", "content", "while", "the", "peptide", "has", "small", "effects", "on", "zwitterionic", "PC", "vesicles,", "observed", "through", "studies", "of", "zeta", "potential", "and", "vesicle", "leakage", "11", ".", "BP100", "does", "not", "perturb", "PC", "bilayers", "even", "at", "high", "peptide/lipid", "ratio", "and", "causes", "membrane", "thinning", "on", "mixed", "DMPC/DMPG", "bilayers", "where", "a", "stronger", "effect", "appears", "in", "anionic", "DMPG", "lipids", "compared", "to", "zwitterionic", "DMPC", "lipids", "12", "." ]
Original work titled: 'Binding and Flip as Initial Steps for BP-100 Antimicrobial Actions' (Scientific Reports/Nature Publishing Group UK) by the following authors: Peter Park; Leandro R. Franco; Hernan Chaimovich; Kaline Coutinho; Iolanda M. Cuccovia; Filipe S. Lima DOI: 10.1038/s41598-019-45075-5	5388809896c7b2a9adf5d708f6ea4b08	CC-BY	http://creativecommons.org/licenses/by/4.0/	4.0	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]	[ "BP100", "does", "not", "perturb", "PC", "bilayers", "even", "at", "high", "peptide/lipid", "ratio", "and", "causes", "membrane", "thinning", "on", "mixed", "DMPC/DMPG", "bilayers", "where", "a", "stronger", "effect", "appears", "in", "anionic", "DMPG", "lipids", "compared", "to", "zwitterionic", "DMPC", "lipids", "12", ".", "In", "zwitterionic-lipid-enriched", "mammalian", "membranes,", "BP100", "would", "bind", "to", "membranes", "through", "electrostatic", "interactions", "and", "the", "absence", "of", "a", "helix-promoting", "environment", "would", "prevent", "helix", "formation", "and", "even", "with", "peptide", "flip,", "as", "in", "our", "α-BP100", "in", "DPPC", "simulation,", "it", "could", "lead", "to", "mild", "membrane", "thinning", "11", ",", "12", ".", "On", "the", "other", "hand,", "bacterial", "membranes", "with", "high", "content", "of", "anionic", "lipids", "on", "the", "outer", "part", "of", "the", "membrane,", "could", "promote", "peptide", "binding,", "alpha-helix", "nucleation,", "and", "propagation,", "leading", "to", "peptide", "flip", "and", "more", "pronounced", "membrane", "thinning,", "which", "is", "consistent", "with", "our", "observations", "from", "α-BP100", "in", "DPPG,", "α-BP100", "in", "PCPG-R", "and", "α-BP100", "(res1–5)", "in", "DPPG", "sets.", "Although", "we", "could", "not", "detect", "membrane", "thinning", "in", "our", "simulations", "(Table", "S2", "),", "it", "should", "be", "noted", "that", "our", "simulations", "had", "only", "one", "peptide", "on", "128-lipid-bilayers.", "A", "more", "pronounced", "effect", "on", "the", "membrane", "might", "be", "observed", "by", "increasing", "the", "number", "of", "peptides", "in", "the", "simulations.", "DPPG", "subdomain", "formation", "Lipid", "clustering,", "or", "subdomain", "formation,", "induced", "by", "CAMPs", "is", "well", "established", "5", ",", "14", ",", "35", "–", "37", ",", "42", "–", "45", ".", "Through", "electrostatic", "interactions,", "CAMPs", "clusters", "anionic", "phosphatidylglycerol", "(PG)", "or", "cardiolipin", "(CL)", "lipids", "on", "the", "outer", "membrane", "of", "bacteria,", "inducing", "phase", "separation", "and", "phase", "boundary", "defects", "between", "lipid", "domains", "and", "the", "rest", "of", "the", "membrane,", "increasing", "membrane", "permeability", "36", ".", "Epand", "et", "al.", "first", "proposed", "it", "45", ",", "in", "a", "study", "with", "oligomers", "of", "lysine", "(OAK)." ]
Original work titled: 'Binding and Flip as Initial Steps for BP-100 Antimicrobial Actions' (Scientific Reports/Nature Publishing Group UK) by the following authors: Peter Park; Leandro R. Franco; Hernan Chaimovich; Kaline Coutinho; Iolanda M. Cuccovia; Filipe S. Lima DOI: 10.1038/s41598-019-45075-5	5388809896c7b2a9adf5d708f6ea4b08	CC-BY	http://creativecommons.org/licenses/by/4.0/	4.0	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]	[ "Lipid", "phase", "separation", "was", "later", "observed", "for", "other", "cAMPs", "and", "cell-penetrating-peptides", "37", ",", "45", ",", "46", ".", "Although", "not", "so", "pronounced,", "DSC", "also", "detected", "BP100", "ability", "to", "promote", "lipid", "phase", "separation", "on", "POPE/TOCL", "(75:25)", "vesicles", "37", ".", "Lipid", "phase", "separation", "promoted", "by", "CAMPs", "has", "also", "been", "observed", "in", "computational", "modeling", "studies.", "In", "a", "coarse-grained", "MD", "simulation", "study", "35", ",", "lipid", "cluster", "promotion", "was", "seen", "in", "POPE/POPG", "(70:30)", "membranes", "by", "Ltc1,", "a", "linear", "alpha-helical", "cAMP", "with", "overall", "+10", "charge.", "Simulations", "showed", "Ltc1", "induced", "POPG", "domains", "in", "small", "(256", "lipids)", "and", "large", "membranes", "(512", "or", "2048", "lipids).", "Also,", "due", "to", "peptide-POPG", "charge", "neutralization,", "Ltc1-induced", "anionic", "domains", "seem", "to", "facilitate", "peptide", "oligomerization,", "enhancing", "peptide", "activity", "on", "bacterial", "model", "membranes", "35", ".", "Likewise,", "our", "simulations", "suggest", "that", "BP100", "promotes", "PG", "aggregation.", "Two", "DPPC:", "DPPG", "(50:50)", "mixed", "bilayers", "were", "designed", "to", "explore", "lipid", "aggregation", "by", "the", "peptide.", "One", "membrane", "was", "composed", "of", "randomly", "mixed", "(PCPG-NR)", "and", "in", "the", "other,", "a", "4", "×", "4", "DPPG", "raft", "(PCPG-R)", "was", "positioned", "in", "the", "middle", "of", "both", "monolayers", "(see", "Methods", "1", "and", "Fig.", "1", ").", "BP100", "was", "able", "to", "cluster", "DPPGs", "in", "PCPG-NR,", "which", "can", "be", "observed", "by", "the", "amount", "of", "DPPG", "in", "contact", "with", "BP100", "(Table", "2", ").", "From", "a", "total", "of", "11", "lipids", "in", "the", "closer", "contact", "with", "BP100,", "8.3", "in", "average", "are", "DPPG", "corresponding", "to", "75%", "of", "the", "lipid", "in", "the", "vicinity", "of", "the", "peptide.", "Additionally,", "this", "DPPG", "clustering", "can", "also", "be", "observed", "in", "lipid", "raft", "size", "distribution", "(Fig.", "S6E", "),", "reaching", "similar", "values", "of", "DPPG/peptide", "contact", "in", "α-BP100", "in", "PCPG-R", "simulation", "(Fig.", "10", ")", "and", "DPPG", "lipid", "raft", "size", "probability", "(Fig.", "S6D", ")." ]
Original work titled: 'Binding and Flip as Initial Steps for BP-100 Antimicrobial Actions' (Scientific Reports/Nature Publishing Group UK) by the following authors: Peter Park; Leandro R. Franco; Hernan Chaimovich; Kaline Coutinho; Iolanda M. Cuccovia; Filipe S. Lima DOI: 10.1038/s41598-019-45075-5	5388809896c7b2a9adf5d708f6ea4b08	CC-BY	http://creativecommons.org/licenses/by/4.0/	4.0	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]	[ "S6D", ").", "These", "data", "suggest", "that", "even", "a", "short-lengthened", "CAMP", "as", "BP100", "can", "promote", "anionic", "lipid", "clustering", "and", "also", "maintain", "it,", "supporting", "the", "experimental", "findings", "37", ".", "BP100", "also", "adsorbs", "on", "pure", "zwitterionic", "PC", "membranes", "and", "promotes", "DPPC", "clustering", "as", "observed", "in", "Figs", "S5", "A", "and", "S6A", ".", "However,", "possibly", "due", "to", "the", "presence", "of", "positively", "charged", "choline", "headgroups", "(Fig.", "1d", "-", "left),", "secondary", "structure", "is", "lost", "(Fig.", "5a", ")", "and", "the", "peptide", "turns", "into", "random", "coil,", "resulting", "in", "an", "increase", "of", "available", "interaction", "surface", "area", "with", "the", "DPPC", "headgroups,", "which", "is", "reflected", "in", "a", "broad", "distribution", "in", "lipid", "raft", "size", "distribution", "(Fig.", "S5A", ").", "Polar/Apolar", "pair", "analysis", "for", "α-BP100", "in", "PCPG-R", "(Fig.", "11", ")", "helps", "to", "explain", "lipid", "aggregation.", "We", "computed", "the", "ten", "most", "frequent", "apolar", "and", "polar", "pairs", "between", "peptide", "and", "lipids.", "The", "number", "of", "polar", "pairs", "between", "the", "peptide", "and", "DPPG", "is", "higher", "than", "those", "with", "DPPC", "and", "is", "maintained", "even", "after", "the", "flip", "(~390", "ns).", "As", "expected,", "+1", "charged", "amino", "group", "(NZ)", "from", "Lysines", "side", "chains", "are", "the", "main", "participants", "in", "polar", "pairings", "(Figs", "S7", "–", "S13", "),", "interacting", "with", "DPPG", "headgroup", "glycerol", "(OC2,", "OC3,", "Fig.", "1d", "-", "right),", "phosphate", "group", "(P),", "and", "carbonyl", "groups", "(C21,", "C31,", "O21,", "O22,", "O31,", "O32)", "from", "chains", "sn1", "and", "sn2", "(Figs", "S9", ",", "S10", ",", "S12", ",", "S13", ").", "Peptide", "flip", "seems", "to", "contribute", "to", "lipid", "clustering.", "Polar/apolar", "pairs", "analysis", "(Fig.", "11", ")", "and", "pair", "frequency", "(Figs", "S8", ",", "S9", ")", "for", "the", "previous", "simulation,", "reveals", "that", "apolar", "pairs", "between", "BP100", "and", "both", "lipids", "rise", "after", "peptide", "flip", "occurs", "(~390", "ns),", "intensifying", "peptide-membrane", "interaction.", "The", "same", "phenomena", "were", "observed", "for", "other", "simulations", "with", "peptide", "flip", "(Figs", "S7", ",", "S10", "and", "S13", ")." ]
Original work titled: 'Binding and Flip as Initial Steps for BP-100 Antimicrobial Actions' (Scientific Reports/Nature Publishing Group UK) by the following authors: Peter Park; Leandro R. Franco; Hernan Chaimovich; Kaline Coutinho; Iolanda M. Cuccovia; Filipe S. Lima DOI: 10.1038/s41598-019-45075-5	5388809896c7b2a9adf5d708f6ea4b08	CC-BY	http://creativecommons.org/licenses/by/4.0/	4.0	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]	[ "Peptide", "flip", "seems", "to", "contribute", "to", "lipid", "clustering.", "Polar/apolar", "pairs", "analysis", "(Fig.", "11", ")", "and", "pair", "frequency", "(Figs", "S8", ",", "S9", ")", "for", "the", "previous", "simulation,", "reveals", "that", "apolar", "pairs", "between", "BP100", "and", "both", "lipids", "rise", "after", "peptide", "flip", "occurs", "(~390", "ns),", "intensifying", "peptide-membrane", "interaction.", "The", "same", "phenomena", "were", "observed", "for", "other", "simulations", "with", "peptide", "flip", "(Figs", "S7", ",", "S10", "and", "S13", ").", "As", "long", "as", "peptide", "flip", "had", "occurred,", "apolar", "residue", "side", "chains", "(from", "Leu3,", "Phe4,", "Ile7,", "Leu8", "and", "Tyr10,", "and", "Leu11)", "were", "in", "close", "contact", "mainly", "with", "groups", "of", "the", "lipid", "tails", "(Figs", "S7", "–", "S10", ",", "S13", ").", "The", "mechanisms", "of", "bacterial", "toxicity", "via", "lipid", "clustering", "induced", "by", "CAMPs", "still", "has", "to", "be", "investigated.", "Moreover,", "possibly", "more", "than", "one", "mechanism", "could", "be", "involved", "in", "the", "process", "of", "bacterial", "killing.", "Evidence", "suggest", "lipid", "clustering", "by", "CAMPs", "could", "lead", "to", "negative", "charge", "concentration", "on", "membranes,", "promoting", "CAMPs", "attachment,", "leading", "to", "pore", "formation", "5", ".", "Anionic", "lipid", "clustering", "would", "have", "surrounding", "interfaces", "with", "the", "rest", "of", "the", "membrane", "which", "could", "lead", "to", "phase", "boundary", "defects,", "leading", "to", "slow", "leakage", "of", "inner", "cell", "content", "32", ".", "Also,", "CAMPs", "and", "cell-penetrating", "peptides", "could", "induce", "negative", "membrane", "curvature,", "enabling", "the", "internalization", "of", "peptides", "into", "cells,", "leading", "to", "intracellular", "killing", "mechanisms.", "The", "formation", "of", "lipid", "clusters", "patches", "would", "also", "lead", "to", "anomalies", "in", "membrane", "protein", "function,", "membrane", "fluidity,", "and", "membrane", "polarization.", "In", "a", "recent", "study", "5", "with", "cWFW,", "a", "cyclic", "antimicrobial", "peptide,", "it", "was", "shown", "in", "vitro", "and", "in", "vivo", "that", "cWFW", "promotes", "lipid", "phase", "separation,", "a", "sharp", "decrease", "in", "membrane", "fluidity.", "The", "significant", "phase", "separation", "appears", "to", "cause", "disorganization", "of", "membrane", "proteins,", "inhibiting", "cell", "wall", "synthesis", "and", "inducing", "autolysis.", "BP100", "mode", "of", "action", "on", "membranes", "is", "dependent", "on", "peptide/lipid", "ratio", "11", ",", "47", "." ]
Original work titled: 'Binding and Flip as Initial Steps for BP-100 Antimicrobial Actions' (Scientific Reports/Nature Publishing Group UK) by the following authors: Peter Park; Leandro R. Franco; Hernan Chaimovich; Kaline Coutinho; Iolanda M. Cuccovia; Filipe S. Lima DOI: 10.1038/s41598-019-45075-5	5388809896c7b2a9adf5d708f6ea4b08	CC-BY	http://creativecommons.org/licenses/by/4.0/	4.0	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]	[ "Also,", "due", "to", "peptide-POPG", "charge", "neutralization,", "Ltc1-induced", "anionic", "domains", "seem", "to", "facilitate", "peptide", "oligomerization,", "enhancing", "peptide", "activity", "on", "bacterial", "model", "membranes", "35", ".", "Likewise,", "our", "simulations", "suggest", "that", "BP100", "promotes", "PG", "aggregation.", "Two", "DPPC:", "DPPG", "(50:50)", "mixed", "bilayers", "were", "designed", "to", "explore", "lipid", "aggregation", "by", "the", "peptide.", "One", "membrane", "was", "composed", "of", "randomly", "mixed", "(PCPG-NR)", "and", "in", "the", "other,", "a", "4", "×", "4", "DPPG", "raft", "(PCPG-R)", "was", "positioned", "in", "the", "middle", "of", "both", "monolayers", "(see", "Methods", "1", "and", "Fig.", "1", ").", "BP100", "was", "able", "to", "cluster", "DPPGs", "in", "PCPG-NR,", "which", "can", "be", "observed", "by", "the", "amount", "of", "DPPG", "in", "contact", "with", "BP100", "(Table", "2", ").", "From", "a", "total", "of", "11", "lipids", "in", "the", "closer", "contact", "with", "BP100,", "8.3", "in", "average", "are", "DPPG", "corresponding", "to", "75%", "of", "the", "lipid", "in", "the", "vicinity", "of", "the", "peptide.", "Additionally,", "this", "DPPG", "clustering", "can", "also", "be", "observed", "in", "lipid", "raft", "size", "distribution", "(Fig.", "S6E", "),", "reaching", "similar", "values", "of", "DPPG/peptide", "contact", "in", "α-BP100", "in", "PCPG-R", "simulation", "(Fig.", "10", ")", "and", "DPPG", "lipid", "raft", "size", "probability", "(Fig.", "S6D", ").", "These", "data", "suggest", "that", "even", "a", "short-lengthened", "CAMP", "as", "BP100", "can", "promote", "anionic", "lipid", "clustering", "and", "also", "maintain", "it,", "supporting", "the", "experimental", "findings", "37", ".", "BP100", "also", "adsorbs", "on", "pure", "zwitterionic", "PC", "membranes", "and", "promotes", "DPPC", "clustering", "as", "observed", "in", "Figs", "S5", "A", "and", "S6A", ".", "However,", "possibly", "due", "to", "the", "presence", "of", "positively", "charged", "choline", "headgroups", "(Fig.", "1d", "-", "left),", "secondary", "structure", "is", "lost", "(Fig.", "5a", ")", "and", "the", "peptide", "turns", "into", "random", "coil,", "resulting", "in", "an", "increase", "of", "available", "interaction", "surface", "area", "with", "the", "DPPC", "headgroups,", "which", "is", "reflected", "in", "a", "broad", "distribution", "in", "lipid", "raft", "size", "distribution", "(Fig.", "S5A", ")." ]
Original work titled: 'Binding and Flip as Initial Steps for BP-100 Antimicrobial Actions' (Scientific Reports/Nature Publishing Group UK) by the following authors: Peter Park; Leandro R. Franco; Hernan Chaimovich; Kaline Coutinho; Iolanda M. Cuccovia; Filipe S. Lima DOI: 10.1038/s41598-019-45075-5	5388809896c7b2a9adf5d708f6ea4b08	CC-BY	http://creativecommons.org/licenses/by/4.0/	4.0	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]	[ "Although", "we", "could", "not", "detect", "membrane", "thinning", "in", "our", "simulations", "(Table", "S2", "),", "it", "should", "be", "noted", "that", "our", "simulations", "had", "only", "one", "peptide", "on", "128-lipid-bilayers.", "A", "more", "pronounced", "effect", "on", "the", "membrane", "might", "be", "observed", "by", "increasing", "the", "number", "of", "peptides", "in", "the", "simulations.", "DPPG", "subdomain", "formation", "Lipid", "clustering,", "or", "subdomain", "formation,", "induced", "by", "CAMPs", "is", "well", "established", "5", ",", "14", ",", "35", "–", "37", ",", "42", "–", "45", ".", "Through", "electrostatic", "interactions,", "CAMPs", "clusters", "anionic", "phosphatidylglycerol", "(PG)", "or", "cardiolipin", "(CL)", "lipids", "on", "the", "outer", "membrane", "of", "bacteria,", "inducing", "phase", "separation", "and", "phase", "boundary", "defects", "between", "lipid", "domains", "and", "the", "rest", "of", "the", "membrane,", "increasing", "membrane", "permeability", "36", ".", "Epand", "et", "al.", "first", "proposed", "it", "45", ",", "in", "a", "study", "with", "oligomers", "of", "lysine", "(OAK).", "Upon", "the", "addition", "of", "OAK", "in", "1-palmitoyl-2-oleoyl", "phosphatidylethanolamine", "(POPE)", "and", "tetraoleoyl", "cardiolipin", "(TOCL)", "mixed", "vesicles,", "transition", "temperature", "shift", "was", "observed", "through", "differential", "scanning", "calorimetry,", "indicating", "lipid", "phase", "separation", "45", ".", "Lipid", "phase", "separation", "was", "later", "observed", "for", "other", "cAMPs", "and", "cell-penetrating-peptides", "37", ",", "45", ",", "46", ".", "Although", "not", "so", "pronounced,", "DSC", "also", "detected", "BP100", "ability", "to", "promote", "lipid", "phase", "separation", "on", "POPE/TOCL", "(75:25)", "vesicles", "37", ".", "Lipid", "phase", "separation", "promoted", "by", "CAMPs", "has", "also", "been", "observed", "in", "computational", "modeling", "studies.", "In", "a", "coarse-grained", "MD", "simulation", "study", "35", ",", "lipid", "cluster", "promotion", "was", "seen", "in", "POPE/POPG", "(70:30)", "membranes", "by", "Ltc1,", "a", "linear", "alpha-helical", "cAMP", "with", "overall", "+10", "charge.", "Simulations", "showed", "Ltc1", "induced", "POPG", "domains", "in", "small", "(256", "lipids)", "and", "large", "membranes", "(512", "or", "2048", "lipids)." ]
Original work titled: 'Binding and Flip as Initial Steps for BP-100 Antimicrobial Actions' (Scientific Reports/Nature Publishing Group UK) by the following authors: Peter Park; Leandro R. Franco; Hernan Chaimovich; Kaline Coutinho; Iolanda M. Cuccovia; Filipe S. Lima DOI: 10.1038/s41598-019-45075-5	5388809896c7b2a9adf5d708f6ea4b08	CC-BY	http://creativecommons.org/licenses/by/4.0/	4.0	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]	[ "For", "BP100", "alpha-helical", "structure", "formation", "is", "favored", "in", "negatively", "charged", "membranes", "8", ".", "In", "our", "simulations,", "BP100", "entirely", "flipped", "in", "DPPG", "enriched", "regions", "of", "the", "membrane.", "Peptide", "flip", "was", "detected", "in", "α-BP100", "in", "DPPG,", "α-BP100", "(res1–5)", "in", "DPPG", "and", "α-BP100", "in", "PCPG-R", "systems.", "No", "peptide", "flip", "was", "detected", "in", "the", "other", "constrained", "BP100", "simulations", "(α-BP100", "(res4–8)", "in", "DPPG", "and", "α-BP100", "(res7–11)", "in", "DPPG).", "However,", "it", "is", "hasty", "to", "affirm", "that", "it", "is", "unlikely", "to", "expect", "peptide", "flip", "to", "happen", "in", "those", "systems", "with", "600", "ns", "of", "simulation", "time.", "For", "instance,", "peptide", "flip", "was", "observed", "after", "1.4", "µs", "of", "simulation", "in", "α-BP100", "in", "DPPG.", "Hydration", "analysis", "(Fig.", "8b", ")", "and", "density", "profile", "(Fig.", "S4A,B", ")", "for", "α-BP100", "in", "DPPC", "show", "also", "that", "BP100", "flipped.", "However,", "the", "alpha-helix", "secondary", "structure", "is", "mostly", "lost", "(Fig.", "5a", ").", "For", "this", "reason,", "BP100", "amphiphilic", "apolar-polar", "facet", "separation", "(Fig.", "2c", ")", "is", "lost.", "Additionally,", "the", "apolar", "moiety", "of", "the", "peptide", "could", "have", "a", "crucial", "role", "in", "peptide", "flip.", "Hydration", "analysis", "(Fig.", "8", ")", "suggests", "peptide", "flip", "results", "in", "peptide", "dehydration", "and", "concomitantly", "enhances", "peptide/lipid", "interaction", "(Fig.", "11", "),", "increasing", "specially", "apolar", "contacts", "(Fig.", "11", ").", "Similar", "behavior", "was", "observed", "in", "a", "study", "of", "the", "interaction", "of", "micelles", "with", "polyatomic", "counterions", "with", "apolar", "and", "polar", "moieties.", "Experimental", "results", "and", "MD", "simulations", "showed", "that", "counterions", "with", "the", "same", "apolar", "groups", "but", "different", "polar", "groups", "resulted", "in", "similar", "ionic", "affinities", "for", "dodecyltrimethylammonium", "micelles,", "and", "the", "simulations", "showed", "that", "counterion", "adsorption", "to", "the", "micelles", "was", "related", "with", "the", "dehydration", "of", "the", "apolar", "group", "of", "the", "counterions", "rather", "than", "by", "the", "polar", "group", "41", "." ]
Original work titled: 'Binding and Flip as Initial Steps for BP-100 Antimicrobial Actions' (Scientific Reports/Nature Publishing Group UK) by the following authors: Peter Park; Leandro R. Franco; Hernan Chaimovich; Kaline Coutinho; Iolanda M. Cuccovia; Filipe S. Lima DOI: 10.1038/s41598-019-45075-5	5388809896c7b2a9adf5d708f6ea4b08	CC-BY	http://creativecommons.org/licenses/by/4.0/	4.0	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]	[ "The", "5–9", "region", "shows", "high", "stability", "in", "all", "constraint-free", "α-BP100/membranes", "simulations", "and", "has", "the", "overall", "lowest", "energy", "barrier", "in", "the", "helix", "propensity", "scale", "40", ".", "DPPG", "seems", "to", "have", "a", "helix-stabilizing", "effect", "on", "BP100.", "All", "the", "simulations", "with", "α-BP100", "in", "DPPG-containing-membranes", "showed", "high", "alpha-helical", "content,", "including", "the", "region", "of", "residues", "5", "to", "9.", "Our", "helicity", "results", "from", "the", "simulations", "with", "α-BP100", "in", "pure", "DPPG", "(73%)", "and", "in", "PCPG", "(50:50)", "mixed", "bilayers", "(54%)", "are", "remarkably", "close", "to", "those", "reported", "in", "experimental", "studies:", "54%", "in", "POPC:POPG", "(50:50)", "11", "and", "61%", "in", "DMPC/DMPG", "(75:25)", "LUVs", "10", ",", "and", "maximum", "observable", "alpha-helix", "spectrum", "for", "BP100", "in", "pure", "POPG", "vesicles", "11", "proving", "that", "BP100", "alpha-helical", "structure", "is", "dependent", "on", "PG", "content", "11", ".", "For", "L-BP100", "simulations", "with", "DPPG,", "PCPG-R,", "and", "PCPG-NR,", "no", "secondary", "structure", "formation", "was", "detected", "(Fig.", "S3", "),", "with", "the", "peptide", "being", "in", "a", "random", "conformation.", "Non-biased", "random", "peptide", "simulations", "require", "much", "longer", "simulation", "time", "to", "sample", "the", "peptide", "conformational", "potential", "landscape", "or", "might", "dwell", "in", "several", "local", "minimum-energy", "states.", "Peptide", "flip", "BP100", "is", "too", "short", "to", "span", "the", "bilayer", "thickness,", "especially", "in", "the", "alpha-helical", "conformation,", "and", "thus", "single", "molecule", "pore", "formation", "is", "an", "unlikely", "scenario.", "NMR", "data", "of", "BP100", "in", "DMPC:", "DMPG", "(3:1)", "10", "shows", "that", "upon", "binding", "to", "negatively", "charged", "membranes,", "alpha-helical", "BP100", "positions", "parallel", "to", "the", "membrane", "as", "in", "a", "surface-bound", "orientation,", "and", "has", "an", "azimuthal", "rotation", "angle", "close", "to", "160°,", "with", "Lysine", "residues", "facing", "the", "solvent.", "This", "last", "arrangement", "is", "commonly", "observed", "with", "other", "CAMPs", "30", "–", "33", ".", "Peptide/membrane", "simulations", "with", "initially", "alpha-helical", "BP100", "had", "its", "polar", "moiety", "facing", "the", "membrane,", "for", "being", "the", "most", "probable", "scenario", "in", "a", "physical", "environment." ]
Original work titled: 'Binding and Flip as Initial Steps for BP-100 Antimicrobial Actions' (Scientific Reports/Nature Publishing Group UK) by the following authors: Peter Park; Leandro R. Franco; Hernan Chaimovich; Kaline Coutinho; Iolanda M. Cuccovia; Filipe S. Lima DOI: 10.1038/s41598-019-45075-5	5388809896c7b2a9adf5d708f6ea4b08	CC-BY	http://creativecommons.org/licenses/by/4.0/	4.0	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]	[ "The", "negatively", "charged", "membrane", "interface", "could", "promote", "the", "initial", "peptide", "folding.", "To", "support", "this,", "we", "performed", "three", "600", "ns-long", "simulations", "with", "constrained", "alpha", "helices", "of", "BP100", "on", "three", "regions:", "residues", "1", "to", "5", "(Lys-Lys-Leu-Phe-Lys),", "4", "to", "8", "(Phe-Lys-Lys-Ile-Leu)", "and", "7", "to", "11", "(Ile-Leu-Lys-Tyr-Leu)", "in", "pure", "DPPG", "bilayers.", "The", "secondary", "structure", "analysis", "of", "the", "constrained", "BP100", "simulations", "yielded", "different", "outcomes.", "Constraint", "on", "residues", "1", "to", "5", "rapidly", "induced", "almost", "full", "alpha-helix", "content", "from", "Lys2", "to", "Lys9", "(Fig.", "6A", "),", "reaching", "73%", "of", "helicity,", "similar", "to", "α-BP100", "in", "DPPG", "without", "constraints", "(Fig.", "5B", ").", "Constraint", "on", "residues", "4", "to", "8", "also", "showed", "a", "helix", "formation", "tendency", "(overall", "63%", "helicity,", "5", "out", "of", "11", "residues,", "from", "Phe4", "to", "Lys9).", "In", "sharp", "contrast,", "constraints", "on", "residues", "7", "to", "11", "(36%", "of", "helicity,", "4", "out", "of", "11", "residues,", "from", "Lys7", "to", "Tyr10)", "had", "no", "effects", "on", "the", "secondary", "structure", "formation", "of", "BP100", "during", "600", "ns", "simulation", "(Fig.", "6C", "),", "indicating", "that", "this", "region", "has", "little", "influence", "on", "initial", "peptide", "folding.", "Pace", "and", "Scholtz", "40", ",", "based", "on", "experimental", "studies,", "proposed", "a", "helix", "propensity", "scale", "as", "Δ(ΔG)", "values", "relative", "to", "Alanine", "set", "to", "zero.", "On", "the", "Pace", "and", "Scholtz", "scale,", "the", "5–9", "region", "has", "the", "highest", "helix", "promoting", "residues", "(overall", "helix", "propensity", "of", "1.4", "kcal/mol).", "We", "find", "1.53", "kcal/mol", "for", "residues", "1", "to", "5", "(Lys-Lys-Leu-Phe-Lys),", "1.68", "kcal/mol", "for", "residues", "4", "to", "8", "(Phe-Lys-Lys-Ile-Leu),", "and", "1.62", "kcal/mol", "for", "residues", "7–11", "(Ile-Leu-Lys-Tyr-Leu)." ]
Original work titled: 'Binding and Flip as Initial Steps for BP-100 Antimicrobial Actions' (Scientific Reports/Nature Publishing Group UK) by the following authors: Peter Park; Leandro R. Franco; Hernan Chaimovich; Kaline Coutinho; Iolanda M. Cuccovia; Filipe S. Lima DOI: 10.1038/s41598-019-45075-5	5388809896c7b2a9adf5d708f6ea4b08	CC-BY	http://creativecommons.org/licenses/by/4.0/	4.0	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]	[ "Also,", "after", "the", "flip,", "apolar", "contacts", "between", "BP100", "and", "DPPG", "were", "more", "frequent", "than", "with", "DPPC", "(Fig.", "11b", ").", "The", "higher", "peptide/DPPG", "apolar", "contact", "frequency", "after", "the", "flip", "is", "also", "observed", "for", "other", "simulations", "with", "peptide", "flip", "(Figs", "S7", "–", "10", ",", "13).", "Discussion", "Peptide", "secondary", "structure", "CD", "spectra", "of", "BP100", "in", "solution", "and", "POPC", "LUVs", "show", "no", "secondary", "structure", "10", ",", "11", ",", "30", "Our", "simulations", "with", "BP100", "in", "solution,", "and", "DPPC", "membrane", "exhibited", "the", "same", "pattern.", "α-BP100", "and", "L-BP100", "in", "solution", "showed", "similar", "behavior,", "with", "a", "prevalence", "of", "random", "conformation", "(Fig.", "4", ").", "In", "a", "related", "MD", "study", "of", "AMPs", "interacting", "with", "membranes", "17", ",", "an", "8", "µs-long", "all-atom", "MD", "simulation", "of", "BP100", "in", "DMPC", "at", "35◽", "the", "authors", "reported", "a", "full", "helix", "length", "during", "1.5", "µs", "and", "a", "subsequent", "unfolding", "event", "of", "Lysines", "at", "positions", "1", "and", "2,", "resulting", "in", "81%", "of", "helicity", "on", "a", "pure", "zwitterionic", "bilayer.", "However,", "as", "reported", "for", "other", "simulated", "peptides", "in", "the", "same", "work,", "the", "forcefield", "used", "could", "result", "in", "an", "over-helical", "artifact", "17", ".", "A", "Brownian", "Dynamics", "simulation", "study", "of", "BP100", "confined", "inside", "an", "implicit", "POPC", "membrane", "reports", "a", "stable", "alpha-helix", "18", ".", "However,", "no", "experimental", "data", "confirms", "that", "BP100", "diffuses", "freely", "in", "the", "membrane", "hydrophobic", "space", "and", "no", "secondary", "structure", "formation", "is", "reported", "for", "pure", "POPC", "vesicles", "11", ".", "In", "our", "simulations", "of", "α-BP100", "and", "L-BP100", "in", "DPPC", "membrane,", "the", "peptide", "quickly", "approached", "the", "membrane", "and", "remained", "on", "the", "surface", "during", "all", "simulation.", "Peptide-lipid", "pair", "analysis", "(Fig.", "S7", ")", "showed", "that", "cationic", "Lysine", "residues", "interacted", "mainly", "with", "phosphate", "groups", "of", "the", "DPPC", "bilayer,", "evidencing", "that", "electrostatic", "interactions", "were", "present.", "In", "the", "case", "of", "L-BP100", "in", "DPPC,", "no", "alpha-helical", "structure", "formation", "was", "observed", "(Fig.", "S3", "),", "and", "for", "α-BP100,", "the", "peptide", "alpha-helix", "conformation", "was", "mostly", "lost,", "although", "one", "helix", "turn", "from", "residues", "5", "to", "9", "remained", "(Fig." ]
Original work titled: 'Binding and Flip as Initial Steps for BP-100 Antimicrobial Actions' (Scientific Reports/Nature Publishing Group UK) by the following authors: Peter Park; Leandro R. Franco; Hernan Chaimovich; Kaline Coutinho; Iolanda M. Cuccovia; Filipe S. Lima DOI: 10.1038/s41598-019-45075-5	5388809896c7b2a9adf5d708f6ea4b08	CC-BY	http://creativecommons.org/licenses/by/4.0/	4.0	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]	[ "In", "the", "last", "500", "ns", "of", "simulation,", "N(0.5)", "was", "approximately", "178", "±", "11", "in", "DPPC,", "145", "±", "7", "in", "DPPG,", "145", "±", "13", "in", "PCPG-NR,", "and", "148", "±", "3", "in", "PCPG-R.", "No", "peptide", "flip", "was", "detected", "in", "the", "trajectories", "for", "those", "simulations.", "However,", "in", "the", "peptide/membrane", "simulations", "with", "α-BP100", "as", "a", "starting", "configuration", "(Fig.", "8b", "),", "N", "(0.5)", "lowered", "in", "DPPC", "(starting", "at", "~700", "ns),", "DPPG", "(~1500", "ns)", "and", "PCPG-R", "(~390", "ns).", "Alongside", "with", "dehydration,", "a", "peptide-flip", "was", "observed", "in", "DPPG", "and", "PCPG-R.", "For", "the", "α-", "BP100", "in", "DPPC", "simulation,", "we", "observed", "a", "semi-flip,", "as", "the", "peptide", "alpha-helical", "conformation", "was", "only", "38%", "(Fig.", "5a", "),", "suggesting", "that", "the", "peptide", "overall", "polar/apolar", "segregation", "(Fig.", "2c", ")", "was", "lost.", "The", "peptide", "flip", "transition", "time", "varied", "from", "100", "to", "400", "ns.", "During", "the", "peptide-flip,", "in", "the", "simulations", "of", "α-BP100", "in", "DPPG", "and", "PCPG-R,", "the", "mean", "number", "N(0.5)", "was", "reduced", "from", "147", "±", "5", "and", "142", "±", "7", "to", "76", "±", "4", "and", "75", "±", "4,", "respectively.", "These", "represent", "on", "average", "a", "reduction", "of", "approximately", "48%", "in", "the", "number", "of", "water", "molecules", "in", "the", "hydration", "shell", "of", "α-BP100.", "In", "DPPC,", "we", "detected", "a", "smaller", "decrease", "in", "the", "hydration", "of", "α-BP100,", "around", "45%", "(from", "172", "±", "8", "to", "94", "±", "2),", "having", "around", "20", "water", "molecules", "more", "after", "the", "semi-flip.", "Figure", "9", "shows", "the", "density", "profile", "before", "and", "after", "peptide", "flip", "for", "α-BP100", "in", "DPPG", "and", "PCPG-R.", "We", "chose", "residues", "Lys5", "and", "Ile7", "to", "illustrate", "the", "changes", "in", "the", "mean", "position", "of", "hydrophobic", "and", "hydrophilic", "residues", "with", "respect", "to", "the", "membrane", "due", "to", "the", "peptide", "flip.", "These", "residues", "are", "polar", "and", "apolar,", "respectively,", "and", "located", "opposite", "to", "each", "other", "when", "in", "an", "alpha-helix", "conformation", "(Fig.", "2c", ")." ]
Original work titled: 'Binding and Flip as Initial Steps for BP-100 Antimicrobial Actions' (Scientific Reports/Nature Publishing Group UK) by the following authors: Peter Park; Leandro R. Franco; Hernan Chaimovich; Kaline Coutinho; Iolanda M. Cuccovia; Filipe S. Lima DOI: 10.1038/s41598-019-45075-5	5388809896c7b2a9adf5d708f6ea4b08	CC-BY	http://creativecommons.org/licenses/by/4.0/	4.0	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]	[ "α-BP100", "with", "constraints", "on", "residues", "1–5", "(Lys-Lys-Leu-Phe-Lys)", "acquired", "identical", "helicity", "(73%)", "to", "α-BP100", "with", "no", "constraints", "at", "the", "same", "conditions", "(Fig.", "5b", "),", "after", "50", "ns", "of", "simulation", "(Fig.", "6a", "),", "with", "a", "helix", "spanning", "from", "Lys2", "to", "Lys9", "(Fig.", "6a", ").", "Constraints", "on", "residues", "4–8", "(Phe-Lys-Lys-Ile-Leu)", "showed", "an", "overall", "52%", "of", "helicity", "(Fig.", "6b", "),", "with", "a", "helix", "spanning", "from", "Phe4", "to", "Lys9", "(Fig.", "6b", ").", "Constraints", "on", "residues", "7–11", "(Ile-Leu-Lys-Tyr-Leu)", "did", "not", "affect", "the", "rest", "of", "the", "peptide", "conformation", "(Fig.", "6c", ")", "in", "600", "ns", "of", "simulation.", "Peptide", "flip", "Simulation", "trajectories", "analyses", "(Fig.", "7", ")", "revealed", "that", "the", "peptide", "in", "alpha-helix", "conformation", "initially", "adsorbed", "at", "the", "DPPG-containing", "membranes", "interface", "with", "its", "hydrophilic", "facet", "in", "contact", "with", "the", "membrane,", "leaving", "the", "hydrophobic", "facet", "exposed", "to", "water.", "We", "observed", "that", "the", "alpha-helix", "rotated,", "inserting", "the", "hydrophobic", "facet", "into", "the", "hydrophobic", "region", "of", "the", "membrane.", "We", "define", "this", "dynamic", "phenomenon,", "observed", "in", "our", "simulations,", "as", "peptide", "flip.", "Although", "this", "final", "peptide", "orientation", "is", "known", "31", "–", "34", ",", "no", "MD", "simulation", "on", "peptide", "flip", "has", "been", "reported.", "Figure", "7", "Peptide", "flip", "observed", "from", "above", "in", "α", "-BP100", "in", "DPPG", "set", "after", "circa", "1400", "ns", "of", "simulation.", "In", "blue,", "polar", "facet", "and", "in", "green,", "the", "apolar", "facet.", "Peptide", "flip", "was", "also", "observed", "in", "α", "-BP100", "in", "DPPC,", "α", "-BP100", "in", "PCPG-R,", "and", "α", "-BP100", "res(1–5)", "in", "DPPG", "simulations.", "The", "peptide", "flip", "caused", "dehydration", "(Fig.", "8", ").", "When", "in", "contact", "with", "membranes,", "depending", "on", "the", "secondary", "structure", "of", "the", "peptide", "and", "the", "lipid", "nature,", "the", "hydration", "of", "the", "peptide", "was", "slightly", "different." ]
Original work titled: 'Binding and Flip as Initial Steps for BP-100 Antimicrobial Actions' (Scientific Reports/Nature Publishing Group UK) by the following authors: Peter Park; Leandro R. Franco; Hernan Chaimovich; Kaline Coutinho; Iolanda M. Cuccovia; Filipe S. Lima DOI: 10.1038/s41598-019-45075-5	5388809896c7b2a9adf5d708f6ea4b08	CC-BY	http://creativecommons.org/licenses/by/4.0/	4.0	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]	[ "In", "all", "cases,", "the", "peptide", "was", "rapidly", "adsorbed", "on", "the", "membranes", "and", "diffused", "laterally.", "Figure", "5", "shows", "that", "the", "BP100", "alpha-helical", "conformation", "was", "proportional", "to", "PG", "content,", "as", "the", "alpha-helix", "percentage", "in", "DPPC", "is", "considerably", "smaller", "than", "that", "observed", "in", "DPPG-containing", "membranes.", "Alpha-helix", "formed", "in", "the", "5", "to", "9", "residues", "region", "(Lys-Lys-Ile-Leu-Lys)", "was", "highly", "stable", "in", "all", "simulations.", "Figure", "5", "Secondary", "structure", "analyses", "of", "α", "-BP100", "in", "DPPC", "(", "a", "),", "DPPG", "(", "b", "),", "PCPG-R", "(", "c", ")", "and", "PCPG-NR", "(", "d", ").", "In", "DPPC,", "α-BP100", "alpha-helix", "conformation", "reached", "a", "plateau", "at", "38%", "helicity", "throughout", "the", "simulation,", "being", "relatively", "less", "stable", "than", "α-BP100", "in", "bilayers", "containing", "DPPG,", "where", "a", "higher", "propensity", "of", "maintaining", "its", "conformation", "was", "observed.", "For", "pure", "DPPG", "(Fig.", "5b", ")", "we", "found", "73%", "(8", "out", "of", "11", "residues),", "and", "for", "both", "PCPG", "(1:1)", "membranes", "we", "report", "54%", "(6", "out", "of", "11)", "of", "helicity", "(Fig.", "5c,d", ").", "No", "alpha-helix", "formation", "was", "detected", "in", "L-BP100", "on", "bilayers", "simulations", "(Fig.", "S3", ").", "Therefore,", "the", "1.8", "µs", "simulation", "was", "not", "enough", "to", "present", "a", "spontaneous", "peptide", "folding.", "The", "alpha-helix", "formed", "in", "the", "region", "of", "the", "residues", "5", "to", "9", "showed", "higher", "stability", "in", "all", "simulations", "with", "α-BP100", "in", "bilayers", "(Fig.", "5", ").", "This", "secondary", "structure", "pattern", "led", "us", "to", "suggest", "that", "the", "residues", "5", "to", "9", "are", "related", "to", "helix", "nucleation,", "in", "which", "the", "formation", "of", "this", "helix", "core", "could", "be", "the", "first", "step", "in", "the", "AMP", "actions.", "Following", "this", "assumption,", "we", "tested", "three", "conformations", "with", "α-BP100", "torsionally", "constrained", "in", "three", "regions:", "res1–5,", "res4–8,", "res7–11", "(Fig.", "3", ")", "and", "simulated", "with", "pure", "DPPG", "membranes.", "Figure", "6", "shows", "the", "evolution", "of", "the", "secondary", "structure", "in", "each", "simulation." ]
Original work titled: 'Binding and Flip as Initial Steps for BP-100 Antimicrobial Actions' (Scientific Reports/Nature Publishing Group UK) by the following authors: Peter Park; Leandro R. Franco; Hernan Chaimovich; Kaline Coutinho; Iolanda M. Cuccovia; Filipe S. Lima DOI: 10.1038/s41598-019-45075-5	5388809896c7b2a9adf5d708f6ea4b08	CC-BY	http://creativecommons.org/licenses/by/4.0/	4.0	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]	[ "Figure", "4", "shows", "that", "BP100", "conformation", "in", "solution", "was,", "predominantly,", "random", "coil.", "The", "peptide", "lost", "the", "initial", "alpha", "helix", "conformation", "in", "approximately", "40", "ns", "when", "starting", "with", "an", "alpha-helix", "configuration", "and", "occasionally", "formed", "an", "alpha-helix", "turn", "in", "the", "5–9", "residue", "region", "(Fig.", "4a", ").", "For", "L-BP100", "in", "solution,", "we", "observed", "a", "similar", "pattern", "(Fig.", "4b", ").", "Circular", "Dichroism", "(CD)", "shows", "that", "BP100", "is", "random", "in", "solution", "10", ",", "11", ",", "30", ",", "and", "our", "simulations", "reproduced", "these", "data.", "Figure", "4", "Secondary", "structure", "analyses", "graphs", "of", "α", "-BP100", "(", "a", ")", "and", "L", "-BP100", "(", "b", ")", "in", "solution.", "In", "both", "cases,", "the", "peptide", "shows", "predominance", "in", "random", "coil", "structure", "(orange)", "with", "occasional", "formation", "of", "1", "alpha", "helix", "turn", "(blue)", "in", "residues", "5", "to", "9.", "Peptide", "in", "bilayers", "BP100", "conformation,", "antimicrobial", "activity,", "and", "PG", "content", "are", "related", "11", ".", "We", "simulated", "α-BP100", "and", "L-BP100", "on", "DPPC,", "DPPG,", "PCPG-R,", "and", "PCPG-NR", "at", "323", "K,", "above", "DPPG", "and", "DPPC", "transition", "temperatures.", "In", "all", "cases,", "the", "peptide", "was", "rapidly", "adsorbed", "on", "the", "membranes", "and", "diffused", "laterally.", "Figure", "5", "shows", "that", "the", "BP100", "alpha-helical", "conformation", "was", "proportional", "to", "PG", "content,", "as", "the", "alpha-helix", "percentage", "in", "DPPC", "is", "considerably", "smaller", "than", "that", "observed", "in", "DPPG-containing", "membranes.", "Alpha-helix", "formed", "in", "the", "5", "to", "9", "residues", "region", "(Lys-Lys-Ile-Leu-Lys)", "was", "highly", "stable", "in", "all", "simulations.", "Figure", "5", "Secondary", "structure", "analyses", "of", "α", "-BP100", "in", "DPPC", "(", "a", "),", "DPPG", "(", "b", "),", "PCPG-R", "(", "c", ")", "and", "PCPG-NR", "(", "d", ").", "In", "DPPC,", "α-BP100", "alpha-helix", "conformation", "reached", "a", "plateau", "at", "38%", "helicity", "throughout", "the", "simulation,", "being", "relatively", "less", "stable", "than", "α-BP100", "in", "bilayers", "containing", "DPPG,", "where", "a", "higher", "propensity", "of", "maintaining", "its", "conformation", "was", "observed.", "For", "pure", "DPPG", "(Fig." ]
Original work titled: 'Binding and Flip as Initial Steps for BP-100 Antimicrobial Actions' (Scientific Reports/Nature Publishing Group UK) by the following authors: Peter Park; Leandro R. Franco; Hernan Chaimovich; Kaline Coutinho; Iolanda M. Cuccovia; Filipe S. Lima DOI: 10.1038/s41598-019-45075-5	5388809896c7b2a9adf5d708f6ea4b08	CC-BY	http://creativecommons.org/licenses/by/4.0/	4.0	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]	[ "The", "time", "window", "selected", "for", "computing", "these", "RDFs", "includes", "that", "of", "the", "membrane", "bound", "peptide", "250", "ns-before", "and", "250", "ns-after", "the", "peptide", "flip.", "The", "pairs", "with", "distinguishable", "RDF", "peaks", "and", "following", "minimum", "were", "used", "to", "analyze", "the", "number", "of", "polar", "and", "apolar", "contacts", "between", "lipids", "and", "peptide.", "A", "cutoff", "distance", "for", "each", "pair", "was", "defined", "from", "the", "position", "of", "the", "first", "minimum", "in", "the", "RDF", "curve,", "and", "a", "contact", "was", "defined", "as", "a", "pair", "of", "atoms", "at", "smaller", "distance", "than", "their", "corresponding", "cutoff", "distance.", "The", "simulations", "were", "analyzed", "and", "the", "total", "number", "of", "polar", "and", "apolar", "contacts", "as", "a", "function", "of", "time", "was", "obtained.", "Additionally,", "some", "polar", "and", "apolar", "pairs", "were", "analyzed", "individually.", "Peptide", "hydration", "The", "time", "evolution", "of", "the", "solvent", "shell", "surrounding", "the", "peptide", "in", "its", "α", "and", "L", "conformations", "in", "all", "simulated", "membranes", "was", "analyzed", "using", "the", "minimum", "distance", "distribution", "function", "(MDDF)", "29", "between", "the", "peptide", "and", "the", "water", "molecules,", "as", "well", "as", "the", "average", "number", "of", "water", "molecules", "N(r),", "within", "a", "distance", "r", "=", "0.5", "nm,", "named", "here", "as", "N(0.5).", "For", "comparison", "the", "MDDF", "of", "BP100", "in", "water", "was", "used", "to", "define", "the", "bulk", "water", "hydration", "shell", "at", "the", "same", "distance.", "Results", "The", "17", "sets", "of", "simulations", "(Table", "1", ")", "were", "run", "for", "more", "than", "25", "µs", "of", "simulation", "time,", "and", "each", "unconstrained", "peptide/membrane", "simulation", "had", "at", "least", "1.6", "µs", "of", "simulation.", "After", "comparing", "the", "simulated", "membrane", "properties", "with", "experimental", "and", "other", "computational", "studies", "(Tables", "S1", "and", "S2", "),", "we", "systematically", "analyzed", "the", "peptide", "conformation", "in", "solution", "and", "on", "bilayers,", "peptide", "trajectory,", "and", "dynamics", "on", "membranes", "and", "the", "effect", "of", "BP100", "on", "model", "bilayers.", "In", "the", "following", "sections,", "we", "describe", "our", "results.", "Secondary", "structure", "Peptide", "in", "solution", "To", "study", "BP100", "secondary", "structure", "in", "water,", "we", "did", "simulations", "for", "more", "than", "2", "µs", "with", "both", "α-BP100", "and", "L-BP100", "initial", "conformations.", "Figure", "4", "shows", "that", "BP100", "conformation", "in", "solution", "was,", "predominantly,", "random", "coil.", "The", "peptide", "lost", "the", "initial", "alpha", "helix", "conformation", "in", "approximately", "40", "ns", "when", "starting", "with", "an", "alpha-helix", "configuration", "and", "occasionally", "formed", "an", "alpha-helix", "turn", "in", "the", "5–9", "residue", "region", "(Fig.", "4a", ")." ]
Original work titled: 'Binding and Flip as Initial Steps for BP-100 Antimicrobial Actions' (Scientific Reports/Nature Publishing Group UK) by the following authors: Peter Park; Leandro R. Franco; Hernan Chaimovich; Kaline Coutinho; Iolanda M. Cuccovia; Filipe S. Lima DOI: 10.1038/s41598-019-45075-5	5388809896c7b2a9adf5d708f6ea4b08	CC-BY	http://creativecommons.org/licenses/by/4.0/	4.0	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]	[ "For", "all", "these", "initial", "conditions,", "we", "obtained", "the", "same", "final", "location", "and", "orientation", "of", "the", "peptide", "that", "will", "be", "discussed", "in", "the", "results", "section.", "To", "investigate", "the", "influence", "of", "small", "core", "alpha-helical", "sequences", "in", "BP100", "to", "its", "stability", "when", "interacting", "with", "bilayers,", "constrained", "simulations", "of", "BP100", "in", "DPPG", "membranes", "were", "performed.", "The", "alpha-helix", "dihedral", "angles", "(ϕ", "=", "−60°;", "ψ", "=", "−40°)", "in", "3", "different", "regions", "were", "fixed:", "1–5", "(Lys-Lys-Leu-Phe-Lys),", "4–8", "(Phe-Lys-Lys-Ile-Leu)", "and", "7–11", "(Ile-Leu-Lys-Tyr-Leu)", "residues", "(Fig.", "3", ").", "We", "maintained", "the", "constrained", "regions", "during", "the", "simulations.", "Figure", "3", "Starting", "structures", "for", "peptides", "with", "permanent", "constrained", "dihedral", "angles.", "Following", "the", "previous", "lipid", "membrane", "systems,", "energy-minimization,", "NVT,", "and", "NPT", "ensembles", "were", "used", "in", "the", "equilibration", "stage", "of", "the", "MD", "simulation.", "Simulation", "details", "MD", "simulations", "were", "carried", "out", "with", "a", "2", "fs", "time-step", "with", "a", "Leap-Frog", "integrator", "24", ",", "in", "isobaric-isothermal", "(NPT)", "ensemble,", "at", "323", "K", "(50", "°C)", "with", "temperature", "coupling", "treated", "separately", "for", "BP100,", "lipids,", "water", "and", "ions", "with", "the", "V-rescale", "thermostat", "25", ".", "Atmospheric", "pressure", "of", "1", "bar", "was", "kept", "with", "the", "Berendsen", "barostat", "26", "and", "semi-isotropic", "pressure", "coupling", "was", "used", "for", "all", "systems.", "All", "bonds", "were", "constrained", "with", "LINCS", "27", "algorithm.", "Long-range", "electrostatic", "correction", "was", "treated", "by", "a", "Particle-mesh-Ewald", "method", "28", "with", "a", "real-space", "cut-off", "of", "1.5", "nm.", "van", "der", "Waals", "interactions", "were", "truncated", "at", "1.5", "nm", "distance", "with", "a", "switch", "function", "from", "1.4", "nm.", "Simulation", "analyses", "Lipid/peptide", "contacts", "For", "the", "computation", "of", "lipid", "contacts", "with", "BP100", "and", "pair", "frequency,", "we", "labeled", "some", "lipid(s)", "and", "BP100", "atoms", "as", "“polar”", "or", "“apolar”,", "based", "on", "charges." ]
Original work titled: 'Binding and Flip as Initial Steps for BP-100 Antimicrobial Actions' (Scientific Reports/Nature Publishing Group UK) by the following authors: Peter Park; Leandro R. Franco; Hernan Chaimovich; Kaline Coutinho; Iolanda M. Cuccovia; Filipe S. Lima DOI: 10.1038/s41598-019-45075-5	5388809896c7b2a9adf5d708f6ea4b08	CC-BY	http://creativecommons.org/licenses/by/4.0/	4.0	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]	[ "One", "membrane", "was", "composed", "of", "randomly", "distributed", "lipids", "(PCPG-NR)", "on", "both", "leaflets", "and", "the", "other,", "a", "4", "×", "4", "DPPG", "raft", "was", "placed", "in", "the", "center", "of", "both", "monolayers", "(PCPG-R)", "and", "the", "remaining", "48", "lipids", "were", "randomly", "distributed", "(Fig.", "2", ").", "Figure", "2", "Initial", "membrane", "configurations", "membranes.", "TIP3P", "water", "molecules", "were", "used", "to", "solvate", "our", "systems,", "with", "an", "approximately", "53", "water/lipid", "ratio.", "Na", "+", "ions", "(Aqvist", "21", ")", "were", "included", "to", "counter-balance", "charges", "of", "membranes", "containing", "DPPG.", "All", "bilayer", "sets", "were", "minimized", "and", "equilibrated", "for", "20", "ps", "in", "a", "NVT", "ensemble", "and", "thereafter,", "in", "NPT", "conditions", "for", "50", "ns.", "After", "that,", "the", "bilayers", "were", "simulated", "for", "860", "ns", "(DPPC),", "1100", "ns", "(DPPG)", "and", "1200", "ns", "(for", "both", "PCPG-R", "and", "PCPG-NR).", "The", "area", "per", "lipid", "and", "membrane", "thickness", "were", "calculated", "for", "all", "membranes", "and", "thNen", "compared", "with", "experimental", "data", "and", "those", "obtained", "by", "Slipids", "authors", "(Tables", "S1", "and", "S2", ").", "The", "last", "trajectory", "frames", "of", "the", "membrane", "simulations", "were", "used", "to", "build", "our", "peptide-lipid", "systems.", "Peptide-in-solution", "and", "peptide-lipid", "systems", "Following", "a", "study", "by", "Beauchamp", "et", "al.", "22", ",", "ff99sb-ildn-NMR", "force", "field", "was", "chosen", "to", "characterize", "BP100", "in", "our", "modeling", "due", "to", "its", "good", "performance", "in", "simulating", "peptides", "and", "proteins", "structures", "in", "TIP3P", "water", "when", "compared", "with", "NMR", "measurements.", "BP100", "(H-Lys-Lys-Leu-Phe-Lys-Lys-Ile-Leu-Lys-Tyr-Leu-NH", "2", ")", "has", "an", "amidated", "C-terminal", "and", "a", "+6", "charge", "at", "physiological", "pH,", "with", "all", "its", "Lysines", "and", "N-terminal", "amine", "protonated.", "To", "study", "secondary", "structure", "behavior", "of", "BP100", "both", "in", "solution", "and", "in", "bilayers,", "two", "initial", "BP100", "conformations", "were", "used:", "linear", "BP100", "(", "L", "-BP100)", "and", "alpha-helical", "BP100", "(", "α", "-BP100)", "(Fig.", "1", "a,b", ")." ]
Original work titled: 'Binding and Flip as Initial Steps for BP-100 Antimicrobial Actions' (Scientific Reports/Nature Publishing Group UK) by the following authors: Peter Park; Leandro R. Franco; Hernan Chaimovich; Kaline Coutinho; Iolanda M. Cuccovia; Filipe S. Lima DOI: 10.1038/s41598-019-45075-5	5388809896c7b2a9adf5d708f6ea4b08	CC-BY	http://creativecommons.org/licenses/by/4.0/	4.0	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]	[ "Table", "1", "shows", "all", "simulation", "systems", "and", "its", "simulation", "time.", "The", "program", "used", "to", "analyze", "the", "hydration", "shell", "of", "the", "peptide", "using", "the", "Minimum", "Distance", "Distribution", "Function", "was", "developed", "in", "our", "group.", "Table", "1", "Table", "containing", "all", "MD", "simulation", "sets", "carried", "out", "in", "this", "work.", "For", "bilayers,", "we", "used", "Slipids", "forcefield", "and", "ff99sb-ildn-NMR", "for", "BP100.", "All", "sets", "were", "simulated", "at", "323", "K", "(above", "DPPC", "and", "DPPG", "transition", "temperatures)", "and", "1", "bar.", "L", "-BP100", "indicate", "constraint-free", "simulations", "using", "random", "coil", "BP100", "as", "peptide", "starting", "configuration", "and", "α", "-BP100,", "as", "alpha", "helix.", "Res1–5,", "res4–8", "and", "res7–11", "indicate", "simulations", "with", "BP100", "with", "permanent", "constraints", "on", "the", "referred", "residues.", "Simulation", "sets", "Simulations", "Peptide/Lipid", "Waters/Lipid", "Time", "(ns)", "Bilayers", "DPPC", "0/128", "54", "860", "DPPG", "53", "1100", "PCPG-R", "0/[64/64]", "54", "1200", "PCPG-NR", "52", "1200", "Peptide", "in", "water", "L", "-BP100", "in", "water", "1/0", "—", "2000", "α", "-BP100", "in", "water", "—", "2850", "Peptide", "with", "bilayers", "L", "-BP100", "in", "DPPC", "1/128", "54", "1700", "α", "-BP100", "in", "DPPC", "54", "2000", "L", "-BP100", "in", "DPPG", "1/128", "53", "1700", "α", "-BP100", "in", "DPPG", "53", "2000", "L", "-BP100", "in", "PCPG-R", "1/[64/64]", "54", "1600", "α", "-BP100", "in", "PCPG-R", "54", "2000", "L", "-BP100", "in", "PCPG-NR", "1/[64/64]", "52", "1700", "α", "-BP100", "in", "PCPG-NR", "52", "2000", "Partially", "constrained", "peptide", "in", "DPPG", "α-", "BP100", "(res1–5)", "in", "DPPG", "1/128", "54", "600", "α-", "BP100", "(res4–8)", "in", "DPPG", "54", "600", "α-", "BP100", "(res7–11)", "in", "DPPG", "54", "600", "Lipid", "bilayers", "We", "used", "Slipids", "forcefield", "19", "parameters", "were", "chosen", "to", "simulate", "DPPC,", "DPPG,", "and", "DPPC/DPPG", "mixed", "bilayers." ]
Original work titled: 'Binding and Flip as Initial Steps for BP-100 Antimicrobial Actions' (Scientific Reports/Nature Publishing Group UK) by the following authors: Peter Park; Leandro R. Franco; Hernan Chaimovich; Kaline Coutinho; Iolanda M. Cuccovia; Filipe S. Lima DOI: 10.1038/s41598-019-45075-5	5388809896c7b2a9adf5d708f6ea4b08	CC-BY	http://creativecommons.org/licenses/by/4.0/	4.0	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]	[ "A", "detailed", "description", "of", "peptide/membrane", "interactions", "at", "the", "atomic", "scale", "may", "help", "to", "gain", "information", "on", "CAMPs", "disruption", "mechanisms,", "permitting", "the", "rational", "design", "of", "new", "derivatives", "and,", "therefore,", "the", "better", "therapeutic", "use", "of", "these", "novel", "antimicrobials.", "Molecular", "Dynamics", "(MD)", "simulations", "provide", "atomic-level", "insights", "and", "have", "been", "widely", "used", "to", "study", "the", "interaction", "of", "AMPs", "with", "membranes", "15", "–", "18", ".", "MD", "simulations", "were", "also", "utilized", "to", "study", "BP100’s", "structure", "and", "activity:", "Wang", "Y.", "et", "al.", "17", "performed", "an", "8", "µs-long", "MD", "simulation", "of", "BP100", "in", "DMPC", "bilayer", "and", "found", "that", "BP100", "remained", "in", "the", "surface-bound-state", "inserting", "through", "its", "C-terminus.", "They", "also", "reported", "the", "unfolding", "of", "BP100", "N-terminus", "(Lys1", "and", "Lys2)", "after", "1.5", "µs,", "resulting", "in", "a", "tilt", "angle", "of", "97°", "and", "81%", "helicity", "10", ",", "17", ".", "In", "a", "study", "with", "Brownian", "Dynamics", "simulations", "with", "a", "coarse-grained", "peptide", "model,", "Alves", "et", "al.", "18", "simulated", "BP100", "confined", "in", "model", "membranes", "at", "293", "K", "for", "1", "µs", "each", "and", "reported", "the", "high", "stability", "of", "BP100", "pre-folded", "alpha", "helix", "and", "a", "threefold", "decrease", "in", "its", "lateral", "diffusion", "in", "POPC:", "POPG", "membranes", "relative", "to", "that", "in", "POPC", "membrane", "18", ".", "In", "this", "work", "we", "report", "simulations,", "in", "solution", "and", "membranes,", "extending", "for", "more", "than", "25", "µs", "of", "BP100", "and", "membranes", "of", "1,2-dipalmitoyl-sn-glycerol-3-phosphocholine", "(DPPC),", "1,2-dipalmitoyl-sn-glycerol-3-phosphoglycerol", "(DPPG),", "and", "DPPC:", "DPPG", "mixtures", "(1:1).", "We", "systematically", "investigated", "the", "dependence", "of", "BP100", "secondary", "structure", "on", "DPPG", "lipids", "which", "agrees", "with", "experimental", "findings", "11", ".", "We", "also", "analyzed", "the", "contribution", "of", "PG-containing", "lipid", "rafts", "on", "BP100", "conformation", "and", "behavior.", "In", "most", "simulations", "containing", "DPPG", "lipids,", "we", "observed", "the", "occurrence", "of", "a", "dynamic", "transition", "of", "the", "peptide", "adsorbed", "at", "the", "membrane", "interface,", "where", "the", "apolar", "facet", "of", "the", "BP100", "(Fig." ]
Original work titled: 'Binding and Flip as Initial Steps for BP-100 Antimicrobial Actions' (Scientific Reports/Nature Publishing Group UK) by the following authors: Peter Park; Leandro R. Franco; Hernan Chaimovich; Kaline Coutinho; Iolanda M. Cuccovia; Filipe S. Lima DOI: 10.1038/s41598-019-45075-5	5388809896c7b2a9adf5d708f6ea4b08	CC-BY	http://creativecommons.org/licenses/by/4.0/	4.0	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]	[ "Due", "to", "their", "potential", "advantage", "as", "antimicrobials,", "new", "AMPs", "are", "increasingly", "being", "isolated", "or", "synthesized", "and", "their", "properties", "investigated.", "Although", "increasing", "evidence", "shows", "that", "some", "AMPs", "may", "also", "act", "intracellularly,", "inhibiting", "proteins", "1", ",", "nucleic", "acids", "1", "–", "4", "and", "cell-wall", "synthesis", "1", "–", "5", "and", "inducing", "cell", "apoptosis", "1", ",", "3", ",", "5", ",", "most", "of", "them", "kill", "cells", "by", "disturbing", "the", "membrane’s", "integrity", "1", ",", "2", ",", "6", ",", "7", ".", "Several", "CAMPs", "seem", "to", "disturb", "the", "membrane", "of", "cells", "by", "self-aggregation", "on", "the", "membrane", "and", "forming", "pores", "beyond", "a", "peptide/lipid", "(P/L)", "ratio", "threshold", "1", ",", "2", ".", "BP100", "(H-KKLFKKILKYL-NH", "2", "),", "is", "a", "hybrid", "CAMP", "synthesized", "by", "combinatorial", "chemistry", "involving", "parts", "of", "two", "natural", "AMPs,", "melittin,", "and", "cecropin", "A", "8", ".", "BP100", "shows", "high", "antimicrobial", "activity", "and", "selectivity", "against", "some", "Gram-negative", "bacteria,", "with", "a", "promising", "minimal", "inhibitory", "concentration", "ranging", "from", "2.5", "to", "5", "µM", "and", "low", "cytotoxicity", "against", "mammalian", "cells", "making", "this", "peptide", "an", "exciting", "candidate", "for", "therapeutic", "use", "8", ".", "BP100", "conformation", "and", "activity", "on", "model", "membranes", "have", "been", "extensively", "analyzed", "with", "experimental", "techniques", "9", "–", "13", ".", "BP100", "has", "a", "random", "coil", "conformation", "in", "solution", "and", "zwitterionic", "bilayers", "but", "acquires", "predominantly", "alpha-helical", "and", "amphipathic", "conformation", "in", "the", "presence", "of", "negatively", "charged", "membranes.", "BP100", "is", "highly", "mobile", "on", "the", "membrane", "surface", "and", "orients", "parallel", "in", "predominantly", "negatively", "charged", "vesicles", "9", ",", "10", ".", "BP100", "secondary", "structure", "formation", "and", "bacteria", "killing", "performance", "seem", "to", "be", "directly", "related", "to", "negative", "charge", "content", "in", "membranes,", "thus", "explaining", "its", "high", "selectivity", "towards", "negative", "bacterial", "membrane", "and", "low", "cytotoxicity", "against", "predominantly", "less", "negatively", "charged", "mammalian", "cell", "membranes", "11", ",", "14", ".", "Experimental", "approaches", "to", "investigate", "peptide/membrane", "interactions", "mainly", "focus", "macroscopic-averaged", "insight", "on", "a", "mesoscopic", "scale.", "A", "detailed", "description", "of", "peptide/membrane", "interactions", "at", "the", "atomic", "scale", "may", "help", "to", "gain", "information", "on", "CAMPs", "disruption", "mechanisms,", "permitting", "the", "rational", "design", "of", "new", "derivatives", "and,", "therefore,", "the", "better", "therapeutic", "use", "of", "these", "novel", "antimicrobials." ]
Original work titled: 'Gut microbiome associated with chemotherapy-induced diarrhea from the CapeOX regimen as adjuvant chemotherapy in resected stage III colorectal cancer' (Gut Pathogens/BioMed Central) by the following authors: Zuo Fei; Yin Lijuan; Yang Xi; Wu Wei; Zhong Jing; Da Miao; Han Shuwen DOI: 10.1186/s13099-019-0299-4	f7083ca86a7871cc8d04d2500480cbf3	CC-BY	http://creativecommons.org/licenses/by/4.0/	4.0	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]	[ "How", "to", "effectively", "and", "efficiently", "avoid", "or", "to", "alleviate", "the", "toxicity", "and", "side", "effects", "is", "a", "critical", "clinical", "problem", "that", "should", "be", "solved.", "CID", "is", "a", "common", "side", "effect", "of", "the", "digestive", "system", "in", "the", "antitumor", "treatment", "process", "of", "cytotoxic", "drugs.", "The", "typical", "clinical", "characteristics", "of", "CID", "are", "as", "follows:", "symptoms", "range", "from", "loose", "stool", "without", "pain", "to", "severe,", "watery", "diarrhea", "with", "abdominal", "pain;", "symptoms", "typically", "last", "5", "to", "7", "days", "and", "may", "occur", "during", "or", "after", "chemotherapy;", "and", "patients", "with", "CID", "have", "a", "poor", "treatment", "response", "to", "gentamicin,", "berberine,", "and", "furoxone", "[", "9", "].", "CID", "can", "lead", "to", "weakness,", "electrolyte", "disorders,", "renal", "failure,", "blood", "volume", "reductions,", "shock,", "and", "even", "death", "[", "10", "].", "Its", "occurrence", "can", "result", "in", "delaying", "chemotherapy,", "increasing", "hospitalization", "time", "and", "costs,", "aggravating", "the", "psychological", "stress", "of", "patients,", "reducing", "the", "treatment", "compliance", "of", "patients", "and", "even", "altering", "the", "entire", "chemotherapy", "plan", "[", "11", "].", "A", "unique", "microecosystem", "and", "characteristic", "microbial", "community", "lives", "in", "the", "colorectal", "regions", "owing", "to", "their", "function", "of", "storing", "feces", "[", "12", "].", "Accumulating", "evidence", "points", "to", "the", "gut", "microbiome", "being", "involved", "in", "CRC", "[", "13", "].", "For", "example,", "some", "researchers", "have", "reported", "that", "Streptococcus", "bovis", "[", "14", "]", "and", "Trichophyton", "tonsurans", "[", "15", "]", "are", "specific", "bacteria", "involved", "in", "colorectal", "cancer;", "Castellarin", "et", "al.", "[", "16", "]", "found", "that", "Thanatephorus", "cucumeris", "infection", "is", "prevalent", "in", "CRC", "tissue", "specimens", "and", "Kostic", "et", "al.", "[", "17", "],", "found", "that", "Thanatephorus", "cucumeris", "can", "generate", "a", "proinflammatory", "microenvironment", "that", "is", "conducive", "to", "the", "progression", "of", "CRC", "through", "recruitment", "of", "tumor-infiltrating", "immune", "cells.", "Moreover,", "many", "enzymes,", "peptides", "and", "small", "molecules", "secreted", "by", "the", "intestinal", "gut", "microbiome", "are", "involved", "in", "activating", "and", "regulating", "important", "signaling", "molecules", "and", "signaling", "pathways", "involved", "in", "the", "progression", "of", "CRC", "[", "18", ",", "19", "].", "Diarrhea", "and", "gut", "microbiome", "disorders", "interact", "as", "both", "cause", "and", "effect.", "Diarrhea", "can", "disrupt", "the", "balance", "of", "the", "gut", "microenvironment." ]
Original work titled: 'Gut microbiome associated with chemotherapy-induced diarrhea from the CapeOX regimen as adjuvant chemotherapy in resected stage III colorectal cancer' (Gut Pathogens/BioMed Central) by the following authors: Zuo Fei; Yin Lijuan; Yang Xi; Wu Wei; Zhong Jing; Da Miao; Han Shuwen DOI: 10.1186/s13099-019-0299-4	f7083ca86a7871cc8d04d2500480cbf3	CC-BY	http://creativecommons.org/licenses/by/4.0/	4.0	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]	[ "Its", "occurrence", "can", "result", "in", "delaying", "chemotherapy,", "increasing", "hospitalization", "time", "and", "costs,", "aggravating", "the", "psychological", "stress", "of", "patients,", "reducing", "the", "treatment", "compliance", "of", "patients", "and", "even", "altering", "the", "entire", "chemotherapy", "plan", "[", "11", "].", "A", "unique", "microecosystem", "and", "characteristic", "microbial", "community", "lives", "in", "the", "colorectal", "regions", "owing", "to", "their", "function", "of", "storing", "feces", "[", "12", "].", "Accumulating", "evidence", "points", "to", "the", "gut", "microbiome", "being", "involved", "in", "CRC", "[", "13", "].", "For", "example,", "some", "researchers", "have", "reported", "that", "Streptococcus", "bovis", "[", "14", "]", "and", "Methanococcus", "voltae", "[", "15", "]", "are", "specific", "bacteria", "involved", "in", "colorectal", "cancer;", "Castellarin", "et", "al.", "[", "16", "]", "found", "that", "Drosophila", "americana", "infection", "is", "prevalent", "in", "CRC", "tissue", "specimens", "and", "Kostic", "et", "al.", "[", "17", "],", "found", "that", "Drosophila", "americana", "can", "generate", "a", "proinflammatory", "microenvironment", "that", "is", "conducive", "to", "the", "progression", "of", "CRC", "through", "recruitment", "of", "tumor-infiltrating", "immune", "cells.", "Moreover,", "many", "enzymes,", "peptides", "and", "small", "molecules", "secreted", "by", "the", "intestinal", "gut", "microbiome", "are", "involved", "in", "activating", "and", "regulating", "important", "signaling", "molecules", "and", "signaling", "pathways", "involved", "in", "the", "progression", "of", "CRC", "[", "18", ",", "19", "].", "Diarrhea", "and", "gut", "microbiome", "disorders", "interact", "as", "both", "cause", "and", "effect.", "Diarrhea", "can", "disrupt", "the", "balance", "of", "the", "gut", "microenvironment.", "Meanwhile,", "the", "invasion", "of", "exogenous", "pathogenic", "microorganisms", "and", "the", "imbalance", "of", "intestinal", "microbes", "can", "lead", "to", "diarrhea", "[", "20", "].", "For", "example,", "the", "invasion", "of", "some", "pathogenic", "bacteria", "including", "Shigella,", "Salmonella", "and", "Klebsiella", "[", "21", ",", "22", "],", "and", "the", "abundance", "changes", "of", "intestinal", "parasitic", "microbes", "include", "Geothlypis", "tolmiei,", "Gratiola", "brevifolia,", "and", "Aeromonas", "can", "induce", "diarrhea", "[", "23", "–", "25", "].", "Chemotherapy", "has", "been", "widely", "used", "in", "the", "clinic", "as", "an", "effective", "therapy", "for", "colorectal", "cancer,", "but", "diarrhea", "caused", "by", "chemotherapeutic", "drugs", "often", "affects", "the", "implementation", "of", "chemotherapy", "regimens", "[", "26", "]." ]
Original work titled: 'Gut microbiome associated with chemotherapy-induced diarrhea from the CapeOX regimen as adjuvant chemotherapy in resected stage III colorectal cancer' (Gut Pathogens/BioMed Central) by the following authors: Zuo Fei; Yin Lijuan; Yang Xi; Wu Wei; Zhong Jing; Da Miao; Han Shuwen DOI: 10.1186/s13099-019-0299-4	f7083ca86a7871cc8d04d2500480cbf3	CC-BY	http://creativecommons.org/licenses/by/4.0/	4.0	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]	[ "Moreover,", "many", "enzymes,", "peptides", "and", "small", "molecules", "secreted", "by", "the", "intestinal", "gut", "microbiome", "are", "involved", "in", "activating", "and", "regulating", "important", "signaling", "molecules", "and", "signaling", "pathways", "involved", "in", "the", "progression", "of", "CRC", "[", "18", ",", "19", "].", "Diarrhea", "and", "gut", "microbiome", "disorders", "interact", "as", "both", "cause", "and", "effect.", "Diarrhea", "can", "disrupt", "the", "balance", "of", "the", "gut", "microenvironment.", "Meanwhile,", "the", "invasion", "of", "exogenous", "pathogenic", "microorganisms", "and", "the", "imbalance", "of", "intestinal", "microbes", "can", "lead", "to", "diarrhea", "[", "20", "].", "For", "example,", "the", "invasion", "of", "some", "pathogenic", "bacteria", "including", "Shigella,", "Salmonella", "and", "Klebsiella", "[", "21", ",", "22", "],", "and", "the", "abundance", "changes", "of", "intestinal", "parasitic", "microbes", "include", "Pterodroma", "neglecta,", "Banisteriopsis", "caapi,", "and", "Aeromonas", "can", "induce", "diarrhea", "[", "23", "–", "25", "].", "Chemotherapy", "has", "been", "widely", "used", "in", "the", "clinic", "as", "an", "effective", "therapy", "for", "colorectal", "cancer,", "but", "diarrhea", "caused", "by", "chemotherapeutic", "drugs", "often", "affects", "the", "implementation", "of", "chemotherapy", "regimens", "[", "26", "].", "Many", "probiotics", "and", "antibiotics", "play", "a", "positive", "role", "in", "the", "treatment", "of", "infectious", "diarrhea", "by", "regulating", "the", "gut", "microbiome", "[", "27", ",", "28", "].", "The", "study", "of", "relationships", "between", "gut", "microbiome", "and", "CID", "may", "provide", "a", "new", "direction", "for", "solving", "this", "clinical", "problem.", "In", "the", "present", "study,", "we", "aimed", "to", "explore", "the", "association", "between", "the", "gut", "microorganisms", "and", "CID", "of", "the", "CapeOX", "regimen", "in", "resected", "stage", "III", "CRC", "and", "to", "provide", "some", "research", "methods", "and", "research", "ideas", "for", "further", "exploring", "the", "relationship", "between", "intestinal", "microbes", "and", "CID.", "The", "results", "may", "provide", "a", "fresh", "approach", "to", "the", "prevention", "and", "treatment", "of", "CID", "from", "a", "microbiological", "perspective.", "Subjects", "and", "methods", "Subjects", "Patients", "with", "CRC", "treated", "at", "Huzhou", "Central", "Hospital", "from", "January", "2016", "to", "January", "2018", "were", "studied.", "The", "clinical", "protocols", "involving", "the", "patients", "and", "the", "informed", "consent", "form", "were", "approved", "by", "the", "Ethics", "Committee", "of", "Huzhou", "Central", "Hospital", "(No.", "201601023)." ]
Original work titled: 'Gut microbiome associated with chemotherapy-induced diarrhea from the CapeOX regimen as adjuvant chemotherapy in resected stage III colorectal cancer' (Gut Pathogens/BioMed Central) by the following authors: Zuo Fei; Yin Lijuan; Yang Xi; Wu Wei; Zhong Jing; Da Miao; Han Shuwen DOI: 10.1186/s13099-019-0299-4	f7083ca86a7871cc8d04d2500480cbf3	CC-BY	http://creativecommons.org/licenses/by/4.0/	4.0	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]	[ "②", "Patients", "with", "other", "intestinal", "diseases,", "such", "as", "ulcerative", "colitis", "and", "Crohn’s", "disease.", "③", "Alternation", "of", "chemotherapy", "regimen", "and", "chemotherapeutic", "dosage", "or", "the", "occurrence", "of", "progression", "of", "the", "disease", "(PD)", "during", "the", "8", "cycles", "of", "the", "CapeOX", "regimen.", "④", "Patients", "who", "accepted", "neo-adjuvant", "chemotherapy.", "⑤", "Patients", "with", "a", "history", "of", "the", "use", "of", "oral", "microbial", "agents", "within", "1", "month", "before", "chemotherapy.", "⑥", "Patients", "with", "another", "primary", "cancer.", "⑦", "Patients", "with", "known", "primary", "organ", "failure.", "⑧", "Patients", "who", "could", "not", "obtained", "the", "stool", "samples", "(n", "=", "15)", "or", "obtained", "unqualified", "stool", "samples.", "All", "of", "the", "subjects", "signed", "informed", "consent", "under", "the", "guidelines", "approved", "by", "the", "Ethics", "Committee", "of", "Huzhou", "Central", "Hospital.", "CRC", "patients", "with", "and", "without", "CID", "were", "including", "in", "the", "experimental", "group", "and", "control", "group,", "respectively.", "According", "to", "National", "Cancer", "Institute", "Common", "Toxicity", "Criteria", "(NCI", "CTC)", "V3.0", "[", "30", "]", "CID", "grade", "1", "is", "defined", "as", "the", "number", "of", "defecations", "increased", "to", "less", "than", "4", "times", "a", "day", "and", "an", "excretion", "volume", "slightly", "increased.", "During", "a", "course", "of", "8", "cycles", "of", "chemotherapy", "administered", "over", "nearly", "half", "a", "year,", "there", "are", "many", "factors", "that", "can", "cause", "diarrhea,", "and", "these", "factors", "interfere", "with", "the", "diagnosis", "of", "CID.", "Clinical", "intervention", "measures,", "such", "as", "using", "antibiotics", "and", "antidiarrheal", "drugs,", "may", "be", "performed", "and", "the", "chemotherapy", "regimen", "may", "be", "changed", "in", "patients", "with", "CID", "grade", "3", "and", "grade", "4.", "Therefore,", "we", "did", "not", "include", "patients", "with", "grade", "1,", "grade", "3", "and", "grade", "4", "in", "the", "experimental", "group.", "CID", "grade", "2", "is", "defined", "as", "the", "number", "of", "defecations", "increased", "to", "4–6", "times", "per", "day", "or", "nocturnal", "stools,", "with", "the", "amount", "of", "excretion", "increased", "but", "with", "no", "interference", "in", "daily", "life.", "All", "of", "the", "subjects", "recruited", "into", "the", "experimental", "group", "were", "CID", "grade", "2", "in", "the", "present", "study.", "Collection", "of", "clinical", "data", "and", "stool", "samples", "Basic", "information", "and", "clinical", "serological", "indicators", "were", "obtained", "from", "the", "medical", "record", "management", "system", "of", "Huzhou", "Central", "Hospital", "with", "informed", "consent", "from", "patients.", "Stool", "samples", "of", "the", "patients", "were", "collected", "in", "the", "2", "weeks", "after", "the", "8", "cycles", "of", "chemotherapy.", "Stool", "samples", "were", "collected", "in", "the", "morning", "prior", "to", "breakfast." ]
Original work titled: 'Gut microbiome associated with chemotherapy-induced diarrhea from the CapeOX regimen as adjuvant chemotherapy in resected stage III colorectal cancer' (Gut Pathogens/BioMed Central) by the following authors: Zuo Fei; Yin Lijuan; Yang Xi; Wu Wei; Zhong Jing; Da Miao; Han Shuwen DOI: 10.1186/s13099-019-0299-4	f7083ca86a7871cc8d04d2500480cbf3	CC-BY	http://creativecommons.org/licenses/by/4.0/	4.0	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]	[ "During", "a", "course", "of", "8", "cycles", "of", "chemotherapy", "administered", "over", "nearly", "half", "a", "year,", "there", "are", "many", "factors", "that", "can", "cause", "diarrhea,", "and", "these", "factors", "interfere", "with", "the", "diagnosis", "of", "CID.", "Clinical", "intervention", "measures,", "such", "as", "using", "antibiotics", "and", "antidiarrheal", "drugs,", "may", "be", "performed", "and", "the", "chemotherapy", "regimen", "may", "be", "changed", "in", "patients", "with", "CID", "grade", "3", "and", "grade", "4.", "Therefore,", "we", "did", "not", "include", "patients", "with", "grade", "1,", "grade", "3", "and", "grade", "4", "in", "the", "experimental", "group.", "CID", "grade", "2", "is", "defined", "as", "the", "number", "of", "defecations", "increased", "to", "4–6", "times", "per", "day", "or", "nocturnal", "stools,", "with", "the", "amount", "of", "excretion", "increased", "but", "with", "no", "interference", "in", "daily", "life.", "All", "of", "the", "subjects", "recruited", "into", "the", "experimental", "group", "were", "CID", "grade", "2", "in", "the", "present", "study.", "Collection", "of", "clinical", "data", "and", "stool", "samples", "Basic", "information", "and", "clinical", "serological", "indicators", "were", "obtained", "from", "the", "medical", "record", "management", "system", "of", "Huzhou", "Central", "Hospital", "with", "informed", "consent", "from", "patients.", "Stool", "samples", "of", "the", "patients", "were", "collected", "in", "the", "2", "weeks", "after", "the", "8", "cycles", "of", "chemotherapy.", "Stool", "samples", "were", "collected", "in", "the", "morning", "prior", "to", "breakfast.", "An", "approximately", "5–10", "g", "stool", "sample", "was", "collected", "after", "defecation", "without", "the", "use", "of", "a", "purgative", "or", "lubricant.", "Within", "half", "an", "hour,", "the", "stool", "samples", "were", "stored", "in", "an", "ultra-low", "temperature", "freezer.", "The", "sample", "preservation", "time", "was", "not", "beyond", "1", "month.", "Finally,", "17", "stool", "samples", "from", "CRC", "patients", "were", "analyzed", "after", "the", "patients", "had", "signed", "informed", "consent", "forms", "and", "the", "unqualified", "specimens", "were", "eliminated.", "Intestinal", "microorganism", "detection", "DNA", "extraction", "and", "PCR", "amplification", "A", "E.Z.N.A.", "®", "Stool", "DNA", "Kit", "(Omega", "Bio-Tek,", "Norcross,", "GA,", "U.S.)", "was", "used", "to", "extract", "total", "DNA", "from", "the", "stool", "samples", "according", "to", "the", "manufacturer’s", "protocols.", "The", "nanodrop", "ND-1000", "spectrophotometer", "(LabTech,", "Washington,", "DC,", "USA)", "with", "the", "absorbances", "at", "260", "nm", "and", "280", "nm", "(A260/A280)", "was", "used", "to", "determine", "the", "quality", "and", "quantity", "of", "the", "purified", "DNA.", "DNA", "integrity", "was", "further", "verified", "by", "electrophoresis", "through", "a", "2.0%", "(w/v)", "agarose", "gel." ]
Original work titled: 'Gut microbiome associated with chemotherapy-induced diarrhea from the CapeOX regimen as adjuvant chemotherapy in resected stage III colorectal cancer' (Gut Pathogens/BioMed Central) by the following authors: Zuo Fei; Yin Lijuan; Yang Xi; Wu Wei; Zhong Jing; Da Miao; Han Shuwen DOI: 10.1186/s13099-019-0299-4	f7083ca86a7871cc8d04d2500480cbf3	CC-BY	http://creativecommons.org/licenses/by/4.0/	4.0	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]	[ "Intestinal", "microorganism", "detection", "DNA", "extraction", "and", "PCR", "amplification", "A", "E.Z.N.A.", "®", "Stool", "DNA", "Kit", "(Omega", "Bio-Tek,", "Norcross,", "GA,", "U.S.)", "was", "used", "to", "extract", "total", "DNA", "from", "the", "stool", "samples", "according", "to", "the", "manufacturer’s", "protocols.", "The", "nanodrop", "ND-1000", "spectrophotometer", "(LabTech,", "Washington,", "DC,", "USA)", "with", "the", "absorbances", "at", "260", "nm", "and", "280", "nm", "(A260/A280)", "was", "used", "to", "determine", "the", "quality", "and", "quantity", "of", "the", "purified", "DNA.", "DNA", "integrity", "was", "further", "verified", "by", "electrophoresis", "through", "a", "2.0%", "(w/v)", "agarose", "gel.", "PCR", "(95", "°C", "for", "3", "min,", "followed", "by", "25", "cycles", "at", "95", "°C", "for", "30", "s,", "55", "°C", "for", "30", "s,", "and", "72", "°C", "for", "45", "s", "and", "a", "final", "extension", "at", "72", "°C", "for", "5", "min)", "was", "used", "to", "amplify", "the", "V3–V4", "region", "of", "the", "bacterial", "16S", "ribosomal", "RNA", "gene", "(the", "primers", "of", "16S", "V3–V4", "rDNA", "are", "as", "follows:", "forward,", "CCTACGGGNGGCWGCAG", "and", "reverse,", "GACTACHVGGGTATCTAATCC).", "PCR", "amplifications", "were", "performed", "in", "triplicate", "in", "a", "25", "μL", "mixture", "containing", "5", "μL", "of", "DNA", "template,", "2", "μL", "of", "Nextera", "XT", "Index", "Primer", "1", "(10", "M),", "2", "μL", "of", "Nextera", "XT", "Index", "Primer", "2", "(10", "M)", "and", "16", "μL", "ddH", "2", "O.", "Amplicons", "were", "extracted", "from", "2%", "agarose", "gels,", "purified", "using", "the", "AxyPrep", "DNA", "Gel", "Extraction", "Kit", "(Axygen", "Biosciences,", "Union", "City,", "CA,", "USA)", "and", "quantified", "using", "QuantiFluor™-ST", "(Promega,", "U.S.)", "according", "to", "the", "manufacturer’s", "instructions.", "Library", "construction", "and", "sequencing", "The", "MiSeq", "library", "was", "constructed", "as", "follows:", "purified", "PCR", "products", "were", "quantified", "by", "Qubit", "®", "3.0", "(Life", "Technologies,", "Invitrogen).", "PCR", "products", "were", "ligated", "with", "Y", "adapter." ]
Original work titled: 'Gut microbiome associated with chemotherapy-induced diarrhea from the CapeOX regimen as adjuvant chemotherapy in resected stage III colorectal cancer' (Gut Pathogens/BioMed Central) by the following authors: Zuo Fei; Yin Lijuan; Yang Xi; Wu Wei; Zhong Jing; Da Miao; Han Shuwen DOI: 10.1186/s13099-019-0299-4	f7083ca86a7871cc8d04d2500480cbf3	CC-BY	http://creativecommons.org/licenses/by/4.0/	4.0	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]	[ "An", "Illumina", "Pair-End", "library", "was", "constructed", "using", "pooled", "DNA", "products,", "and", "the", "amplicon", "library", "was", "pair-end", "sequenced", "(2", "×", "250)", "on", "an", "Illumina", "MiSeq", "platform", "(Shanghai", "BIOZERON", "Co.,", "Ltd.)", "according", "to", "standard", "protocols", "(MiSeq", "V3", "or", "V4", "sequencing", "kit,", "Hua", "Ya", "Regenerative", "Medicine", "Biological", "Engineering", "Technology", "CO.,", "LTD,", "Shanghai,", "China).", "Sequencing", "data", "bioinformatics", "analysis", "Sequencing", "data", "processing", "and", "optimization", "were", "performed", "according", "to", "the", "criteria", "at", "http://en.wikipedia.org/wiki/Fastq", ".", "Cutadapt", "(version", "1.11)", "was", "used", "to", "demultiplex", "and", "quality", "filter", "the", "raw", "fastq", "files.", "Pandaseq", "(version", "2.9)", "was", "used", "to", "assemble", "PE", "reads;", "only", "sequences", "that", "overlapped", "longer", "than", "10", "bp", "were", "assembled", "according", "to", "their", "overlap", "sequence.", "Mosaic", "sequences", "and", "sequences", "longer", "than", "300–480", "bp", "were", "discarded.", "In", "addition,", "the", "reads", "that", "receiving", "an", "average", "quality", "score", "<", "20", "were", "discarded.", "The", "Silva", "database", "was", "used", "for", "comparison", "of", "16S", "rRNA", "gene", "sequences", "[", "31", "]", "and", "the", "GeneBank", "database", "was", "used", "to", "analyze", "functional", "genes", "[", "32", "].", "Mothur", "software", "[", "33", "]", "(", "http://www.mothur.org/wiki/Main_Page", ")", "was", "used", "to", "analyze", "the", "microbial", "diversity.", "OTU", "(operational", "taxonomic", "units),", "as", "the", "artificial", "classification", "unit,", "was", "used", "to", "estimate", "the", "number", "of", "species", "in", "each", "sample,", "and", "the", "similarity", "threshold", "was", "97%.", "The", "coverage", "(", "http://www.mothur.org/wiki/Coverage", ")", "was", "used", "as", "the", "sequencing", "depth", "index.", "The", "ACE", "estimator", "(", "http://www.mothur.org/wiki/Ace", ")", "and", "Chao", "estimator", "(", "http://www.mothur.org/wiki/Chao", ")", "were", "used", "to", "estimate", "the", "gut", "microbial", "community", "richness.", "The", "Shannon", "index", "(", "http://www.mothur.org/wiki/Shannon", ")", "and", "Simpson", "index", "(", "http://www.mothur.org/wiki/Simpson", ")", "were", "used", "to", "estimate", "the", "gut", "microbial", "community", "diversity." ]
Original work titled: 'Gut microbiome associated with chemotherapy-induced diarrhea from the CapeOX regimen as adjuvant chemotherapy in resected stage III colorectal cancer' (Gut Pathogens/BioMed Central) by the following authors: Zuo Fei; Yin Lijuan; Yang Xi; Wu Wei; Zhong Jing; Da Miao; Han Shuwen DOI: 10.1186/s13099-019-0299-4	f7083ca86a7871cc8d04d2500480cbf3	CC-BY	http://creativecommons.org/licenses/by/4.0/	4.0	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]	[ "Mothur", "software", "[", "33", "]", "(", "http://www.mothur.org/wiki/Main_Page", ")", "was", "used", "to", "analyze", "the", "microbial", "diversity.", "OTU", "(operational", "taxonomic", "units),", "as", "the", "artificial", "classification", "unit,", "was", "used", "to", "estimate", "the", "number", "of", "species", "in", "each", "sample,", "and", "the", "similarity", "threshold", "was", "97%.", "The", "coverage", "(", "http://www.mothur.org/wiki/Coverage", ")", "was", "used", "as", "the", "sequencing", "depth", "index.", "The", "ACE", "estimator", "(", "http://www.mothur.org/wiki/Ace", ")", "and", "Chao", "estimator", "(", "http://www.mothur.org/wiki/Chao", ")", "were", "used", "to", "estimate", "the", "gut", "microbial", "community", "richness.", "The", "Shannon", "index", "(", "http://www.mothur.org/wiki/Shannon", ")", "and", "Simpson", "index", "(", "http://www.mothur.org/wiki/Simpson", ")", "were", "used", "to", "estimate", "the", "gut", "microbial", "community", "diversity.", "The", "pie", "charts", "were", "used", "to", "describe", "the", "distribution", "of", "microorganisms", "at", "the", "species", "level.", "Proportions", "less", "than", "1%", "were", "included", "in", "“Others”,", "considering", "the", "best", "visual", "presentation.", "Venn", "diagrams", "were", "implemented", "by", "Venn", "diagram.", "We", "performed", "clustering", "on", "genera", "obtained", "from", "the", "RDP", "Classifier", "by", "means", "of", "the", "complete", "linkage", "hierarchical", "clustering", "technique", "using", "the", "R", "package", "HCLUST", "(", "http://sekhon.berkeley.edu/stats/html/hclust.html", ").", "The", "basic", "process", "of", "LDA", "analysis", "[", "34", "]", "was", "as", "follows:", "First,", "non-parametric", "Kruskal–Wallis", "rank", "sum", "test", "was", "used", "to", "detect", "the", "significant", "difference", "of", "abundance", "among", "species", "between", "the", "two", "groups", "of", "samples.", "Then", "Wilcoxon", "rank", "sum", "test", "was", "used", "to", "analyze", "the", "difference", "between", "groups", "based", "on", "the", "significant", "difference", "species.", "Finally,", "LDA", "was", "used", "to", "reduce", "the", "dimension", "of", "data", "and", "evaluate", "the", "influence", "of", "significantly", "different", "species", "(LDA", "score).", "LDA", "effect", "size", "more", "than", "2", "was", "included", "in", "the", "figure.", "The", "genes", "of", "the", "16S", "corresponding", "species", "and", "their", "copy", "number", "have", "been", "generally", "known,", "and", "these", "genes", "can", "be", "compared", "with", "databases", "(e.g.", "KEGG,", "NOG)", "to", "predict", "the", "possible", "metabolic", "capacity", "of", "these", "species." ]
Original work titled: 'Gut microbiome associated with chemotherapy-induced diarrhea from the CapeOX regimen as adjuvant chemotherapy in resected stage III colorectal cancer' (Gut Pathogens/BioMed Central) by the following authors: Zuo Fei; Yin Lijuan; Yang Xi; Wu Wei; Zhong Jing; Da Miao; Han Shuwen DOI: 10.1186/s13099-019-0299-4	f7083ca86a7871cc8d04d2500480cbf3	CC-BY	http://creativecommons.org/licenses/by/4.0/	4.0	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]	[ "According", "to", "the", "NCCN", "guidelines,", "the", "CapeOX", "regimen", "for", "resected", "stage", "III", "CRC", "has", "been", "defined", "as", "8", "cycles", "of", "capecitabine", "(1000", "mg/m", "2", "twice", "daily)", "combined", "with", "oxaliplatin", "(130", "mg/m", "2", "every", "3", "weeks)", "[", "36", "].", "CID", "is", "one", "of", "the", "most", "common", "side", "effects", "of", "the", "CapeOX", "regimen", "[", "37", "].", "The", "degree", "of", "diarrhea", "caused", "by", "different", "chemotherapeutic", "agents", "varies.", "Among", "the", "chemotherapeutic", "drugs", "for", "colorectal", "cancer,", "the", "most", "common", "drugs", "that", "cause", "diarrhea", "are", "fluorouracil,", "irinotecan", "and", "platinum,", "and", "the", "incidence", "of", "diarrhea", "associated", "with", "these", "drugs", "can", "be", "as", "high", "as", "50–80%", "[", "38", "].", "Our", "previous", "clinical", "investigation", "found", "that", "the", "probability", "of", "CID", "increased", "with", "an", "increase", "of", "chemotherapeutic", "frequency", "and", "chemotherapeutic", "dosage", "and", "most", "cases", "of", "CID", "occur", "within", "2", "weeks", "after", "chemotherapy.", "Therefore,", "in", "the", "present", "study,", "stool", "samples", "from", "the", "patients", "were", "collected", "in", "2", "weeks", "after", "the", "8", "cycles", "of", "chemotherapy", "of", "the", "CapeOX", "regimen", "were", "completed.", "Studies", "of", "Carroll", "et", "al.", "[", "39", "]", "suggested", "that", "the", "richness", "of", "16S", "rRNA", "sequences", "was", "significantly", "decreased", "in", "patients", "with", "diarrhea-predominant", "irritable", "bowel", "syndrome.", "Lee", "[", "40", "]", "has", "reported", "the", "community", "diversity", "of", "gut", "microbiome", "is", "lower", "in", "patients", "with", "kidney", "posttransplant", "diarrhea.", "Similar", "results", "have", "been", "reported", "in", "dogs", "with", "acute", "diarrhea", "[", "41", "].", "The", "research", "on", "these", "diarrhea", "diseases", "is", "consistent", "with", "our", "findings.", "We", "found", "that", "the", "gut", "microbial", "community", "richness", "and", "community", "diversity", "was", "lower", "in", "CRC", "patients", "with", "CID", "in", "the", "present", "study.", "The", "decrease", "of", "microbial", "diversity", "may", "be", "related", "to", "the", "imbalance", "of", "gut", "microbiome.", "The", "dominant", "pathogenic", "bacteria", "leads", "to", "the", "reduction", "of", "the", "resident", "normal", "microbiota", "through", "the", "plunder", "of", "nutrients", "or", "the", "killing", "effect", "of", "bacterial", "toxic", "metabolites.", "Our", "results", "from", "the", "microbial", "community", "structure", "analysis", "showed", "Caridina", "spongicola", "occupied", "the", "highest", "proportion", "(31.22%)", "of", "gut", "microbiome", "in", "CRC", "patients", "with", "CID." ]
Original work titled: 'Gut microbiome associated with chemotherapy-induced diarrhea from the CapeOX regimen as adjuvant chemotherapy in resected stage III colorectal cancer' (Gut Pathogens/BioMed Central) by the following authors: Zuo Fei; Yin Lijuan; Yang Xi; Wu Wei; Zhong Jing; Da Miao; Han Shuwen DOI: 10.1186/s13099-019-0299-4	f7083ca86a7871cc8d04d2500480cbf3	CC-BY	http://creativecommons.org/licenses/by/4.0/	4.0	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]	[ "Our", "previous", "clinical", "investigation", "found", "that", "the", "probability", "of", "CID", "increased", "with", "an", "increase", "of", "chemotherapeutic", "frequency", "and", "chemotherapeutic", "dosage", "and", "most", "cases", "of", "CID", "occur", "within", "2", "weeks", "after", "chemotherapy.", "Therefore,", "in", "the", "present", "study,", "stool", "samples", "from", "the", "patients", "were", "collected", "in", "2", "weeks", "after", "the", "8", "cycles", "of", "chemotherapy", "of", "the", "CapeOX", "regimen", "were", "completed.", "Studies", "of", "Carroll", "et", "al.", "[", "39", "]", "suggested", "that", "the", "richness", "of", "16S", "rRNA", "sequences", "was", "significantly", "decreased", "in", "patients", "with", "diarrhea-predominant", "irritable", "bowel", "syndrome.", "Lee", "[", "40", "]", "has", "reported", "the", "community", "diversity", "of", "gut", "microbiome", "is", "lower", "in", "patients", "with", "kidney", "posttransplant", "diarrhea.", "Similar", "results", "have", "been", "reported", "in", "dogs", "with", "acute", "diarrhea", "[", "41", "].", "The", "research", "on", "these", "diarrhea", "diseases", "is", "consistent", "with", "our", "findings.", "We", "found", "that", "the", "gut", "microbial", "community", "richness", "and", "community", "diversity", "was", "lower", "in", "CRC", "patients", "with", "CID", "in", "the", "present", "study.", "The", "decrease", "of", "microbial", "diversity", "may", "be", "related", "to", "the", "imbalance", "of", "gut", "microbiome.", "The", "dominant", "pathogenic", "bacteria", "leads", "to", "the", "reduction", "of", "the", "resident", "normal", "microbiota", "through", "the", "plunder", "of", "nutrients", "or", "the", "killing", "effect", "of", "bacterial", "toxic", "metabolites.", "Our", "results", "from", "the", "microbial", "community", "structure", "analysis", "showed", "Paxillus", "involutus", "occupied", "the", "highest", "proportion", "(31.22%)", "of", "gut", "microbiome", "in", "CRC", "patients", "with", "CID.", "Lu", "et", "al.", "[", "42", "]", "reported", "that", "the", "rate", "of", "Paxillus", "involutus", "was", "approximately", "0.5%", "in", "Beijing", "by", "culturing", "the", "stool", "pathogens", "from", "outpatients", "with", "diarrhea", "syndromes", "using", "the", "Vitek2", "Compact", "instrument.", "Zhang", "et", "al.", "[", "22", "]", "only", "isolated", "43", "Paxillus", "involutus", "strains", "from", "551", "stool", "specimens", "from", "diarrhea", "patients.", "Although", "the", "study", "may", "have", "be", "interfered", "by", "other", "factors", "such", "as", "geographical", "location,", "nosocomial", "infection,", "or", "pollution", "contamination", "in", "the", "fecal", "collection", "process.", "The", "increased", "proportion", "of", "Paxillus", "involutus", "in", "patients", "with", "CID", "remains", "a", "phenomenon", "of", "concern.", "Microorganisms", "can", "adjust", "and", "modify", "their", "surroundings", "due", "to", "their", "metabolic", "products.", "A", "series", "of", "enzymes", "and", "genes", "participate", "in", "the", "process", "of", "metabolism", "[", "12", "]." ]
Original work titled: 'Gut microbiome associated with chemotherapy-induced diarrhea from the CapeOX regimen as adjuvant chemotherapy in resected stage III colorectal cancer' (Gut Pathogens/BioMed Central) by the following authors: Zuo Fei; Yin Lijuan; Yang Xi; Wu Wei; Zhong Jing; Da Miao; Han Shuwen DOI: 10.1186/s13099-019-0299-4	f7083ca86a7871cc8d04d2500480cbf3	CC-BY	http://creativecommons.org/licenses/by/4.0/	4.0	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]	[ "Fig.", "4", "Functional", "analysis.", "The", "Picrust", "software", "was", "used", "to", "analyze", "the", "pathway", "based", "on", "the", "KEGG", "database.", "The", "significant", "differences", "in", "functional", "metabolism", "are", "shown", "in", "the", "figure", "Discussion", "The", "CapeOX", "regimen", "is", "recommended", "as", "the", "postoperative", "adjuvant", "chemotherapy", "regimen", "in", "resected", "CRC", "patients", "with", "stage", "III", "or", "high-risk", "stage", "II", "[", "35", "].", "The", "high-risk", "factors", "in", "stage", "II", "may", "affect", "the", "accuracy", "of", "experimental", "results,", "Thus,", "CRC", "patients", "with", "stage", "III", "were", "recruited", "in", "the", "present", "study.", "According", "to", "the", "NCCN", "guidelines,", "the", "CapeOX", "regimen", "for", "resected", "stage", "III", "CRC", "has", "been", "defined", "as", "8", "cycles", "of", "capecitabine", "(1000", "mg/m", "2", "twice", "daily)", "combined", "with", "oxaliplatin", "(130", "mg/m", "2", "every", "3", "weeks)", "[", "36", "].", "CID", "is", "one", "of", "the", "most", "common", "side", "effects", "of", "the", "CapeOX", "regimen", "[", "37", "].", "The", "degree", "of", "diarrhea", "caused", "by", "different", "chemotherapeutic", "agents", "varies.", "Among", "the", "chemotherapeutic", "drugs", "for", "colorectal", "cancer,", "the", "most", "common", "drugs", "that", "cause", "diarrhea", "are", "fluorouracil,", "irinotecan", "and", "platinum,", "and", "the", "incidence", "of", "diarrhea", "associated", "with", "these", "drugs", "can", "be", "as", "high", "as", "50–80%", "[", "38", "].", "Our", "previous", "clinical", "investigation", "found", "that", "the", "probability", "of", "CID", "increased", "with", "an", "increase", "of", "chemotherapeutic", "frequency", "and", "chemotherapeutic", "dosage", "and", "most", "cases", "of", "CID", "occur", "within", "2", "weeks", "after", "chemotherapy.", "Therefore,", "in", "the", "present", "study,", "stool", "samples", "from", "the", "patients", "were", "collected", "in", "2", "weeks", "after", "the", "8", "cycles", "of", "chemotherapy", "of", "the", "CapeOX", "regimen", "were", "completed.", "Studies", "of", "Carroll", "et", "al.", "[", "39", "]", "suggested", "that", "the", "richness", "of", "16S", "rRNA", "sequences", "was", "significantly", "decreased", "in", "patients", "with", "diarrhea-predominant", "irritable", "bowel", "syndrome.", "Lee", "[", "40", "]", "has", "reported", "the", "community", "diversity", "of", "gut", "microbiome", "is", "lower", "in", "patients", "with", "kidney", "posttransplant", "diarrhea.", "Similar", "results", "have", "been", "reported", "in", "dogs", "with", "acute", "diarrhea", "[", "41", "].", "The", "research", "on", "these", "diarrhea", "diseases", "is", "consistent", "with", "our", "findings." ]
Original work titled: 'Gut microbiome associated with chemotherapy-induced diarrhea from the CapeOX regimen as adjuvant chemotherapy in resected stage III colorectal cancer' (Gut Pathogens/BioMed Central) by the following authors: Zuo Fei; Yin Lijuan; Yang Xi; Wu Wei; Zhong Jing; Da Miao; Han Shuwen DOI: 10.1186/s13099-019-0299-4	f7083ca86a7871cc8d04d2500480cbf3	CC-BY	http://creativecommons.org/licenses/by/4.0/	4.0	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]	[ "The", "increased", "proportion", "of", "Petroica", "boodang", "in", "patients", "with", "CID", "remains", "a", "phenomenon", "of", "concern.", "Microorganisms", "can", "adjust", "and", "modify", "their", "surroundings", "due", "to", "their", "metabolic", "products.", "A", "series", "of", "enzymes", "and", "genes", "participate", "in", "the", "process", "of", "metabolism", "[", "12", "].", "Functional", "analysis", "of", "these", "enzymes", "and", "genes", "would", "be", "conducive", "to", "understand", "the", "whole", "microecological", "environment.", "In", "the", "present", "study,", "we", "screened", "75", "differentiated", "microorganisms", "at", "the", "species", "level", "by", "using", "LDA", "effect", "size", "analysis", "as", "well", "as", "23", "pathways", "associated", "with", "differential", "microorganisms", "by", "using", "KEGG", "databases.", "These", "differential", "pathways", "are", "related", "to", "microbial", "metabolites,", "cell", "proliferation", "and", "death,", "immune", "system,", "and", "many", "other", "aspects.", "These", "differentiated", "microorganisms,", "their", "metabolic", "products", "and", "the", "relevant", "pathways", "make", "up", "the", "intestinal", "microecosystem", "that", "causes", "CID.", "These", "results", "may", "provide", "characteristic", "microorganisms", "or", "potential", "molecular", "targets", "for", "the", "treatment", "and", "prevention", "of", "CID.", "It", "must", "be", "emphasized", "that", "small", "sample", "size", "and", "potential", "sample", "contamination", "may", "affect", "the", "accuracy", "of", "the", "present", "study.", "Strict", "inclusion", "and", "exclusion", "criteria", "was", "performed", "in", "this", "study.", "Subjects", "in", "the", "experimental", "group", "were", "only", "included", "the", "resected", "stage", "III", "colorectal", "cancer", "(CRC)", "patients", "who", "voluntarily", "accepted", "and", "completed", "8", "cycles", "of", "the", "CapeOX", "regimen", "and", "accompanied", "with", "grade", "2", "of", "CID.", "Thus,", "the", "small", "sample", "size", "limits", "the", "applicability", "of", "the", "findings.", "A", "multi-center,", "large", "study", "will", "provide", "more", "powerful", "data", "to", "support", "the", "clarification", "of", "the", "microbial", "differences", "in", "CRC", "patients", "with", "CID.", "Conclusion", "Chemotherapy", "induced", "diarrhea", "(CID)", "is", "a", "common", "side", "effect", "in", "patients", "receiving", "chemotherapy", "for", "cancer.", "In", "the", "present", "study,", "We", "found", "that", "the", "gut", "microbial", "community", "structure", "and", "community", "diversity", "have", "changed", "in", "CRC", "patients", "with", "CID.", "The", "gut", "microbial", "community", "richness", "and", "community", "diversity", "were", "lower", "in", "CID.", "Petroica", "boodang", "was", "the", "most", "predominant", "species", "among", "the", "gut", "microbiome", "in", "CRC", "patients", "with", "CID.", "It", "may", "provide", "novel", "insights", "into", "the", "prevention", "and", "treatment", "of", "patients", "with", "CID", "to", "improve", "patients’", "quality", "of", "life", "and", "chemotherapy", "tolerance." ]
Original work titled: 'Gut microbiome associated with chemotherapy-induced diarrhea from the CapeOX regimen as adjuvant chemotherapy in resected stage III colorectal cancer' (Gut Pathogens/BioMed Central) by the following authors: Zuo Fei; Yin Lijuan; Yang Xi; Wu Wei; Zhong Jing; Da Miao; Han Shuwen DOI: 10.1186/s13099-019-0299-4	f7083ca86a7871cc8d04d2500480cbf3	CC-BY	http://creativecommons.org/licenses/by/4.0/	4.0	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]	[ "Lee", "[", "40", "]", "has", "reported", "the", "community", "diversity", "of", "gut", "microbiome", "is", "lower", "in", "patients", "with", "kidney", "posttransplant", "diarrhea.", "Similar", "results", "have", "been", "reported", "in", "dogs", "with", "acute", "diarrhea", "[", "41", "].", "The", "research", "on", "these", "diarrhea", "diseases", "is", "consistent", "with", "our", "findings.", "We", "found", "that", "the", "gut", "microbial", "community", "richness", "and", "community", "diversity", "was", "lower", "in", "CRC", "patients", "with", "CID", "in", "the", "present", "study.", "The", "decrease", "of", "microbial", "diversity", "may", "be", "related", "to", "the", "imbalance", "of", "gut", "microbiome.", "The", "dominant", "pathogenic", "bacteria", "leads", "to", "the", "reduction", "of", "the", "resident", "normal", "microbiota", "through", "the", "plunder", "of", "nutrients", "or", "the", "killing", "effect", "of", "bacterial", "toxic", "metabolites.", "Our", "results", "from", "the", "microbial", "community", "structure", "analysis", "showed", "Porphyromonas", "endodontalis", "occupied", "the", "highest", "proportion", "(31.22%)", "of", "gut", "microbiome", "in", "CRC", "patients", "with", "CID.", "Lu", "et", "al.", "[", "42", "]", "reported", "that", "the", "rate", "of", "Porphyromonas", "endodontalis", "was", "approximately", "0.5%", "in", "Beijing", "by", "culturing", "the", "stool", "pathogens", "from", "outpatients", "with", "diarrhea", "syndromes", "using", "the", "Vitek2", "Compact", "instrument.", "Zhang", "et", "al.", "[", "22", "]", "only", "isolated", "43", "Porphyromonas", "endodontalis", "strains", "from", "551", "stool", "specimens", "from", "diarrhea", "patients.", "Although", "the", "study", "may", "have", "be", "interfered", "by", "other", "factors", "such", "as", "geographical", "location,", "nosocomial", "infection,", "or", "pollution", "contamination", "in", "the", "fecal", "collection", "process.", "The", "increased", "proportion", "of", "Porphyromonas", "endodontalis", "in", "patients", "with", "CID", "remains", "a", "phenomenon", "of", "concern.", "Microorganisms", "can", "adjust", "and", "modify", "their", "surroundings", "due", "to", "their", "metabolic", "products.", "A", "series", "of", "enzymes", "and", "genes", "participate", "in", "the", "process", "of", "metabolism", "[", "12", "].", "Functional", "analysis", "of", "these", "enzymes", "and", "genes", "would", "be", "conducive", "to", "understand", "the", "whole", "microecological", "environment.", "In", "the", "present", "study,", "we", "screened", "75", "differentiated", "microorganisms", "at", "the", "species", "level", "by", "using", "LDA", "effect", "size", "analysis", "as", "well", "as", "23", "pathways", "associated", "with", "differential", "microorganisms", "by", "using", "KEGG", "databases.", "These", "differential", "pathways", "are", "related", "to", "microbial", "metabolites,", "cell", "proliferation", "and", "death,", "immune", "system,", "and", "many", "other", "aspects.", "These", "differentiated", "microorganisms,", "their", "metabolic", "products", "and", "the", "relevant", "pathways", "make", "up", "the", "intestinal", "microecosystem", "that", "causes", "CID." ]
Original work titled: 'Gut microbiome associated with chemotherapy-induced diarrhea from the CapeOX regimen as adjuvant chemotherapy in resected stage III colorectal cancer' (Gut Pathogens/BioMed Central) by the following authors: Zuo Fei; Yin Lijuan; Yang Xi; Wu Wei; Zhong Jing; Da Miao; Han Shuwen DOI: 10.1186/s13099-019-0299-4	f7083ca86a7871cc8d04d2500480cbf3	CC-BY	http://creativecommons.org/licenses/by/4.0/	4.0	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]	[ "The", "innermost", "layer", "shows", "the", "taxonomic", "tree.", "The", "circle", "from", "the", "inside", "to", "the", "outside", "represents", "different", "taxon", "levels", "from", "phylum", "to", "genus.", "Yellow", "circles", "represent", "no", "statistical", "difference", "in", "species", "between", "the", "two", "groups,", "and", "red", "circles", "and", "green", "circles", "represent", "the", "higher", "abundance", "of", "genus", "in", "the", "control", "group", "and", "the", "chemotherapy-induced", "diarrhea", "group,", "respectively.", "The", "lowercase", "English", "letters", "corresponding", "to", "the", "different", "bacteria", "are", "shown", "in", "the", "legends", "The", "functional", "analysis", "of", "16S", "rRNA", "genes", "associated", "with", "CID", "during", "the", "CapeOX", "regimen", "for", "CRC", "It", "has", "been", "confirmed", "that", "many", "gene", "function", "annotation", "databases", "are", "associated", "with", "corresponding", "16S", "rRNA", "gene", "sequences.", "Functional", "analysis", "of", "enzymes", "and", "genes", "would", "be", "conducive", "to", "understand", "the", "whole", "microecological", "environment.", "As", "shown", "in", "Fig.", "4", ",", "the", "figure", "shows", "the", "results", "of", "the", "functional", "analysis.", "Overall,", "23", "pathways", "(p", "<", "0.001)", "associated", "with", "statistically", "significant", "differences", "might", "be", "involved", "in", "CID", "during", "the", "CapeOX", "regimen", "for", "adjuvant", "chemotherapy", "in", "resected", "stage", "III", "colorectal", "cancer.", "These", "differential", "pathways", "are", "related", "to", "microbial", "metabolites,", "cell", "proliferation", "and", "death,", "immune", "system,", "and", "many", "other", "aspects.", "Fig.", "4", "Functional", "analysis.", "The", "Picrust", "software", "was", "used", "to", "analyze", "the", "pathway", "based", "on", "the", "KEGG", "database.", "The", "significant", "differences", "in", "functional", "metabolism", "are", "shown", "in", "the", "figure", "Discussion", "The", "CapeOX", "regimen", "is", "recommended", "as", "the", "postoperative", "adjuvant", "chemotherapy", "regimen", "in", "resected", "CRC", "patients", "with", "stage", "III", "or", "high-risk", "stage", "II", "[", "35", "].", "The", "high-risk", "factors", "in", "stage", "II", "may", "affect", "the", "accuracy", "of", "experimental", "results,", "Thus,", "CRC", "patients", "with", "stage", "III", "were", "recruited", "in", "the", "present", "study.", "According", "to", "the", "NCCN", "guidelines,", "the", "CapeOX", "regimen", "for", "resected", "stage", "III", "CRC", "has", "been", "defined", "as", "8", "cycles", "of", "capecitabine", "(1000", "mg/m", "2", "twice", "daily)", "combined", "with", "oxaliplatin", "(130", "mg/m", "2", "every", "3", "weeks)", "[", "36", "].", "CID", "is", "one", "of", "the", "most", "common", "side", "effects", "of", "the", "CapeOX", "regimen", "[", "37", "].", "The", "degree", "of", "diarrhea", "caused", "by", "different", "chemotherapeutic", "agents", "varies." ]
Original work titled: 'Gut microbiome associated with chemotherapy-induced diarrhea from the CapeOX regimen as adjuvant chemotherapy in resected stage III colorectal cancer' (Gut Pathogens/BioMed Central) by the following authors: Zuo Fei; Yin Lijuan; Yang Xi; Wu Wei; Zhong Jing; Da Miao; Han Shuwen DOI: 10.1186/s13099-019-0299-4	f7083ca86a7871cc8d04d2500480cbf3	CC-BY	http://creativecommons.org/licenses/by/4.0/	4.0	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]	[ "The", "cladogram", "in", "Fig.", "3", "c", "displays", "the", "composition", "and", "proportion", "of", "microorganisms", "at", "different", "taxonomic", "levels.", "The", "cladogram", "showed", "that", "the", "abundance", "of", "these", "bacteria", "including", "Actinomycetaceae,", "Micrococcaceae,", "Bacteroidaceae,", "Porphyromonadaceae,", "Ruminococcaceae,", "Erysipelotrichaceae,", "Leptotrichiaceae,", "Enterobacteriaceae", "(Klebsiella", "belongs", "to", "Enterobacteriaceae)", "and", "Synergistaceae", "had", "significant", "differences", "at", "family", "level", "between", "the", "two", "groups.", "Fig.", "3", "Differential", "microbes", "analysis.", "The", "samples", "were", "divided", "into", "two", "groups", "according", "to", "patients", "with", "or", "without", "CID.", "The", "number", "of", "OTUs", "that", "were", "exclusive", "or", "shared", "by", "the", "two", "groups", "were", "visualized", "by", "a", "Venn", "Chart", "(", "a", ").", "The", "strip", "figure", "in", "b", "displays", "the", "LDA", "effect", "size", "analysis.", "LDA", "effect", "size", "analysis", "was", "used", "to", "compare", "the", "differences", "in", "microbial", "abundance", "between", "the", "two", "groups", "(", "b", ").", "LDA", "scores", "over", "2", "mean", "that", "the", "differences", "are", "statistically", "significant", "(p", "<", "0.05).", "The", "cladogram", "in", "c", "displays", "the", "composition", "and", "proportion", "of", "microorganisms", "at", "different", "taxonomic", "levels.", "The", "innermost", "layer", "shows", "the", "taxonomic", "tree.", "The", "circle", "from", "the", "inside", "to", "the", "outside", "represents", "different", "taxon", "levels", "from", "phylum", "to", "genus.", "Yellow", "circles", "represent", "no", "statistical", "difference", "in", "species", "between", "the", "two", "groups,", "and", "red", "circles", "and", "green", "circles", "represent", "the", "higher", "abundance", "of", "genus", "in", "the", "control", "group", "and", "the", "chemotherapy-induced", "diarrhea", "group,", "respectively.", "The", "lowercase", "English", "letters", "corresponding", "to", "the", "different", "bacteria", "are", "shown", "in", "the", "legends", "The", "functional", "analysis", "of", "16S", "rRNA", "genes", "associated", "with", "CID", "during", "the", "CapeOX", "regimen", "for", "CRC", "It", "has", "been", "confirmed", "that", "many", "gene", "function", "annotation", "databases", "are", "associated", "with", "corresponding", "16S", "rRNA", "gene", "sequences.", "Functional", "analysis", "of", "enzymes", "and", "genes", "would", "be", "conducive", "to", "understand", "the", "whole", "microecological", "environment.", "As", "shown", "in", "Fig.", "4", ",", "the", "figure", "shows", "the", "results", "of", "the", "functional", "analysis." ]

Original work titled: 'Binding and Flip as Initial Steps for BP-100 Antimicrobial Actions' (Scientific Reports/Nature Publishing Group UK) by the following authors: Peter Park; Leandro R. Franco; Hernan Chaimovich; Kaline Coutinho; Iolanda M. Cuccovia; Filipe S. Lima DOI: 10.1038/s41598-019-45075-5

5388809896c7b2a9adf5d708f6ea4b08

CC-BY

http://creativecommons.org/licenses/by/4.0/

4.0

[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]

[ "Introduction", "Cationic", "antimicrobial", "peptides", "(CAMPs)", "are", "short-length,", "amphiphilic,", "rich", "in", "basic", "residues", "of", "the", "innate", "immune", "system", "of", "complex", "organisms,", "serving", "as", "the", "first", "defense", "line", "against", "pathogens.", "CAMPs", "can", "potentially", "give", "rise", "to", "a", "new", "generation", "of", "drugs", "due", "to", "their", "broad", "spectrum", "of", "antimicrobial", "activity", "against", "bacteria,", "rare", "cases", "of", "the", "appearance", "of", "AMP-resistant", "bacteria,", "selectivity,", "and", "rapid", "effects.", "Due", "to", "their", "potential", "advantage", "as", "antimicrobials,", "new", "AMPs", "are", "increasingly", "being", "isolated", "or", "synthesized", "and", "their", "properties", "investigated.", "Although", "increasing", "evidence", "shows", "that", "some", "AMPs", "may", "also", "act", "intracellularly,", "inhibiting", "proteins", "1", ",", "nucleic", "acids", "1", "–", "4", "and", "cell-wall", "synthesis", "1", "–", "5", "and", "inducing", "cell", "apoptosis", "1", ",", "3", ",", "5", ",", "most", "of", "them", "kill", "cells", "by", "disturbing", "the", "membrane’s", "integrity", "1", ",", "2", ",", "6", ",", "7", ".", "Several", "CAMPs", "seem", "to", "disturb", "the", "membrane", "of", "cells", "by", "self-aggregation", "on", "the", "membrane", "and", "forming", "pores", "beyond", "a", "peptide/lipid", "(P/L)", "ratio", "threshold", "1", ",", "2", ".", "BP100", "(H-KKLFKKILKYL-NH", "2", "),", "is", "a", "hybrid", "CAMP", "synthesized", "by", "combinatorial", "chemistry", "involving", "parts", "of", "two", "natural", "AMPs,", "melittin,", "and", "cecropin", "A", "8", ".", "BP100", "shows", "high", "antimicrobial", "activity", "and", "selectivity", "against", "some", "Gram-negative", "bacteria,", "with", "a", "promising", "minimal", "inhibitory", "concentration", "ranging", "from", "2.5", "to", "5", "µM", "and", "low", "cytotoxicity", "against", "mammalian", "cells", "making", "this", "peptide", "an", "exciting", "candidate", "for", "therapeutic", "use", "8", ".", "BP100", "conformation", "and", "activity", "on", "model", "membranes", "have", "been", "extensively", "analyzed", "with", "experimental", "techniques", "9", "–", "13", ".", "BP100", "has", "a", "random", "coil", "conformation", "in", "solution", "and", "zwitterionic", "bilayers", "but", "acquires", "predominantly", "alpha-helical", "and", "amphipathic", "conformation", "in", "the", "presence", "of", "negatively", "charged", "membranes.", "BP100", "is", "highly", "mobile", "on", "the", "membrane", "surface", "and", "orients", "parallel", "in", "predominantly", "negatively", "charged", "vesicles", "9", ",", "10", "." ]

Original work titled: 'Binding and Flip as Initial Steps for BP-100 Antimicrobial Actions' (Scientific Reports/Nature Publishing Group UK) by the following authors: Peter Park; Leandro R. Franco; Hernan Chaimovich; Kaline Coutinho; Iolanda M. Cuccovia; Filipe S. Lima DOI: 10.1038/s41598-019-45075-5

5388809896c7b2a9adf5d708f6ea4b08

CC-BY

http://creativecommons.org/licenses/by/4.0/

4.0

[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]

[ "CAMPs", "can", "potentially", "give", "rise", "to", "a", "new", "generation", "of", "drugs", "due", "to", "their", "broad", "spectrum", "of", "antimicrobial", "activity", "against", "bacteria,", "rare", "cases", "of", "the", "appearance", "of", "AMP-resistant", "bacteria,", "selectivity,", "and", "rapid", "effects.", "Due", "to", "their", "potential", "advantage", "as", "antimicrobials,", "new", "AMPs", "are", "increasingly", "being", "isolated", "or", "synthesized", "and", "their", "properties", "investigated.", "Although", "increasing", "evidence", "shows", "that", "some", "AMPs", "may", "also", "act", "intracellularly,", "inhibiting", "proteins", "1", ",", "nucleic", "acids", "1", "–", "4", "and", "cell-wall", "synthesis", "1", "–", "5", "and", "inducing", "cell", "apoptosis", "1", ",", "3", ",", "5", ",", "most", "of", "them", "kill", "cells", "by", "disturbing", "the", "membrane’s", "integrity", "1", ",", "2", ",", "6", ",", "7", ".", "Several", "CAMPs", "seem", "to", "disturb", "the", "membrane", "of", "cells", "by", "self-aggregation", "on", "the", "membrane", "and", "forming", "pores", "beyond", "a", "peptide/lipid", "(P/L)", "ratio", "threshold", "1", ",", "2", ".", "BP100", "(H-KKLFKKILKYL-NH", "2", "),", "is", "a", "hybrid", "CAMP", "synthesized", "by", "combinatorial", "chemistry", "involving", "parts", "of", "two", "natural", "AMPs,", "melittin,", "and", "cecropin", "A", "8", ".", "BP100", "shows", "high", "antimicrobial", "activity", "and", "selectivity", "against", "some", "Gram-negative", "bacteria,", "with", "a", "promising", "minimal", "inhibitory", "concentration", "ranging", "from", "2.5", "to", "5", "µM", "and", "low", "cytotoxicity", "against", "mammalian", "cells", "making", "this", "peptide", "an", "exciting", "candidate", "for", "therapeutic", "use", "8", ".", "BP100", "conformation", "and", "activity", "on", "model", "membranes", "have", "been", "extensively", "analyzed", "with", "experimental", "techniques", "9", "–", "13", ".", "BP100", "has", "a", "random", "coil", "conformation", "in", "solution", "and", "zwitterionic", "bilayers", "but", "acquires", "predominantly", "alpha-helical", "and", "amphipathic", "conformation", "in", "the", "presence", "of", "negatively", "charged", "membranes.", "BP100", "is", "highly", "mobile", "on", "the", "membrane", "surface", "and", "orients", "parallel", "in", "predominantly", "negatively", "charged", "vesicles", "9", ",", "10", ".", "BP100", "secondary", "structure", "formation", "and", "bacteria", "killing", "performance", "seem", "to", "be", "directly", "related", "to", "negative", "charge", "content", "in", "membranes,", "thus", "explaining", "its", "high", "selectivity", "towards", "negative", "bacterial", "membrane", "and", "low", "cytotoxicity", "against", "predominantly", "less", "negatively", "charged", "mammalian", "cell", "membranes", "11", ",", "14", ".", "Experimental", "approaches", "to", "investigate", "peptide/membrane", "interactions", "mainly", "focus", "macroscopic-averaged", "insight", "on", "a", "mesoscopic", "scale." ]

Original work titled: 'Binding and Flip as Initial Steps for BP-100 Antimicrobial Actions' (Scientific Reports/Nature Publishing Group UK) by the following authors: Peter Park; Leandro R. Franco; Hernan Chaimovich; Kaline Coutinho; Iolanda M. Cuccovia; Filipe S. Lima DOI: 10.1038/s41598-019-45075-5

5388809896c7b2a9adf5d708f6ea4b08

CC-BY

http://creativecommons.org/licenses/by/4.0/

4.0

[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]

[ "BP100", "secondary", "structure", "formation", "and", "bacteria", "killing", "performance", "seem", "to", "be", "directly", "related", "to", "negative", "charge", "content", "in", "membranes,", "thus", "explaining", "its", "high", "selectivity", "towards", "negative", "bacterial", "membrane", "and", "low", "cytotoxicity", "against", "predominantly", "less", "negatively", "charged", "mammalian", "cell", "membranes", "11", ",", "14", ".", "Experimental", "approaches", "to", "investigate", "peptide/membrane", "interactions", "mainly", "focus", "macroscopic-averaged", "insight", "on", "a", "mesoscopic", "scale.", "A", "detailed", "description", "of", "peptide/membrane", "interactions", "at", "the", "atomic", "scale", "may", "help", "to", "gain", "information", "on", "CAMPs", "disruption", "mechanisms,", "permitting", "the", "rational", "design", "of", "new", "derivatives", "and,", "therefore,", "the", "better", "therapeutic", "use", "of", "these", "novel", "antimicrobials.", "Molecular", "Dynamics", "(MD)", "simulations", "provide", "atomic-level", "insights", "and", "have", "been", "widely", "used", "to", "study", "the", "interaction", "of", "AMPs", "with", "membranes", "15", "–", "18", ".", "MD", "simulations", "were", "also", "utilized", "to", "study", "BP100’s", "structure", "and", "activity:", "Wang", "Y.", "et", "al.", "17", "performed", "an", "8", "µs-long", "MD", "simulation", "of", "BP100", "in", "DMPC", "bilayer", "and", "found", "that", "BP100", "remained", "in", "the", "surface-bound-state", "inserting", "through", "its", "C-terminus.", "They", "also", "reported", "the", "unfolding", "of", "BP100", "N-terminus", "(Lys1", "and", "Lys2)", "after", "1.5", "µs,", "resulting", "in", "a", "tilt", "angle", "of", "97°", "and", "81%", "helicity", "10", ",", "17", ".", "In", "a", "study", "with", "Brownian", "Dynamics", "simulations", "with", "a", "coarse-grained", "peptide", "model,", "Alves", "et", "al.", "18", "simulated", "BP100", "confined", "in", "model", "membranes", "at", "293", "K", "for", "1", "µs", "each", "and", "reported", "the", "high", "stability", "of", "BP100", "pre-folded", "alpha", "helix", "and", "a", "threefold", "decrease", "in", "its", "lateral", "diffusion", "in", "POPC:", "POPG", "membranes", "relative", "to", "that", "in", "POPC", "membrane", "18", ".", "In", "this", "work", "we", "report", "simulations,", "in", "solution", "and", "membranes,", "extending", "for", "more", "than", "25", "µs", "of", "BP100", "and", "membranes", "of", "1,2-dipalmitoyl-sn-glycerol-3-phosphocholine", "(DPPC),", "1,2-dipalmitoyl-sn-glycerol-3-phosphoglycerol", "(DPPG),", "and", "DPPC:", "DPPG", "mixtures", "(1:1)." ]

Original work titled: 'Binding and Flip as Initial Steps for BP-100 Antimicrobial Actions' (Scientific Reports/Nature Publishing Group UK) by the following authors: Peter Park; Leandro R. Franco; Hernan Chaimovich; Kaline Coutinho; Iolanda M. Cuccovia; Filipe S. Lima DOI: 10.1038/s41598-019-45075-5

5388809896c7b2a9adf5d708f6ea4b08

CC-BY

http://creativecommons.org/licenses/by/4.0/

4.0

[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]

[ "In", "this", "work", "we", "report", "simulations,", "in", "solution", "and", "membranes,", "extending", "for", "more", "than", "25", "µs", "of", "BP100", "and", "membranes", "of", "1,2-dipalmitoyl-sn-glycerol-3-phosphocholine", "(DPPC),", "1,2-dipalmitoyl-sn-glycerol-3-phosphoglycerol", "(DPPG),", "and", "DPPC:", "DPPG", "mixtures", "(1:1).", "We", "systematically", "investigated", "the", "dependence", "of", "BP100", "secondary", "structure", "on", "DPPG", "lipids", "which", "agrees", "with", "experimental", "findings", "11", ".", "We", "also", "analyzed", "the", "contribution", "of", "PG-containing", "lipid", "rafts", "on", "BP100", "conformation", "and", "behavior.", "In", "most", "simulations", "containing", "DPPG", "lipids,", "we", "observed", "the", "occurrence", "of", "a", "dynamic", "transition", "of", "the", "peptide", "adsorbed", "at", "the", "membrane", "interface,", "where", "the", "apolar", "facet", "of", "the", "BP100", "(Fig.", "1c", "),", "initially", "exposed", "to", "water,", "rotates", "toward", "the", "membrane", "interior,", "leaving", "the", "polar", "facet", "of", "the", "peptide", "exposed", "to", "water.", "This", "process,", "defined", "here", "as", "peptide", "flip,", "could", "be", "part", "of", "CAMPs", "primary", "antimicrobial", "mechanism.", "Constraining", "four", "residues", "of", "the", "peptide", "into", "an", "alpha", "helix", "turn,", "we", "observed", "that", "the", "unconstrained", "regions", "of", "the", "peptide", "rapidly", "acquired", "an", "alpha-helix", "conformation", "in", "DPPG-containing", "membranes,", "suggesting", "that", "the", "formation", "of", "these", "small", "alpha-helical", "nuclei", "in", "peptide/membrane", "interactions", "may", "be", "the", "initial", "step", "for", "the", "peptide", "insertion", "into", "the", "hydrophobic", "core", "of", "the", "membranes.", "Figure", "1", "BP100", "initial", "structures:", "random", "coil", "L", "-BP100", "(", "a", ")", "and", "alpha-helical", "α", "-BP100", "(", "b", ").", "Helical", "wheel", "projection", "(", "c", "),", "Lys5", "and", "Ile7", "were", "used", "as", "representative", "residues", "of", "polar", "and", "apolar", "moieties,", "respectively.", "In", "(", "d", ")", "DPPC", "(in", "blue)", "and", "DPPG", "(in", "yellow).", "Atom", "names", "are", "shown", "for", "peptide", "and", "lipids;", "they", "were", "used", "in", "our", "peptide-lipid", "pair", "analysis.", "Methods", "All", "simulations", "sets", "were", "assembled,", "carried", "out", "and", "analyzed", "using", "GROMACS", "5.0.2", "software", "package." ]

Original work titled: 'Binding and Flip as Initial Steps for BP-100 Antimicrobial Actions' (Scientific Reports/Nature Publishing Group UK) by the following authors: Peter Park; Leandro R. Franco; Hernan Chaimovich; Kaline Coutinho; Iolanda M. Cuccovia; Filipe S. Lima DOI: 10.1038/s41598-019-45075-5

5388809896c7b2a9adf5d708f6ea4b08

CC-BY

http://creativecommons.org/licenses/by/4.0/

4.0

[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]

[ "Simulation", "sets", "Simulations", "Peptide/Lipid", "Waters/Lipid", "Time", "(ns)", "Bilayers", "DPPC", "0/128", "54", "860", "DPPG", "53", "1100", "PCPG-R", "0/[64/64]", "54", "1200", "PCPG-NR", "52", "1200", "Peptide", "in", "water", "L", "-BP100", "in", "water", "1/0", "—", "2000", "α", "-BP100", "in", "water", "—", "2850", "Peptide", "with", "bilayers", "L", "-BP100", "in", "DPPC", "1/128", "54", "1700", "α", "-BP100", "in", "DPPC", "54", "2000", "L", "-BP100", "in", "DPPG", "1/128", "53", "1700", "α", "-BP100", "in", "DPPG", "53", "2000", "L", "-BP100", "in", "PCPG-R", "1/[64/64]", "54", "1600", "α", "-BP100", "in", "PCPG-R", "54", "2000", "L", "-BP100", "in", "PCPG-NR", "1/[64/64]", "52", "1700", "α", "-BP100", "in", "PCPG-NR", "52", "2000", "Partially", "constrained", "peptide", "in", "DPPG", "α-", "BP100", "(res1–5)", "in", "DPPG", "1/128", "54", "600", "α-", "BP100", "(res4–8)", "in", "DPPG", "54", "600", "α-", "BP100", "(res7–11)", "in", "DPPG", "54", "600", "Lipid", "bilayers", "We", "used", "Slipids", "forcefield", "19", "parameters", "were", "chosen", "to", "simulate", "DPPC,", "DPPG,", "and", "DPPC/DPPG", "mixed", "bilayers.", "64-lipids-per-monolayer", "DPPC", "and", "DPPG", "pure", "membrane", "topologies", "were", "taken", "from", "the", "Slipids", "developer", "group", "website", "(http://www.fos.su.se/~sasha/Slipids/Downloads.html).", "Mixed", "bilayers", "of", "DPPC", "and", "DPPG", "containing", "32", "DPPCs", "and", "32", "DPPGs", "in", "each", "leaflet", "were", "constructed", "using", "the", "PACKMOL", "20", "software.", "One", "membrane", "was", "composed", "of", "randomly", "distributed", "lipids", "(PCPG-NR)", "on", "both", "leaflets", "and", "the", "other,", "a", "4", "×", "4", "DPPG", "raft", "was", "placed", "in", "the", "center", "of", "both", "monolayers", "(PCPG-R)", "and", "the", "remaining", "48", "lipids", "were", "randomly", "distributed", "(Fig.", "2", ")." ]

Original work titled: 'Binding and Flip as Initial Steps for BP-100 Antimicrobial Actions' (Scientific Reports/Nature Publishing Group UK) by the following authors: Peter Park; Leandro R. Franco; Hernan Chaimovich; Kaline Coutinho; Iolanda M. Cuccovia; Filipe S. Lima DOI: 10.1038/s41598-019-45075-5

5388809896c7b2a9adf5d708f6ea4b08

CC-BY

http://creativecommons.org/licenses/by/4.0/

4.0

[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]

[ "The", "area", "per", "lipid", "and", "membrane", "thickness", "were", "calculated", "for", "all", "membranes", "and", "thNen", "compared", "with", "experimental", "data", "and", "those", "obtained", "by", "Slipids", "authors", "(Tables", "S1", "and", "S2", ").", "The", "last", "trajectory", "frames", "of", "the", "membrane", "simulations", "were", "used", "to", "build", "our", "peptide-lipid", "systems.", "Peptide-in-solution", "and", "peptide-lipid", "systems", "Following", "a", "study", "by", "Beauchamp", "et", "al.", "22", ",", "ff99sb-ildn-NMR", "force", "field", "was", "chosen", "to", "characterize", "BP100", "in", "our", "modeling", "due", "to", "its", "good", "performance", "in", "simulating", "peptides", "and", "proteins", "structures", "in", "TIP3P", "water", "when", "compared", "with", "NMR", "measurements.", "BP100", "(H-Lys-Lys-Leu-Phe-Lys-Lys-Ile-Leu-Lys-Tyr-Leu-NH", "2", ")", "has", "an", "amidated", "C-terminal", "and", "a", "+6", "charge", "at", "physiological", "pH,", "with", "all", "its", "Lysines", "and", "N-terminal", "amine", "protonated.", "To", "study", "secondary", "structure", "behavior", "of", "BP100", "both", "in", "solution", "and", "in", "bilayers,", "two", "initial", "BP100", "conformations", "were", "used:", "linear", "BP100", "(", "L", "-BP100)", "and", "alpha-helical", "BP100", "(", "α", "-BP100)", "(Fig.", "1", "a,b", ").", "In", "the", "peptide/water", "system,", "one", "peptide", "(", "α", "-BP100", "or", "L-BP100", "initial", "conformation)", "were", "simulated", "in", "a", "cubic", "box", "with", "3975", "TIP3P", "water", "molecules", "for", "more", "than", "1", "microsecond", "with", "its", "+6", "charges", "neutralized", "with", "6", "Cl", "−", "ions", "(Dang", "23", ").", "Simulations", "containing", "peptides", "with", "membranes", "had", "a", "peptide/lipid", "ratio", "of", "1/128", "and", "the", "peptide", "was", "initially", "positioned", "in", "parallel", "orientation", "with", "the", "membrane", "surface", "approximately", "2", "nm", "away.", "For", "the", "α", "-BP100,", "additionally,", "we", "tested", "two", "parallel", "orientations,", "where", "the", "polar", "amino", "acids", "were", "facing", "the", "membrane", "and", "a", "random", "orientation.", "For", "the", "perpendicular", "orientation", "we", "tested", "two", "ways", "with", "either", "the", "C-terminal", "or", "N-terminal", "facing", "the", "interface.", "For", "all", "these", "initial", "conditions,", "we", "obtained", "the", "same", "final", "location", "and", "orientation", "of", "the", "peptide", "that", "will", "be", "discussed", "in", "the", "results", "section." ]

Original work titled: 'Binding and Flip as Initial Steps for BP-100 Antimicrobial Actions' (Scientific Reports/Nature Publishing Group UK) by the following authors: Peter Park; Leandro R. Franco; Hernan Chaimovich; Kaline Coutinho; Iolanda M. Cuccovia; Filipe S. Lima DOI: 10.1038/s41598-019-45075-5

5388809896c7b2a9adf5d708f6ea4b08

CC-BY

http://creativecommons.org/licenses/by/4.0/

4.0

[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]

[ "Atmospheric", "pressure", "of", "1", "bar", "was", "kept", "with", "the", "Berendsen", "barostat", "26", "and", "semi-isotropic", "pressure", "coupling", "was", "used", "for", "all", "systems.", "All", "bonds", "were", "constrained", "with", "LINCS", "27", "algorithm.", "Long-range", "electrostatic", "correction", "was", "treated", "by", "a", "Particle-mesh-Ewald", "method", "28", "with", "a", "real-space", "cut-off", "of", "1.5", "nm.", "van", "der", "Waals", "interactions", "were", "truncated", "at", "1.5", "nm", "distance", "with", "a", "switch", "function", "from", "1.4", "nm.", "Simulation", "analyses", "Lipid/peptide", "contacts", "For", "the", "computation", "of", "lipid", "contacts", "with", "BP100", "and", "pair", "frequency,", "we", "labeled", "some", "lipid(s)", "and", "BP100", "atoms", "as", "“polar”", "or", "“apolar”,", "based", "on", "charges.", "Then,", "the", "radial", "distribution", "function", "(RDF)", "between", "each", "pair", "of", "apolar", "(or", "polar)", "atoms", "of", "the", "lipids/BP100", "system", "were", "computed.", "The", "time", "window", "selected", "for", "computing", "these", "RDFs", "includes", "that", "of", "the", "membrane", "bound", "peptide", "250", "ns-before", "and", "250", "ns-after", "the", "peptide", "flip.", "The", "pairs", "with", "distinguishable", "RDF", "peaks", "and", "following", "minimum", "were", "used", "to", "analyze", "the", "number", "of", "polar", "and", "apolar", "contacts", "between", "lipids", "and", "peptide.", "A", "cutoff", "distance", "for", "each", "pair", "was", "defined", "from", "the", "position", "of", "the", "first", "minimum", "in", "the", "RDF", "curve,", "and", "a", "contact", "was", "defined", "as", "a", "pair", "of", "atoms", "at", "smaller", "distance", "than", "their", "corresponding", "cutoff", "distance.", "The", "simulations", "were", "analyzed", "and", "the", "total", "number", "of", "polar", "and", "apolar", "contacts", "as", "a", "function", "of", "time", "was", "obtained.", "Additionally,", "some", "polar", "and", "apolar", "pairs", "were", "analyzed", "individually.", "Peptide", "hydration", "The", "time", "evolution", "of", "the", "solvent", "shell", "surrounding", "the", "peptide", "in", "its", "α", "and", "L", "conformations", "in", "all", "simulated", "membranes", "was", "analyzed", "using", "the", "minimum", "distance", "distribution", "function", "(MDDF)", "29", "between", "the", "peptide", "and", "the", "water", "molecules,", "as", "well", "as", "the", "average", "number", "of", "water", "molecules", "N(r),", "within", "a", "distance", "r", "=", "0.5", "nm,", "named", "here", "as", "N(0.5).", "For", "comparison", "the", "MDDF", "of", "BP100", "in", "water", "was", "used", "to", "define", "the", "bulk", "water", "hydration", "shell", "at", "the", "same", "distance." ]

Original work titled: 'Binding and Flip as Initial Steps for BP-100 Antimicrobial Actions' (Scientific Reports/Nature Publishing Group UK) by the following authors: Peter Park; Leandro R. Franco; Hernan Chaimovich; Kaline Coutinho; Iolanda M. Cuccovia; Filipe S. Lima DOI: 10.1038/s41598-019-45075-5

5388809896c7b2a9adf5d708f6ea4b08

CC-BY

http://creativecommons.org/licenses/by/4.0/

4.0

[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]

[ "A", "cutoff", "distance", "for", "each", "pair", "was", "defined", "from", "the", "position", "of", "the", "first", "minimum", "in", "the", "RDF", "curve,", "and", "a", "contact", "was", "defined", "as", "a", "pair", "of", "atoms", "at", "smaller", "distance", "than", "their", "corresponding", "cutoff", "distance.", "The", "simulations", "were", "analyzed", "and", "the", "total", "number", "of", "polar", "and", "apolar", "contacts", "as", "a", "function", "of", "time", "was", "obtained.", "Additionally,", "some", "polar", "and", "apolar", "pairs", "were", "analyzed", "individually.", "Peptide", "hydration", "The", "time", "evolution", "of", "the", "solvent", "shell", "surrounding", "the", "peptide", "in", "its", "α", "and", "L", "conformations", "in", "all", "simulated", "membranes", "was", "analyzed", "using", "the", "minimum", "distance", "distribution", "function", "(MDDF)", "29", "between", "the", "peptide", "and", "the", "water", "molecules,", "as", "well", "as", "the", "average", "number", "of", "water", "molecules", "N(r),", "within", "a", "distance", "r", "=", "0.5", "nm,", "named", "here", "as", "N(0.5).", "For", "comparison", "the", "MDDF", "of", "BP100", "in", "water", "was", "used", "to", "define", "the", "bulk", "water", "hydration", "shell", "at", "the", "same", "distance.", "Results", "The", "17", "sets", "of", "simulations", "(Table", "1", ")", "were", "run", "for", "more", "than", "25", "µs", "of", "simulation", "time,", "and", "each", "unconstrained", "peptide/membrane", "simulation", "had", "at", "least", "1.6", "µs", "of", "simulation.", "After", "comparing", "the", "simulated", "membrane", "properties", "with", "experimental", "and", "other", "computational", "studies", "(Tables", "S1", "and", "S2", "),", "we", "systematically", "analyzed", "the", "peptide", "conformation", "in", "solution", "and", "on", "bilayers,", "peptide", "trajectory,", "and", "dynamics", "on", "membranes", "and", "the", "effect", "of", "BP100", "on", "model", "bilayers.", "In", "the", "following", "sections,", "we", "describe", "our", "results.", "Secondary", "structure", "Peptide", "in", "solution", "To", "study", "BP100", "secondary", "structure", "in", "water,", "we", "did", "simulations", "for", "more", "than", "2", "µs", "with", "both", "α-BP100", "and", "L-BP100", "initial", "conformations.", "Figure", "4", "shows", "that", "BP100", "conformation", "in", "solution", "was,", "predominantly,", "random", "coil.", "The", "peptide", "lost", "the", "initial", "alpha", "helix", "conformation", "in", "approximately", "40", "ns", "when", "starting", "with", "an", "alpha-helix", "configuration", "and", "occasionally", "formed", "an", "alpha-helix", "turn", "in", "the", "5–9", "residue", "region", "(Fig.", "4a", ").", "For", "L-BP100", "in", "solution,", "we", "observed", "a", "similar", "pattern", "(Fig.", "4b", ").", "Circular", "Dichroism", "(CD)", "shows", "that", "BP100", "is", "random", "in", "solution", "10", ",", "11", ",", "30", ",", "and", "our", "simulations", "reproduced", "these", "data." ]

Original work titled: 'Binding and Flip as Initial Steps for BP-100 Antimicrobial Actions' (Scientific Reports/Nature Publishing Group UK) by the following authors: Peter Park; Leandro R. Franco; Hernan Chaimovich; Kaline Coutinho; Iolanda M. Cuccovia; Filipe S. Lima DOI: 10.1038/s41598-019-45075-5

5388809896c7b2a9adf5d708f6ea4b08

CC-BY

http://creativecommons.org/licenses/by/4.0/

4.0

[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]

[ "4a", ").", "For", "L-BP100", "in", "solution,", "we", "observed", "a", "similar", "pattern", "(Fig.", "4b", ").", "Circular", "Dichroism", "(CD)", "shows", "that", "BP100", "is", "random", "in", "solution", "10", ",", "11", ",", "30", ",", "and", "our", "simulations", "reproduced", "these", "data.", "Figure", "4", "Secondary", "structure", "analyses", "graphs", "of", "α", "-BP100", "(", "a", ")", "and", "L", "-BP100", "(", "b", ")", "in", "solution.", "In", "both", "cases,", "the", "peptide", "shows", "predominance", "in", "random", "coil", "structure", "(orange)", "with", "occasional", "formation", "of", "1", "alpha", "helix", "turn", "(blue)", "in", "residues", "5", "to", "9.", "Peptide", "in", "bilayers", "BP100", "conformation,", "antimicrobial", "activity,", "and", "PG", "content", "are", "related", "11", ".", "We", "simulated", "α-BP100", "and", "L-BP100", "on", "DPPC,", "DPPG,", "PCPG-R,", "and", "PCPG-NR", "at", "323", "K,", "above", "DPPG", "and", "DPPC", "transition", "temperatures.", "In", "all", "cases,", "the", "peptide", "was", "rapidly", "adsorbed", "on", "the", "membranes", "and", "diffused", "laterally.", "Figure", "5", "shows", "that", "the", "BP100", "alpha-helical", "conformation", "was", "proportional", "to", "PG", "content,", "as", "the", "alpha-helix", "percentage", "in", "DPPC", "is", "considerably", "smaller", "than", "that", "observed", "in", "DPPG-containing", "membranes.", "Alpha-helix", "formed", "in", "the", "5", "to", "9", "residues", "region", "(Lys-Lys-Ile-Leu-Lys)", "was", "highly", "stable", "in", "all", "simulations.", "Figure", "5", "Secondary", "structure", "analyses", "of", "α", "-BP100", "in", "DPPC", "(", "a", "),", "DPPG", "(", "b", "),", "PCPG-R", "(", "c", ")", "and", "PCPG-NR", "(", "d", ").", "In", "DPPC,", "α-BP100", "alpha-helix", "conformation", "reached", "a", "plateau", "at", "38%", "helicity", "throughout", "the", "simulation,", "being", "relatively", "less", "stable", "than", "α-BP100", "in", "bilayers", "containing", "DPPG,", "where", "a", "higher", "propensity", "of", "maintaining", "its", "conformation", "was", "observed.", "For", "pure", "DPPG", "(Fig.", "5b", ")", "we", "found", "73%", "(8", "out", "of", "11", "residues),", "and", "for", "both", "PCPG", "(1:1)", "membranes", "we", "report", "54%", "(6", "out", "of", "11)", "of", "helicity", "(Fig.", "5c,d", ")." ]

Original work titled: 'Binding and Flip as Initial Steps for BP-100 Antimicrobial Actions' (Scientific Reports/Nature Publishing Group UK) by the following authors: Peter Park; Leandro R. Franco; Hernan Chaimovich; Kaline Coutinho; Iolanda M. Cuccovia; Filipe S. Lima DOI: 10.1038/s41598-019-45075-5

5388809896c7b2a9adf5d708f6ea4b08

CC-BY

http://creativecommons.org/licenses/by/4.0/

4.0

[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]

[ "5", ").", "This", "secondary", "structure", "pattern", "led", "us", "to", "suggest", "that", "the", "residues", "5", "to", "9", "are", "related", "to", "helix", "nucleation,", "in", "which", "the", "formation", "of", "this", "helix", "core", "could", "be", "the", "first", "step", "in", "the", "AMP", "actions.", "Following", "this", "assumption,", "we", "tested", "three", "conformations", "with", "α-BP100", "torsionally", "constrained", "in", "three", "regions:", "res1–5,", "res4–8,", "res7–11", "(Fig.", "3", ")", "and", "simulated", "with", "pure", "DPPG", "membranes.", "Figure", "6", "shows", "the", "evolution", "of", "the", "secondary", "structure", "in", "each", "simulation.", "Figure", "6", "Secondary", "structure", "analyses", "graphs", "of", "BP100", "in", "DPPG", "with", "one", "turn", "constraints", "on", "res1–5", "(", "a", "),", "res", "4–8", "(", "b", ")", "and", "res7–11", "(", "c", ").", "α-BP100", "with", "constraints", "on", "residues", "1–5", "(Lys-Lys-Leu-Phe-Lys)", "acquired", "identical", "helicity", "(73%)", "to", "α-BP100", "with", "no", "constraints", "at", "the", "same", "conditions", "(Fig.", "5b", "),", "after", "50", "ns", "of", "simulation", "(Fig.", "6a", "),", "with", "a", "helix", "spanning", "from", "Lys2", "to", "Lys9", "(Fig.", "6a", ").", "Constraints", "on", "residues", "4–8", "(Phe-Lys-Lys-Ile-Leu)", "showed", "an", "overall", "52%", "of", "helicity", "(Fig.", "6b", "),", "with", "a", "helix", "spanning", "from", "Phe4", "to", "Lys9", "(Fig.", "6b", ").", "Constraints", "on", "residues", "7–11", "(Ile-Leu-Lys-Tyr-Leu)", "did", "not", "affect", "the", "rest", "of", "the", "peptide", "conformation", "(Fig.", "6c", ")", "in", "600", "ns", "of", "simulation.", "Peptide", "flip", "Simulation", "trajectories", "analyses", "(Fig.", "7", ")", "revealed", "that", "the", "peptide", "in", "alpha-helix", "conformation", "initially", "adsorbed", "at", "the", "DPPG-containing", "membranes", "interface", "with", "its", "hydrophilic", "facet", "in", "contact", "with", "the", "membrane,", "leaving", "the", "hydrophobic", "facet", "exposed", "to", "water.", "We", "observed", "that", "the", "alpha-helix", "rotated,", "inserting", "the", "hydrophobic", "facet", "into", "the", "hydrophobic", "region", "of", "the", "membrane.", "We", "define", "this", "dynamic", "phenomenon,", "observed", "in", "our", "simulations,", "as", "peptide", "flip." ]

Original work titled: 'Binding and Flip as Initial Steps for BP-100 Antimicrobial Actions' (Scientific Reports/Nature Publishing Group UK) by the following authors: Peter Park; Leandro R. Franco; Hernan Chaimovich; Kaline Coutinho; Iolanda M. Cuccovia; Filipe S. Lima DOI: 10.1038/s41598-019-45075-5

5388809896c7b2a9adf5d708f6ea4b08

CC-BY

http://creativecommons.org/licenses/by/4.0/

4.0

[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]

[ "Peptide", "flip", "was", "also", "observed", "in", "α", "-BP100", "in", "DPPC,", "α", "-BP100", "in", "PCPG-R,", "and", "α", "-BP100", "res(1–5)", "in", "DPPG", "simulations.", "The", "peptide", "flip", "caused", "dehydration", "(Fig.", "8", ").", "When", "in", "contact", "with", "membranes,", "depending", "on", "the", "secondary", "structure", "of", "the", "peptide", "and", "the", "lipid", "nature,", "the", "hydration", "of", "the", "peptide", "was", "slightly", "different.", "However,", "when", "the", "peptide", "flip", "took", "place,", "its", "hydration", "was", "drastically", "altered.", "Figure", "8", "Average", "number", "of", "water", "molecules", "up", "to", "a", "distance", "of", "0.5", "nm,", "N(0.5),", "obtained", "from", "the", "minimum-distance", "distribution", "function", "(MDDF),", "between", "L-BP100", "(", "a", ")", "and", "α", "-BP100", "(", "b", ")", "and", "water", "molecules.", "Vertical", "lines", "indicate", "when", "peptide", "flip", "occurred.", "In", "the", "peptide/membrane", "simulations", "with", "L-BP100", "as", "a", "starting", "configuration", "(Fig.", "8a", "),", "no", "significant", "change", "in", "the", "number", "of", "water", "molecules", "surrounding", "the", "peptide", "was", "observed", "in", "comparison", "the", "150", "obtained", "in", "the", "bulk", "aqueous", "solution.", "In", "the", "last", "500", "ns", "of", "simulation,", "N(0.5)", "was", "approximately", "178", "±", "11", "in", "DPPC,", "145", "±", "7", "in", "DPPG,", "145", "±", "13", "in", "PCPG-NR,", "and", "148", "±", "3", "in", "PCPG-R.", "No", "peptide", "flip", "was", "detected", "in", "the", "trajectories", "for", "those", "simulations.", "However,", "in", "the", "peptide/membrane", "simulations", "with", "α-BP100", "as", "a", "starting", "configuration", "(Fig.", "8b", "),", "N", "(0.5)", "lowered", "in", "DPPC", "(starting", "at", "~700", "ns),", "DPPG", "(~1500", "ns)", "and", "PCPG-R", "(~390", "ns).", "Alongside", "with", "dehydration,", "a", "peptide-flip", "was", "observed", "in", "DPPG", "and", "PCPG-R.", "For", "the", "α-", "BP100", "in", "DPPC", "simulation,", "we", "observed", "a", "semi-flip,", "as", "the", "peptide", "alpha-helical", "conformation", "was", "only", "38%", "(Fig.", "5a", "),", "suggesting", "that", "the", "peptide", "overall", "polar/apolar", "segregation", "(Fig.", "2c", ")", "was", "lost.", "The", "peptide", "flip", "transition", "time", "varied", "from", "100", "to", "400", "ns." ]

Original work titled: 'Binding and Flip as Initial Steps for BP-100 Antimicrobial Actions' (Scientific Reports/Nature Publishing Group UK) by the following authors: Peter Park; Leandro R. Franco; Hernan Chaimovich; Kaline Coutinho; Iolanda M. Cuccovia; Filipe S. Lima DOI: 10.1038/s41598-019-45075-5

5388809896c7b2a9adf5d708f6ea4b08

CC-BY

http://creativecommons.org/licenses/by/4.0/

4.0

[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]

[ "Alongside", "with", "dehydration,", "a", "peptide-flip", "was", "observed", "in", "DPPG", "and", "PCPG-R.", "For", "the", "α-", "BP100", "in", "DPPC", "simulation,", "we", "observed", "a", "semi-flip,", "as", "the", "peptide", "alpha-helical", "conformation", "was", "only", "38%", "(Fig.", "5a", "),", "suggesting", "that", "the", "peptide", "overall", "polar/apolar", "segregation", "(Fig.", "2c", ")", "was", "lost.", "The", "peptide", "flip", "transition", "time", "varied", "from", "100", "to", "400", "ns.", "During", "the", "peptide-flip,", "in", "the", "simulations", "of", "α-BP100", "in", "DPPG", "and", "PCPG-R,", "the", "mean", "number", "N(0.5)", "was", "reduced", "from", "147", "±", "5", "and", "142", "±", "7", "to", "76", "±", "4", "and", "75", "±", "4,", "respectively.", "These", "represent", "on", "average", "a", "reduction", "of", "approximately", "48%", "in", "the", "number", "of", "water", "molecules", "in", "the", "hydration", "shell", "of", "α-BP100.", "In", "DPPC,", "we", "detected", "a", "smaller", "decrease", "in", "the", "hydration", "of", "α-BP100,", "around", "45%", "(from", "172", "±", "8", "to", "94", "±", "2),", "having", "around", "20", "water", "molecules", "more", "after", "the", "semi-flip.", "Figure", "9", "shows", "the", "density", "profile", "before", "and", "after", "peptide", "flip", "for", "α-BP100", "in", "DPPG", "and", "PCPG-R.", "We", "chose", "residues", "Lys5", "and", "Ile7", "to", "illustrate", "the", "changes", "in", "the", "mean", "position", "of", "hydrophobic", "and", "hydrophilic", "residues", "with", "respect", "to", "the", "membrane", "due", "to", "the", "peptide", "flip.", "These", "residues", "are", "polar", "and", "apolar,", "respectively,", "and", "located", "opposite", "to", "each", "other", "when", "in", "an", "alpha-helix", "conformation", "(Fig.", "2c", ").", "Trajectory", "visualization", "and", "density", "profile", "(Figs", "7", "and", "9", ")", "clearly", "show", "the", "distinct", "orientation", "in", "BP100", "hydrophobic", "facet", "before", "and", "after", "peptide", "flip.", "During", "the", "initial", "phase", "of", "approaching", "towards", "the", "membrane,", "BP100", "polar", "side", "faces", "the", "membrane", "with", "its", "N-terminal", "residues", "(Lys1", "and", "Lys2)", "interacting", "with", "the", "bilayer", "headgroups.", "After", "the", "flip,", "the", "apolar", "residues", "facet", "turns", "to", "the", "membrane,", "and", "simultaneously", "inserts", "into", "the", "bilayer,", "below", "the", "carbonyl", "carbons", "(C31)", "of", "the", "lipids", "(Fig.", "9", ").", "Figure", "9", "Peptide", "flip", "observed", "through", "number", "density", "analysis." ]

Original work titled: 'Binding and Flip as Initial Steps for BP-100 Antimicrobial Actions' (Scientific Reports/Nature Publishing Group UK) by the following authors: Peter Park; Leandro R. Franco; Hernan Chaimovich; Kaline Coutinho; Iolanda M. Cuccovia; Filipe S. Lima DOI: 10.1038/s41598-019-45075-5

5388809896c7b2a9adf5d708f6ea4b08

CC-BY

http://creativecommons.org/licenses/by/4.0/

4.0

[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]

[ "After", "the", "flip,", "the", "apolar", "residues", "facet", "turns", "to", "the", "membrane,", "and", "simultaneously", "inserts", "into", "the", "bilayer,", "below", "the", "carbonyl", "carbons", "(C31)", "of", "the", "lipids", "(Fig.", "9", ").", "Figure", "9", "Peptide", "flip", "observed", "through", "number", "density", "analysis.", "(", "a", "and", "b", ")", "show", "respectively", "before", "and", "after", "the", "flip", "in", "α", "-BP100", "in", "DPPG", "simulation;", "c)", "and", "d)", "demonstrate", "the", "flip", "for", "α", "-BP100", "in", "PCPG-R", "simulation.", "Lys5", "represents", "the", "polar", "side", "of", "BP100", "and", "Ile7,", "the", "apolar", "facet", "(Fig.", "2c", ").", "OC3", "(DPPG", "head", "group", "further", "out", "glycerol", "Oxygen),", "N", "chol", "(DPPC", "head", "group", "choline", "Nitrogen),", "P", "(Phosphorus)", "and", "C31", "(first", "carbon", "from", "sn-1", "acyl", "chain)", "are", "shown", "to", "display", "BP100", "insertion", "into", "the", "bilayer", "after", "the", "flip.", "Peptide", "flip", "was", "not", "observed", "in", "α-BP100", "in", "PCPG-NR,", "where", "DPPG", "lipids", "were", "initially", "scattered", "randomly.", "PG", "content", "might", "be", "related", "to", "the", "occurrence", "of", "the", "flip,", "but", "also,", "the", "PG", "content", "in", "the", "vicinity", "of", "BP100.", "Several", "studies", "suggest", "membrane-active", "peptides", "cause", "anionic", "lipid", "clustering,", "or", "subdomain", "formation,", "upon", "binding", "to", "bilayers", "containing", "neutral", "and", "charged", "phospholipids", "35", "–", "37", ".", "The", "same", "mechanism", "could", "be", "involved", "in", "BP100/bilayers", "interactions.", "Lipid", "clustering", "The", "distribution", "of", "the", "lipids", "in", "the", "vicinity", "of", "BP100", "was", "evaluated", "by", "computing", "the", "total", "number", "of", "lipids", "in", "contact", "with", "α-BP100", "as", "a", "function", "of", "time", "(Fig.", "S5", "),", "the", "time-averaged", "values", "(Table", "2", ",", "Fig.", "10", "),", "and", "the", "lipid", "raft", "size", "distribution", "(Fig.", "S6", ").", "Table", "2", "Average", "number", "of", "lipids", "in", "contact", "with", "BP100", "in", "simulations", "using", "α", "-BP100", "as", "the", "peptide", "starting", "configuration,", "except", "α", "-BP100", "(1–5),", "which", "had", "permanent", "constraints", "on", "residues", "1", "to", "5.", "Standard", "deviations", "are", "shown", "in", "parenthesis." ]

Original work titled: 'Binding and Flip as Initial Steps for BP-100 Antimicrobial Actions' (Scientific Reports/Nature Publishing Group UK) by the following authors: Peter Park; Leandro R. Franco; Hernan Chaimovich; Kaline Coutinho; Iolanda M. Cuccovia; Filipe S. Lima DOI: 10.1038/s41598-019-45075-5

5388809896c7b2a9adf5d708f6ea4b08

CC-BY

http://creativecommons.org/licenses/by/4.0/

4.0

[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]

[ "Average", "Number", "of", "Lipids", "in", "Contact", "with", "BP100", "Simulation", "Lipid", "in", "Contact", "Average", "α", "-BP100", "in", "DPPC", "DPPC", "10.7", "(±2.6)", "α", "-BP100", "in", "DPPG", "DPPG", "13.1", "(±1.4)", "α", "-BP100", "(1–5)", "in", "DPPG", "DPPG", "13.5", "(±1.9)", "α", "-BP100", "in", "PCPG-R", "Total", "12.3", "(±1.7)", "DPPC", "3.6", "(±1.5)", "DPPG", "8.7", "(±1.2)", "α", "-BP100", "in", "PCPG-NR", "Total", "11.0", "(±1.7)", "DPPC", "2.7", "(±1.3)", "DPPG", "8.3", "(±1.6)", "Figure", "10", "Average", "Number", "of", "DPPCs", "(", "a", ")", "and", "DPPGs", "(", "b", ")", "in", "contact", "with", "BP100", "analyzed", "for", "all", "constraint-free", "simulations", "containing", "BP100", "in", "an", "initially", "alpha", "helical", "conformation", "in", "DPPC,", "DPPG,", "PCPG-R", "and", "PCPG-NR", "membranes.", "Vertical", "lines", "represent", "the", "average", "time", "where", "peptide", "flip", "was", "observed.", "Standard", "deviation", "error", "bars", "are", "represented", "as", "fillings.", "α-BP100", "in", "DPPC", "simulation", "had", "on", "average", "10.7", "peptide/lipid", "contacts", "(Table", "2", ")", "and", "a", "steady", "increase", "in", "the", "number", "of", "contact", "lipids", "(Figs", "10b", "and", "S5a", ").", "This", "increase", "is", "due", "to", "the", "peptide", "losing", "its", "alpha-helical", "conformation", "(Fig.", "5a", "),", "expanding", "the", "available", "peptide", "interaction", "area", "with", "the", "membrane.", "Lipid", "raft", "size", "distribution", "also", "shows", "a", "broader", "distribution", "of", "DPPC", "raft", "size,", "supporting", "this", "observation", "(Fig.", "S6a", ").", "A", "semi-peptide", "flip", "was", "observed", "at", "~700", "ns", "of", "simulation", "and,", "concomitantly,", "while", "BP100", "inserts", "into", "the", "bilayer", "as", "the", "density", "profile", "shows", "(Fig.", "S4a,b", "),", "the", "number", "of", "DPPCs", "in", "contact", "with", "BP100", "increased", "(Fig.", "S5a", ")." ]

Original work titled: 'Binding and Flip as Initial Steps for BP-100 Antimicrobial Actions' (Scientific Reports/Nature Publishing Group UK) by the following authors: Peter Park; Leandro R. Franco; Hernan Chaimovich; Kaline Coutinho; Iolanda M. Cuccovia; Filipe S. Lima DOI: 10.1038/s41598-019-45075-5

5388809896c7b2a9adf5d708f6ea4b08

CC-BY

http://creativecommons.org/licenses/by/4.0/

4.0

[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]

[ "S5a", ").", "α-BP100", "in", "DPPG", "simulation", "shows", "on", "average", "13.1", "DPPGs", "in", "close", "contact", "with", "the", "peptide", "(Table", "2", ").", "The", "number", "of", "DPPGs", "in", "contact", "rose", "after", "the", "flip,", "approximately", "in", "1500", "ns", "of", "simulation", "(Figs", "10a", "and", "S5b", ")", "and", "concurrently,", "BP100", "inserted", "deeply", "into", "the", "membrane", "(Fig.", "7a,b", ").", "Constrained", "α-BP100", "(res1–5)", "in", "DPPG,", "which", "showed", "identical", "alpha-helix", "content", "with", "α-BP100", "in", "DPPG", "(73%,", "Figs", "5b", "and", "6a", "),", "not", "only", "exhibits", "peptide", "flip", "in", "approximately", "300", "ns", "of", "simulation", "but", "also", "has,", "on", "average,", "13.5", "DPPGs", "in", "contact", "with", "BP100", "(Table", "2", ").", "In", "the", "simulation", "with", "α-BP100", "in", "PCPG-NR,", "the", "number", "of", "DPPG", "in", "contact", "with", "the", "peptide", "showed", "a", "slight", "increase", "(Fig.", "10b", "),", "reaching", "the", "average", "value", "observed", "in", "the", "simulation", "with", "PCPG-R", "(Table", "2", ").", "Also,", "lipid", "raft", "size", "probability", "analysis", "(Fig.", "S6d", ")", "showed", "a", "narrower", "peak", "distribution", "for", "DPPGs", "in", "contact", "with", "BP100", "in", "PCPG-R", "system,", "compared", "to", "PCPG-NR", "(Fig.", "S6e", "),", "indicating", "that", "DPPG", "lipid", "raft", "size", "was", "stable.", "Peptide", "flip", "was", "observed", "in", "the", "PCPG-R", "set", "after", "~390", "ns", "of", "simulation", "and", "no", "significant", "variation", "of", "the", "number", "of", "DPPG", "in", "contact", "with", "peptide", "was", "observed.", "Polar", "and", "apolar", "interaction", "analysis", "Peptide", "contact", "analysis", "revealed", "the", "increase", "of", "lipid/peptide", "contacts", "after", "peptide", "flip", "and", "DPPG", "clustering", "on", "PCPG", "membranes.", "We", "analyzed", "the", "nature", "of", "the", "intermolecular", "interactions", "that", "determine", "peptide-membrane", "interactions", "throughout", "the", "simulations.", "We", "calculated", "the", "number", "of", "polar", "and", "apolar", "pair", "contacts", "between", "peptide", "atoms", "and", "membrane", "atoms", "(Figs", "S7", "–", "S13", ").", "Using", "α-BP100", "in", "PCPG-R", "system", "as", "an", "example,", "Fig.", "11", "shows", "the", "sum", "of", "the", "10", "most", "frequent", "apolar/polar", "pairs", "between", "BP100", "with", "DPPC", "and", "DPPG." ]

Original work titled: 'Binding and Flip as Initial Steps for BP-100 Antimicrobial Actions' (Scientific Reports/Nature Publishing Group UK) by the following authors: Peter Park; Leandro R. Franco; Hernan Chaimovich; Kaline Coutinho; Iolanda M. Cuccovia; Filipe S. Lima DOI: 10.1038/s41598-019-45075-5

5388809896c7b2a9adf5d708f6ea4b08

CC-BY

http://creativecommons.org/licenses/by/4.0/

4.0

[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]

[ "Figure", "11", "BP100", "pair", "occurrence", "with", "DPPC", "(", "a", ")", "and", "DPPG", "(", "b", ")", "for", "α", "-BP100", "in", "PCPG-R", "simulation.", "Graphs", "show", "the", "sum", "of", "the", "ten", "most", "frequent", "apolar/polar", "pairs", "during", "the", "simulation.", "Pairs", "were", "calculated", "using", "the", "monolayer", "facing", "the", "peptide.", "Green", "vertical", "lines", "indicate", "when", "peptide", "flip", "occurred", "(circa", "390", "ns).", "The", "total", "number", "of", "pairs,", "regardless", "if", "it", "is", "polar", "or", "apolar,", "between", "BP100", "and", "DPPG", "is", "higher", "than", "that", "with", "DPPC", "(Fig.", "11", "),", "which", "directly", "reflects", "on", "the", "number", "of", "lipids", "in", "contact", "with", "BP100", "(Fig.", "10", ").", "During", "the", "initial", "approach", "of", "the", "peptide", "towards", "the", "bilayer,", "polar", "interactions", "between", "charged", "Lysines", "and", "DPPG", "headgroup", "dominate", "the", "interaction", "(Figs", "11", "b,", "S9", ",", "S10", ",", "S12", "and", "S13", ").", "The", "primary", "interaction", "was", "between", "positively", "charged", "(+1)", "Lysine", "side", "chain", "amino", "group", "(NZ)", "and", "DPPG", "head", "phosphoglycerol", "group", "oxygens", "(OC2,", "OC3),", "even", "after", "peptide", "flip", "(Figs", "S9", ",", "S10", ",", "S12", "and", "S13", ").", "Before", "the", "peptide", "flip,", "the", "number", "of", "polar", "contacts", "is", "higher", "than", "the", "apolar", "contacts", "for", "DPPG/BP100.", "As", "the", "peptide", "starts", "to", "flip,", "the", "number", "of", "apolar", "contacts", "increase,", "while", "the", "polar", "contacts", "decrease.", "After", "the", "peptide", "flip", "is", "completed,", "apolar", "contacts", "are", "as", "numerous", "as", "the", "polar", "contacts", "(Fig.", "11a,b", "and", "S7–10,13", ").", "Also,", "after", "the", "flip,", "apolar", "contacts", "between", "BP100", "and", "DPPG", "were", "more", "frequent", "than", "with", "DPPC", "(Fig.", "11b", ").", "The", "higher", "peptide/DPPG", "apolar", "contact", "frequency", "after", "the", "flip", "is", "also", "observed", "for", "other", "simulations", "with", "peptide", "flip", "(Figs", "S7", "–", "10", ",", "13).", "Discussion", "Peptide", "secondary", "structure", "CD", "spectra", "of", "BP100", "in", "solution", "and", "POPC", "LUVs", "show", "no", "secondary", "structure", "10", ",", "11", ",", "30", "Our", "simulations", "with", "BP100", "in", "solution,", "and", "DPPC", "membrane", "exhibited", "the", "same", "pattern." ]

Original work titled: 'Binding and Flip as Initial Steps for BP-100 Antimicrobial Actions' (Scientific Reports/Nature Publishing Group UK) by the following authors: Peter Park; Leandro R. Franco; Hernan Chaimovich; Kaline Coutinho; Iolanda M. Cuccovia; Filipe S. Lima DOI: 10.1038/s41598-019-45075-5

5388809896c7b2a9adf5d708f6ea4b08

CC-BY

http://creativecommons.org/licenses/by/4.0/

4.0

[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]

[ "The", "primary", "interaction", "was", "between", "positively", "charged", "(+1)", "Lysine", "side", "chain", "amino", "group", "(NZ)", "and", "DPPG", "head", "phosphoglycerol", "group", "oxygens", "(OC2,", "OC3),", "even", "after", "peptide", "flip", "(Figs", "S9", ",", "S10", ",", "S12", "and", "S13", ").", "Before", "the", "peptide", "flip,", "the", "number", "of", "polar", "contacts", "is", "higher", "than", "the", "apolar", "contacts", "for", "DPPG/BP100.", "As", "the", "peptide", "starts", "to", "flip,", "the", "number", "of", "apolar", "contacts", "increase,", "while", "the", "polar", "contacts", "decrease.", "After", "the", "peptide", "flip", "is", "completed,", "apolar", "contacts", "are", "as", "numerous", "as", "the", "polar", "contacts", "(Fig.", "11a,b", "and", "S7–10,13", ").", "Also,", "after", "the", "flip,", "apolar", "contacts", "between", "BP100", "and", "DPPG", "were", "more", "frequent", "than", "with", "DPPC", "(Fig.", "11b", ").", "The", "higher", "peptide/DPPG", "apolar", "contact", "frequency", "after", "the", "flip", "is", "also", "observed", "for", "other", "simulations", "with", "peptide", "flip", "(Figs", "S7", "–", "10", ",", "13).", "Discussion", "Peptide", "secondary", "structure", "CD", "spectra", "of", "BP100", "in", "solution", "and", "POPC", "LUVs", "show", "no", "secondary", "structure", "10", ",", "11", ",", "30", "Our", "simulations", "with", "BP100", "in", "solution,", "and", "DPPC", "membrane", "exhibited", "the", "same", "pattern.", "α-BP100", "and", "L-BP100", "in", "solution", "showed", "similar", "behavior,", "with", "a", "prevalence", "of", "random", "conformation", "(Fig.", "4", ").", "In", "a", "related", "MD", "study", "of", "AMPs", "interacting", "with", "membranes", "17", ",", "an", "8", "µs-long", "all-atom", "MD", "simulation", "of", "BP100", "in", "DMPC", "at", "35◽", "the", "authors", "reported", "a", "full", "helix", "length", "during", "1.5", "µs", "and", "a", "subsequent", "unfolding", "event", "of", "Lysines", "at", "positions", "1", "and", "2,", "resulting", "in", "81%", "of", "helicity", "on", "a", "pure", "zwitterionic", "bilayer.", "However,", "as", "reported", "for", "other", "simulated", "peptides", "in", "the", "same", "work,", "the", "forcefield", "used", "could", "result", "in", "an", "over-helical", "artifact", "17", ".", "A", "Brownian", "Dynamics", "simulation", "study", "of", "BP100", "confined", "inside", "an", "implicit", "POPC", "membrane", "reports", "a", "stable", "alpha-helix", "18", "." ]

Original work titled: 'Binding and Flip as Initial Steps for BP-100 Antimicrobial Actions' (Scientific Reports/Nature Publishing Group UK) by the following authors: Peter Park; Leandro R. Franco; Hernan Chaimovich; Kaline Coutinho; Iolanda M. Cuccovia; Filipe S. Lima DOI: 10.1038/s41598-019-45075-5

5388809896c7b2a9adf5d708f6ea4b08

CC-BY

http://creativecommons.org/licenses/by/4.0/

4.0

[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]

[ "Peptide-lipid", "pair", "analysis", "(Fig.", "S7", ")", "showed", "that", "cationic", "Lysine", "residues", "interacted", "mainly", "with", "phosphate", "groups", "of", "the", "DPPC", "bilayer,", "evidencing", "that", "electrostatic", "interactions", "were", "present.", "In", "the", "case", "of", "L-BP100", "in", "DPPC,", "no", "alpha-helical", "structure", "formation", "was", "observed", "(Fig.", "S3", "),", "and", "for", "α-BP100,", "the", "peptide", "alpha-helix", "conformation", "was", "mostly", "lost,", "although", "one", "helix", "turn", "from", "residues", "5", "to", "9", "remained", "(Fig.", "5A", ").", "The", "minimum", "alpha-helix", "length", "detected", "by", "CD", "spectroscopy", "is", "proposed", "to", "encompass", "seven", "to", "eleven", "residues", "38", ",", "hence", "the", "alpha-helix", "turn", "in", "residues", "5–9", "might", "not", "be", "detected", "by", "CD.", "Alternatively,", "this", "could", "be", "an", "over-helical", "forcefield", "artifact", "22", ",", "but", "it", "also", "indicates", "the", "high", "stability", "of", "the", "alpha-helix", "formed", "by", "the", "(5–9)", "Lys-Lys-Ile-Leu-Lys", "sequence.", "This", "stability", "leads", "us", "to", "conjecture", "that", "BP100", "alpha-helix", "formation", "could", "be", "initiated", "through", "a", "core", "sequence,", "a", "nascent", "helix", "39", ".", "The", "negatively", "charged", "membrane", "interface", "could", "promote", "the", "initial", "peptide", "folding.", "To", "support", "this,", "we", "performed", "three", "600", "ns-long", "simulations", "with", "constrained", "alpha", "helices", "of", "BP100", "on", "three", "regions:", "residues", "1", "to", "5", "(Lys-Lys-Leu-Phe-Lys),", "4", "to", "8", "(Phe-Lys-Lys-Ile-Leu)", "and", "7", "to", "11", "(Ile-Leu-Lys-Tyr-Leu)", "in", "pure", "DPPG", "bilayers.", "The", "secondary", "structure", "analysis", "of", "the", "constrained", "BP100", "simulations", "yielded", "different", "outcomes.", "Constraint", "on", "residues", "1", "to", "5", "rapidly", "induced", "almost", "full", "alpha-helix", "content", "from", "Lys2", "to", "Lys9", "(Fig.", "6A", "),", "reaching", "73%", "of", "helicity,", "similar", "to", "α-BP100", "in", "DPPG", "without", "constraints", "(Fig.", "5B", ").", "Constraint", "on", "residues", "4", "to", "8", "also", "showed", "a", "helix", "formation", "tendency", "(overall", "63%", "helicity,", "5", "out", "of", "11", "residues,", "from", "Phe4", "to", "Lys9)." ]

Original work titled: 'Binding and Flip as Initial Steps for BP-100 Antimicrobial Actions' (Scientific Reports/Nature Publishing Group UK) by the following authors: Peter Park; Leandro R. Franco; Hernan Chaimovich; Kaline Coutinho; Iolanda M. Cuccovia; Filipe S. Lima DOI: 10.1038/s41598-019-45075-5

5388809896c7b2a9adf5d708f6ea4b08

CC-BY

http://creativecommons.org/licenses/by/4.0/

4.0

[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]

[ "We", "find", "1.53", "kcal/mol", "for", "residues", "1", "to", "5", "(Lys-Lys-Leu-Phe-Lys),", "1.68", "kcal/mol", "for", "residues", "4", "to", "8", "(Phe-Lys-Lys-Ile-Leu),", "and", "1.62", "kcal/mol", "for", "residues", "7–11", "(Ile-Leu-Lys-Tyr-Leu).", "Our", "secondary", "structure", "data", "indicates", "that", "BP100", "nascent", "helix", "could", "be", "formed", "either", "in", "the", "region", "between", "residues", "1", "to", "5", "or", "between", "residues", "5", "to", "9.", "We", "favor", "the", "latter", "due", "to", "the", "presence", "of", "positively", "charged", "Lysine", "residues", "in", "the", "N-terminal", "side", "(Lys1", "and", "Lys2)", "which", "could", "produce", "an", "energetically", "unfavorable", "barrier", "to", "initial", "peptide", "folding.", "The", "5–9", "region", "shows", "high", "stability", "in", "all", "constraint-free", "α-BP100/membranes", "simulations", "and", "has", "the", "overall", "lowest", "energy", "barrier", "in", "the", "helix", "propensity", "scale", "40", ".", "DPPG", "seems", "to", "have", "a", "helix-stabilizing", "effect", "on", "BP100.", "All", "the", "simulations", "with", "α-BP100", "in", "DPPG-containing-membranes", "showed", "high", "alpha-helical", "content,", "including", "the", "region", "of", "residues", "5", "to", "9.", "Our", "helicity", "results", "from", "the", "simulations", "with", "α-BP100", "in", "pure", "DPPG", "(73%)", "and", "in", "PCPG", "(50:50)", "mixed", "bilayers", "(54%)", "are", "remarkably", "close", "to", "those", "reported", "in", "experimental", "studies:", "54%", "in", "POPC:POPG", "(50:50)", "11", "and", "61%", "in", "DMPC/DMPG", "(75:25)", "LUVs", "10", ",", "and", "maximum", "observable", "alpha-helix", "spectrum", "for", "BP100", "in", "pure", "POPG", "vesicles", "11", "proving", "that", "BP100", "alpha-helical", "structure", "is", "dependent", "on", "PG", "content", "11", ".", "For", "L-BP100", "simulations", "with", "DPPG,", "PCPG-R,", "and", "PCPG-NR,", "no", "secondary", "structure", "formation", "was", "detected", "(Fig.", "S3", "),", "with", "the", "peptide", "being", "in", "a", "random", "conformation.", "Non-biased", "random", "peptide", "simulations", "require", "much", "longer", "simulation", "time", "to", "sample", "the", "peptide", "conformational", "potential", "landscape", "or", "might", "dwell", "in", "several", "local", "minimum-energy", "states." ]

Original work titled: 'Binding and Flip as Initial Steps for BP-100 Antimicrobial Actions' (Scientific Reports/Nature Publishing Group UK) by the following authors: Peter Park; Leandro R. Franco; Hernan Chaimovich; Kaline Coutinho; Iolanda M. Cuccovia; Filipe S. Lima DOI: 10.1038/s41598-019-45075-5

5388809896c7b2a9adf5d708f6ea4b08

CC-BY

http://creativecommons.org/licenses/by/4.0/

4.0

[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]

[ "For", "L-BP100", "simulations", "with", "DPPG,", "PCPG-R,", "and", "PCPG-NR,", "no", "secondary", "structure", "formation", "was", "detected", "(Fig.", "S3", "),", "with", "the", "peptide", "being", "in", "a", "random", "conformation.", "Non-biased", "random", "peptide", "simulations", "require", "much", "longer", "simulation", "time", "to", "sample", "the", "peptide", "conformational", "potential", "landscape", "or", "might", "dwell", "in", "several", "local", "minimum-energy", "states.", "Peptide", "flip", "BP100", "is", "too", "short", "to", "span", "the", "bilayer", "thickness,", "especially", "in", "the", "alpha-helical", "conformation,", "and", "thus", "single", "molecule", "pore", "formation", "is", "an", "unlikely", "scenario.", "NMR", "data", "of", "BP100", "in", "DMPC:", "DMPG", "(3:1)", "10", "shows", "that", "upon", "binding", "to", "negatively", "charged", "membranes,", "alpha-helical", "BP100", "positions", "parallel", "to", "the", "membrane", "as", "in", "a", "surface-bound", "orientation,", "and", "has", "an", "azimuthal", "rotation", "angle", "close", "to", "160°,", "with", "Lysine", "residues", "facing", "the", "solvent.", "This", "last", "arrangement", "is", "commonly", "observed", "with", "other", "CAMPs", "30", "–", "33", ".", "Peptide/membrane", "simulations", "with", "initially", "alpha-helical", "BP100", "had", "its", "polar", "moiety", "facing", "the", "membrane,", "for", "being", "the", "most", "probable", "scenario", "in", "a", "physical", "environment.", "In", "the", "α-BP100", "in", "DPPG", "(Fig.", "7", "),", "α-BP100", "in", "DPPC,", "α-BP100", "in", "PCPG-R", "and", "α-BP100", "(res1–5)", "in", "DPPG", "simulations", "trajectories,", "we", "observed", "the", "binding", "of", "BP100", "from", "bulk", "solution", "to", "the", "membranes", "with", "its", "Lysines", "residues", "pointing", "towards", "the", "bilayer,", "and", "then,", "the", "peptide", "rotated,", "leaving", "its", "apolar", "facet", "facing", "the", "interior", "of", "the", "bilayer.", "We", "termed", "this", "transition", "peptide", "flip.", "Although", "BP100", "surface-bound", "state", "is", "reported", "12", ",", "17", ",", "no", "previous", "peptide/membrane", "MD", "simulation", "work", "has", "reported", "a", "peptide", "flip", "transition.", "Peptide", "flip", "brings", "significant", "outcomes", "regarding", "BP100", "localization", "in", "the", "membrane,", "in", "peptide/membrane", "interaction", "and", "the", "peptide", "hydration,", "possibly", "being", "a", "crucial", "step", "of", "carpet", "mechanism", "for", "BP100", "and", "other", "CAMPs.", "Through", "the", "density", "profile,", "we", "observed", "deep", "penetration", "of", "the", "peptide", "into", "the", "membrane", "through", "its", "apolar", "residues", "with", "larger", "side-chains,", "after", "the", "flip", "(Fig.", "7", ")." ]

Original work titled: 'Binding and Flip as Initial Steps for BP-100 Antimicrobial Actions' (Scientific Reports/Nature Publishing Group UK) by the following authors: Peter Park; Leandro R. Franco; Hernan Chaimovich; Kaline Coutinho; Iolanda M. Cuccovia; Filipe S. Lima DOI: 10.1038/s41598-019-45075-5

5388809896c7b2a9adf5d708f6ea4b08

CC-BY

http://creativecommons.org/licenses/by/4.0/

4.0

[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]

[ "Through", "the", "density", "profile,", "we", "observed", "deep", "penetration", "of", "the", "peptide", "into", "the", "membrane", "through", "its", "apolar", "residues", "with", "larger", "side-chains,", "after", "the", "flip", "(Fig.", "7", ").", "BP100", "hydration", "analysis", "also", "shows", "a", "decrease", "in", "the", "overall", "peptide", "hydration", "after", "the", "flip", "(Fig.", "8", ").", "Apolar/polar", "pair", "interaction", "analysis", "(Fig.", "11", ")", "revealed", "that", "after", "the", "flip,", "the", "number", "of", "contacts", "between", "apolar", "residues", "from", "the", "lipids", "and", "the", "peptide", "increases", "significantly,", "while", "the", "number", "of", "contacts", "between", "polar", "groups", "of", "the", "lipids", "and", "the", "peptides", "slightly", "decreases.", "In", "other", "words,", "peptide", "flip", "intensifies", "peptide", "binding", "to", "membranes", "burying", "the", "apolar", "residues", "of", "the", "peptide", "deeper", "into", "the", "membrane", "core.", "We", "investigated", "what", "factors", "could", "lead", "to", "the", "occurrence", "of", "BP100", "peptide", "flip.", "Membrane", "composition", "appears", "to", "have", "a", "significant", "role.", "For", "BP100", "alpha-helical", "structure", "formation", "is", "favored", "in", "negatively", "charged", "membranes", "8", ".", "In", "our", "simulations,", "BP100", "entirely", "flipped", "in", "DPPG", "enriched", "regions", "of", "the", "membrane.", "Peptide", "flip", "was", "detected", "in", "α-BP100", "in", "DPPG,", "α-BP100", "(res1–5)", "in", "DPPG", "and", "α-BP100", "in", "PCPG-R", "systems.", "No", "peptide", "flip", "was", "detected", "in", "the", "other", "constrained", "BP100", "simulations", "(α-BP100", "(res4–8)", "in", "DPPG", "and", "α-BP100", "(res7–11)", "in", "DPPG).", "However,", "it", "is", "hasty", "to", "affirm", "that", "it", "is", "unlikely", "to", "expect", "peptide", "flip", "to", "happen", "in", "those", "systems", "with", "600", "ns", "of", "simulation", "time.", "For", "instance,", "peptide", "flip", "was", "observed", "after", "1.4", "µs", "of", "simulation", "in", "α-BP100", "in", "DPPG.", "Hydration", "analysis", "(Fig.", "8b", ")", "and", "density", "profile", "(Fig.", "S4A,B", ")", "for", "α-BP100", "in", "DPPC", "show", "also", "that", "BP100", "flipped.", "However,", "the", "alpha-helix", "secondary", "structure", "is", "mostly", "lost", "(Fig.", "5a", ").", "For", "this", "reason,", "BP100", "amphiphilic", "apolar-polar", "facet", "separation", "(Fig.", "2c", ")", "is", "lost." ]

Original work titled: 'Binding and Flip as Initial Steps for BP-100 Antimicrobial Actions' (Scientific Reports/Nature Publishing Group UK) by the following authors: Peter Park; Leandro R. Franco; Hernan Chaimovich; Kaline Coutinho; Iolanda M. Cuccovia; Filipe S. Lima DOI: 10.1038/s41598-019-45075-5

5388809896c7b2a9adf5d708f6ea4b08

CC-BY

http://creativecommons.org/licenses/by/4.0/

4.0

[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]

[ "For", "instance,", "peptide", "flip", "was", "observed", "after", "1.4", "µs", "of", "simulation", "in", "α-BP100", "in", "DPPG.", "Hydration", "analysis", "(Fig.", "8b", ")", "and", "density", "profile", "(Fig.", "S4A,B", ")", "for", "α-BP100", "in", "DPPC", "show", "also", "that", "BP100", "flipped.", "However,", "the", "alpha-helix", "secondary", "structure", "is", "mostly", "lost", "(Fig.", "5a", ").", "For", "this", "reason,", "BP100", "amphiphilic", "apolar-polar", "facet", "separation", "(Fig.", "2c", ")", "is", "lost.", "Additionally,", "the", "apolar", "moiety", "of", "the", "peptide", "could", "have", "a", "crucial", "role", "in", "peptide", "flip.", "Hydration", "analysis", "(Fig.", "8", ")", "suggests", "peptide", "flip", "results", "in", "peptide", "dehydration", "and", "concomitantly", "enhances", "peptide/lipid", "interaction", "(Fig.", "11", "),", "increasing", "specially", "apolar", "contacts", "(Fig.", "11", ").", "Similar", "behavior", "was", "observed", "in", "a", "study", "of", "the", "interaction", "of", "micelles", "with", "polyatomic", "counterions", "with", "apolar", "and", "polar", "moieties.", "Experimental", "results", "and", "MD", "simulations", "showed", "that", "counterions", "with", "the", "same", "apolar", "groups", "but", "different", "polar", "groups", "resulted", "in", "similar", "ionic", "affinities", "for", "dodecyltrimethylammonium", "micelles,", "and", "the", "simulations", "showed", "that", "counterion", "adsorption", "to", "the", "micelles", "was", "related", "with", "the", "dehydration", "of", "the", "apolar", "group", "of", "the", "counterions", "rather", "than", "by", "the", "polar", "group", "41", ".", "These", "factors", "could", "help", "to", "explain", "BP100", "selectivity", "towards", "negatively", "charged", "bacterial", "membranes", "and", "low", "cytotoxicity.", "Results", "of", "leakage", "from", "the", "inner", "compartment", "of", "LUVs", "upon", "addition", "of", "BP100", "showed", "that", "BP100", "leakage", "ability", "is", "proportional", "to", "PG", "content", "while", "the", "peptide", "has", "small", "effects", "on", "zwitterionic", "PC", "vesicles,", "observed", "through", "studies", "of", "zeta", "potential", "and", "vesicle", "leakage", "11", ".", "BP100", "does", "not", "perturb", "PC", "bilayers", "even", "at", "high", "peptide/lipid", "ratio", "and", "causes", "membrane", "thinning", "on", "mixed", "DMPC/DMPG", "bilayers", "where", "a", "stronger", "effect", "appears", "in", "anionic", "DMPG", "lipids", "compared", "to", "zwitterionic", "DMPC", "lipids", "12", "." ]

Original work titled: 'Binding and Flip as Initial Steps for BP-100 Antimicrobial Actions' (Scientific Reports/Nature Publishing Group UK) by the following authors: Peter Park; Leandro R. Franco; Hernan Chaimovich; Kaline Coutinho; Iolanda M. Cuccovia; Filipe S. Lima DOI: 10.1038/s41598-019-45075-5

5388809896c7b2a9adf5d708f6ea4b08

CC-BY

http://creativecommons.org/licenses/by/4.0/

4.0

[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]

[ "BP100", "does", "not", "perturb", "PC", "bilayers", "even", "at", "high", "peptide/lipid", "ratio", "and", "causes", "membrane", "thinning", "on", "mixed", "DMPC/DMPG", "bilayers", "where", "a", "stronger", "effect", "appears", "in", "anionic", "DMPG", "lipids", "compared", "to", "zwitterionic", "DMPC", "lipids", "12", ".", "In", "zwitterionic-lipid-enriched", "mammalian", "membranes,", "BP100", "would", "bind", "to", "membranes", "through", "electrostatic", "interactions", "and", "the", "absence", "of", "a", "helix-promoting", "environment", "would", "prevent", "helix", "formation", "and", "even", "with", "peptide", "flip,", "as", "in", "our", "α-BP100", "in", "DPPC", "simulation,", "it", "could", "lead", "to", "mild", "membrane", "thinning", "11", ",", "12", ".", "On", "the", "other", "hand,", "bacterial", "membranes", "with", "high", "content", "of", "anionic", "lipids", "on", "the", "outer", "part", "of", "the", "membrane,", "could", "promote", "peptide", "binding,", "alpha-helix", "nucleation,", "and", "propagation,", "leading", "to", "peptide", "flip", "and", "more", "pronounced", "membrane", "thinning,", "which", "is", "consistent", "with", "our", "observations", "from", "α-BP100", "in", "DPPG,", "α-BP100", "in", "PCPG-R", "and", "α-BP100", "(res1–5)", "in", "DPPG", "sets.", "Although", "we", "could", "not", "detect", "membrane", "thinning", "in", "our", "simulations", "(Table", "S2", "),", "it", "should", "be", "noted", "that", "our", "simulations", "had", "only", "one", "peptide", "on", "128-lipid-bilayers.", "A", "more", "pronounced", "effect", "on", "the", "membrane", "might", "be", "observed", "by", "increasing", "the", "number", "of", "peptides", "in", "the", "simulations.", "DPPG", "subdomain", "formation", "Lipid", "clustering,", "or", "subdomain", "formation,", "induced", "by", "CAMPs", "is", "well", "established", "5", ",", "14", ",", "35", "–", "37", ",", "42", "–", "45", ".", "Through", "electrostatic", "interactions,", "CAMPs", "clusters", "anionic", "phosphatidylglycerol", "(PG)", "or", "cardiolipin", "(CL)", "lipids", "on", "the", "outer", "membrane", "of", "bacteria,", "inducing", "phase", "separation", "and", "phase", "boundary", "defects", "between", "lipid", "domains", "and", "the", "rest", "of", "the", "membrane,", "increasing", "membrane", "permeability", "36", ".", "Epand", "et", "al.", "first", "proposed", "it", "45", ",", "in", "a", "study", "with", "oligomers", "of", "lysine", "(OAK)." ]

Original work titled: 'Binding and Flip as Initial Steps for BP-100 Antimicrobial Actions' (Scientific Reports/Nature Publishing Group UK) by the following authors: Peter Park; Leandro R. Franco; Hernan Chaimovich; Kaline Coutinho; Iolanda M. Cuccovia; Filipe S. Lima DOI: 10.1038/s41598-019-45075-5

5388809896c7b2a9adf5d708f6ea4b08

CC-BY

http://creativecommons.org/licenses/by/4.0/

4.0

[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]

[ "Lipid", "phase", "separation", "was", "later", "observed", "for", "other", "cAMPs", "and", "cell-penetrating-peptides", "37", ",", "45", ",", "46", ".", "Although", "not", "so", "pronounced,", "DSC", "also", "detected", "BP100", "ability", "to", "promote", "lipid", "phase", "separation", "on", "POPE/TOCL", "(75:25)", "vesicles", "37", ".", "Lipid", "phase", "separation", "promoted", "by", "CAMPs", "has", "also", "been", "observed", "in", "computational", "modeling", "studies.", "In", "a", "coarse-grained", "MD", "simulation", "study", "35", ",", "lipid", "cluster", "promotion", "was", "seen", "in", "POPE/POPG", "(70:30)", "membranes", "by", "Ltc1,", "a", "linear", "alpha-helical", "cAMP", "with", "overall", "+10", "charge.", "Simulations", "showed", "Ltc1", "induced", "POPG", "domains", "in", "small", "(256", "lipids)", "and", "large", "membranes", "(512", "or", "2048", "lipids).", "Also,", "due", "to", "peptide-POPG", "charge", "neutralization,", "Ltc1-induced", "anionic", "domains", "seem", "to", "facilitate", "peptide", "oligomerization,", "enhancing", "peptide", "activity", "on", "bacterial", "model", "membranes", "35", ".", "Likewise,", "our", "simulations", "suggest", "that", "BP100", "promotes", "PG", "aggregation.", "Two", "DPPC:", "DPPG", "(50:50)", "mixed", "bilayers", "were", "designed", "to", "explore", "lipid", "aggregation", "by", "the", "peptide.", "One", "membrane", "was", "composed", "of", "randomly", "mixed", "(PCPG-NR)", "and", "in", "the", "other,", "a", "4", "×", "4", "DPPG", "raft", "(PCPG-R)", "was", "positioned", "in", "the", "middle", "of", "both", "monolayers", "(see", "Methods", "1", "and", "Fig.", "1", ").", "BP100", "was", "able", "to", "cluster", "DPPGs", "in", "PCPG-NR,", "which", "can", "be", "observed", "by", "the", "amount", "of", "DPPG", "in", "contact", "with", "BP100", "(Table", "2", ").", "From", "a", "total", "of", "11", "lipids", "in", "the", "closer", "contact", "with", "BP100,", "8.3", "in", "average", "are", "DPPG", "corresponding", "to", "75%", "of", "the", "lipid", "in", "the", "vicinity", "of", "the", "peptide.", "Additionally,", "this", "DPPG", "clustering", "can", "also", "be", "observed", "in", "lipid", "raft", "size", "distribution", "(Fig.", "S6E", "),", "reaching", "similar", "values", "of", "DPPG/peptide", "contact", "in", "α-BP100", "in", "PCPG-R", "simulation", "(Fig.", "10", ")", "and", "DPPG", "lipid", "raft", "size", "probability", "(Fig.", "S6D", ")." ]

Original work titled: 'Binding and Flip as Initial Steps for BP-100 Antimicrobial Actions' (Scientific Reports/Nature Publishing Group UK) by the following authors: Peter Park; Leandro R. Franco; Hernan Chaimovich; Kaline Coutinho; Iolanda M. Cuccovia; Filipe S. Lima DOI: 10.1038/s41598-019-45075-5

5388809896c7b2a9adf5d708f6ea4b08

CC-BY

http://creativecommons.org/licenses/by/4.0/

4.0

[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]

[ "S6D", ").", "These", "data", "suggest", "that", "even", "a", "short-lengthened", "CAMP", "as", "BP100", "can", "promote", "anionic", "lipid", "clustering", "and", "also", "maintain", "it,", "supporting", "the", "experimental", "findings", "37", ".", "BP100", "also", "adsorbs", "on", "pure", "zwitterionic", "PC", "membranes", "and", "promotes", "DPPC", "clustering", "as", "observed", "in", "Figs", "S5", "A", "and", "S6A", ".", "However,", "possibly", "due", "to", "the", "presence", "of", "positively", "charged", "choline", "headgroups", "(Fig.", "1d", "-", "left),", "secondary", "structure", "is", "lost", "(Fig.", "5a", ")", "and", "the", "peptide", "turns", "into", "random", "coil,", "resulting", "in", "an", "increase", "of", "available", "interaction", "surface", "area", "with", "the", "DPPC", "headgroups,", "which", "is", "reflected", "in", "a", "broad", "distribution", "in", "lipid", "raft", "size", "distribution", "(Fig.", "S5A", ").", "Polar/Apolar", "pair", "analysis", "for", "α-BP100", "in", "PCPG-R", "(Fig.", "11", ")", "helps", "to", "explain", "lipid", "aggregation.", "We", "computed", "the", "ten", "most", "frequent", "apolar", "and", "polar", "pairs", "between", "peptide", "and", "lipids.", "The", "number", "of", "polar", "pairs", "between", "the", "peptide", "and", "DPPG", "is", "higher", "than", "those", "with", "DPPC", "and", "is", "maintained", "even", "after", "the", "flip", "(~390", "ns).", "As", "expected,", "+1", "charged", "amino", "group", "(NZ)", "from", "Lysines", "side", "chains", "are", "the", "main", "participants", "in", "polar", "pairings", "(Figs", "S7", "–", "S13", "),", "interacting", "with", "DPPG", "headgroup", "glycerol", "(OC2,", "OC3,", "Fig.", "1d", "-", "right),", "phosphate", "group", "(P),", "and", "carbonyl", "groups", "(C21,", "C31,", "O21,", "O22,", "O31,", "O32)", "from", "chains", "sn1", "and", "sn2", "(Figs", "S9", ",", "S10", ",", "S12", ",", "S13", ").", "Peptide", "flip", "seems", "to", "contribute", "to", "lipid", "clustering.", "Polar/apolar", "pairs", "analysis", "(Fig.", "11", ")", "and", "pair", "frequency", "(Figs", "S8", ",", "S9", ")", "for", "the", "previous", "simulation,", "reveals", "that", "apolar", "pairs", "between", "BP100", "and", "both", "lipids", "rise", "after", "peptide", "flip", "occurs", "(~390", "ns),", "intensifying", "peptide-membrane", "interaction.", "The", "same", "phenomena", "were", "observed", "for", "other", "simulations", "with", "peptide", "flip", "(Figs", "S7", ",", "S10", "and", "S13", ")." ]

Original work titled: 'Binding and Flip as Initial Steps for BP-100 Antimicrobial Actions' (Scientific Reports/Nature Publishing Group UK) by the following authors: Peter Park; Leandro R. Franco; Hernan Chaimovich; Kaline Coutinho; Iolanda M. Cuccovia; Filipe S. Lima DOI: 10.1038/s41598-019-45075-5

5388809896c7b2a9adf5d708f6ea4b08

CC-BY

http://creativecommons.org/licenses/by/4.0/

4.0

[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]

[ "Peptide", "flip", "seems", "to", "contribute", "to", "lipid", "clustering.", "Polar/apolar", "pairs", "analysis", "(Fig.", "11", ")", "and", "pair", "frequency", "(Figs", "S8", ",", "S9", ")", "for", "the", "previous", "simulation,", "reveals", "that", "apolar", "pairs", "between", "BP100", "and", "both", "lipids", "rise", "after", "peptide", "flip", "occurs", "(~390", "ns),", "intensifying", "peptide-membrane", "interaction.", "The", "same", "phenomena", "were", "observed", "for", "other", "simulations", "with", "peptide", "flip", "(Figs", "S7", ",", "S10", "and", "S13", ").", "As", "long", "as", "peptide", "flip", "had", "occurred,", "apolar", "residue", "side", "chains", "(from", "Leu3,", "Phe4,", "Ile7,", "Leu8", "and", "Tyr10,", "and", "Leu11)", "were", "in", "close", "contact", "mainly", "with", "groups", "of", "the", "lipid", "tails", "(Figs", "S7", "–", "S10", ",", "S13", ").", "The", "mechanisms", "of", "bacterial", "toxicity", "via", "lipid", "clustering", "induced", "by", "CAMPs", "still", "has", "to", "be", "investigated.", "Moreover,", "possibly", "more", "than", "one", "mechanism", "could", "be", "involved", "in", "the", "process", "of", "bacterial", "killing.", "Evidence", "suggest", "lipid", "clustering", "by", "CAMPs", "could", "lead", "to", "negative", "charge", "concentration", "on", "membranes,", "promoting", "CAMPs", "attachment,", "leading", "to", "pore", "formation", "5", ".", "Anionic", "lipid", "clustering", "would", "have", "surrounding", "interfaces", "with", "the", "rest", "of", "the", "membrane", "which", "could", "lead", "to", "phase", "boundary", "defects,", "leading", "to", "slow", "leakage", "of", "inner", "cell", "content", "32", ".", "Also,", "CAMPs", "and", "cell-penetrating", "peptides", "could", "induce", "negative", "membrane", "curvature,", "enabling", "the", "internalization", "of", "peptides", "into", "cells,", "leading", "to", "intracellular", "killing", "mechanisms.", "The", "formation", "of", "lipid", "clusters", "patches", "would", "also", "lead", "to", "anomalies", "in", "membrane", "protein", "function,", "membrane", "fluidity,", "and", "membrane", "polarization.", "In", "a", "recent", "study", "5", "with", "cWFW,", "a", "cyclic", "antimicrobial", "peptide,", "it", "was", "shown", "in", "vitro", "and", "in", "vivo", "that", "cWFW", "promotes", "lipid", "phase", "separation,", "a", "sharp", "decrease", "in", "membrane", "fluidity.", "The", "significant", "phase", "separation", "appears", "to", "cause", "disorganization", "of", "membrane", "proteins,", "inhibiting", "cell", "wall", "synthesis", "and", "inducing", "autolysis.", "BP100", "mode", "of", "action", "on", "membranes", "is", "dependent", "on", "peptide/lipid", "ratio", "11", ",", "47", "." ]

Original work titled: 'Binding and Flip as Initial Steps for BP-100 Antimicrobial Actions' (Scientific Reports/Nature Publishing Group UK) by the following authors: Peter Park; Leandro R. Franco; Hernan Chaimovich; Kaline Coutinho; Iolanda M. Cuccovia; Filipe S. Lima DOI: 10.1038/s41598-019-45075-5

5388809896c7b2a9adf5d708f6ea4b08

CC-BY

http://creativecommons.org/licenses/by/4.0/

4.0

[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]

[ "Also,", "due", "to", "peptide-POPG", "charge", "neutralization,", "Ltc1-induced", "anionic", "domains", "seem", "to", "facilitate", "peptide", "oligomerization,", "enhancing", "peptide", "activity", "on", "bacterial", "model", "membranes", "35", ".", "Likewise,", "our", "simulations", "suggest", "that", "BP100", "promotes", "PG", "aggregation.", "Two", "DPPC:", "DPPG", "(50:50)", "mixed", "bilayers", "were", "designed", "to", "explore", "lipid", "aggregation", "by", "the", "peptide.", "One", "membrane", "was", "composed", "of", "randomly", "mixed", "(PCPG-NR)", "and", "in", "the", "other,", "a", "4", "×", "4", "DPPG", "raft", "(PCPG-R)", "was", "positioned", "in", "the", "middle", "of", "both", "monolayers", "(see", "Methods", "1", "and", "Fig.", "1", ").", "BP100", "was", "able", "to", "cluster", "DPPGs", "in", "PCPG-NR,", "which", "can", "be", "observed", "by", "the", "amount", "of", "DPPG", "in", "contact", "with", "BP100", "(Table", "2", ").", "From", "a", "total", "of", "11", "lipids", "in", "the", "closer", "contact", "with", "BP100,", "8.3", "in", "average", "are", "DPPG", "corresponding", "to", "75%", "of", "the", "lipid", "in", "the", "vicinity", "of", "the", "peptide.", "Additionally,", "this", "DPPG", "clustering", "can", "also", "be", "observed", "in", "lipid", "raft", "size", "distribution", "(Fig.", "S6E", "),", "reaching", "similar", "values", "of", "DPPG/peptide", "contact", "in", "α-BP100", "in", "PCPG-R", "simulation", "(Fig.", "10", ")", "and", "DPPG", "lipid", "raft", "size", "probability", "(Fig.", "S6D", ").", "These", "data", "suggest", "that", "even", "a", "short-lengthened", "CAMP", "as", "BP100", "can", "promote", "anionic", "lipid", "clustering", "and", "also", "maintain", "it,", "supporting", "the", "experimental", "findings", "37", ".", "BP100", "also", "adsorbs", "on", "pure", "zwitterionic", "PC", "membranes", "and", "promotes", "DPPC", "clustering", "as", "observed", "in", "Figs", "S5", "A", "and", "S6A", ".", "However,", "possibly", "due", "to", "the", "presence", "of", "positively", "charged", "choline", "headgroups", "(Fig.", "1d", "-", "left),", "secondary", "structure", "is", "lost", "(Fig.", "5a", ")", "and", "the", "peptide", "turns", "into", "random", "coil,", "resulting", "in", "an", "increase", "of", "available", "interaction", "surface", "area", "with", "the", "DPPC", "headgroups,", "which", "is", "reflected", "in", "a", "broad", "distribution", "in", "lipid", "raft", "size", "distribution", "(Fig.", "S5A", ")." ]

Original work titled: 'Binding and Flip as Initial Steps for BP-100 Antimicrobial Actions' (Scientific Reports/Nature Publishing Group UK) by the following authors: Peter Park; Leandro R. Franco; Hernan Chaimovich; Kaline Coutinho; Iolanda M. Cuccovia; Filipe S. Lima DOI: 10.1038/s41598-019-45075-5

5388809896c7b2a9adf5d708f6ea4b08

CC-BY

http://creativecommons.org/licenses/by/4.0/

4.0

[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]

[ "Although", "we", "could", "not", "detect", "membrane", "thinning", "in", "our", "simulations", "(Table", "S2", "),", "it", "should", "be", "noted", "that", "our", "simulations", "had", "only", "one", "peptide", "on", "128-lipid-bilayers.", "A", "more", "pronounced", "effect", "on", "the", "membrane", "might", "be", "observed", "by", "increasing", "the", "number", "of", "peptides", "in", "the", "simulations.", "DPPG", "subdomain", "formation", "Lipid", "clustering,", "or", "subdomain", "formation,", "induced", "by", "CAMPs", "is", "well", "established", "5", ",", "14", ",", "35", "–", "37", ",", "42", "–", "45", ".", "Through", "electrostatic", "interactions,", "CAMPs", "clusters", "anionic", "phosphatidylglycerol", "(PG)", "or", "cardiolipin", "(CL)", "lipids", "on", "the", "outer", "membrane", "of", "bacteria,", "inducing", "phase", "separation", "and", "phase", "boundary", "defects", "between", "lipid", "domains", "and", "the", "rest", "of", "the", "membrane,", "increasing", "membrane", "permeability", "36", ".", "Epand", "et", "al.", "first", "proposed", "it", "45", ",", "in", "a", "study", "with", "oligomers", "of", "lysine", "(OAK).", "Upon", "the", "addition", "of", "OAK", "in", "1-palmitoyl-2-oleoyl", "phosphatidylethanolamine", "(POPE)", "and", "tetraoleoyl", "cardiolipin", "(TOCL)", "mixed", "vesicles,", "transition", "temperature", "shift", "was", "observed", "through", "differential", "scanning", "calorimetry,", "indicating", "lipid", "phase", "separation", "45", ".", "Lipid", "phase", "separation", "was", "later", "observed", "for", "other", "cAMPs", "and", "cell-penetrating-peptides", "37", ",", "45", ",", "46", ".", "Although", "not", "so", "pronounced,", "DSC", "also", "detected", "BP100", "ability", "to", "promote", "lipid", "phase", "separation", "on", "POPE/TOCL", "(75:25)", "vesicles", "37", ".", "Lipid", "phase", "separation", "promoted", "by", "CAMPs", "has", "also", "been", "observed", "in", "computational", "modeling", "studies.", "In", "a", "coarse-grained", "MD", "simulation", "study", "35", ",", "lipid", "cluster", "promotion", "was", "seen", "in", "POPE/POPG", "(70:30)", "membranes", "by", "Ltc1,", "a", "linear", "alpha-helical", "cAMP", "with", "overall", "+10", "charge.", "Simulations", "showed", "Ltc1", "induced", "POPG", "domains", "in", "small", "(256", "lipids)", "and", "large", "membranes", "(512", "or", "2048", "lipids)." ]

Original work titled: 'Binding and Flip as Initial Steps for BP-100 Antimicrobial Actions' (Scientific Reports/Nature Publishing Group UK) by the following authors: Peter Park; Leandro R. Franco; Hernan Chaimovich; Kaline Coutinho; Iolanda M. Cuccovia; Filipe S. Lima DOI: 10.1038/s41598-019-45075-5

5388809896c7b2a9adf5d708f6ea4b08

CC-BY

http://creativecommons.org/licenses/by/4.0/

4.0

[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]

[ "For", "BP100", "alpha-helical", "structure", "formation", "is", "favored", "in", "negatively", "charged", "membranes", "8", ".", "In", "our", "simulations,", "BP100", "entirely", "flipped", "in", "DPPG", "enriched", "regions", "of", "the", "membrane.", "Peptide", "flip", "was", "detected", "in", "α-BP100", "in", "DPPG,", "α-BP100", "(res1–5)", "in", "DPPG", "and", "α-BP100", "in", "PCPG-R", "systems.", "No", "peptide", "flip", "was", "detected", "in", "the", "other", "constrained", "BP100", "simulations", "(α-BP100", "(res4–8)", "in", "DPPG", "and", "α-BP100", "(res7–11)", "in", "DPPG).", "However,", "it", "is", "hasty", "to", "affirm", "that", "it", "is", "unlikely", "to", "expect", "peptide", "flip", "to", "happen", "in", "those", "systems", "with", "600", "ns", "of", "simulation", "time.", "For", "instance,", "peptide", "flip", "was", "observed", "after", "1.4", "µs", "of", "simulation", "in", "α-BP100", "in", "DPPG.", "Hydration", "analysis", "(Fig.", "8b", ")", "and", "density", "profile", "(Fig.", "S4A,B", ")", "for", "α-BP100", "in", "DPPC", "show", "also", "that", "BP100", "flipped.", "However,", "the", "alpha-helix", "secondary", "structure", "is", "mostly", "lost", "(Fig.", "5a", ").", "For", "this", "reason,", "BP100", "amphiphilic", "apolar-polar", "facet", "separation", "(Fig.", "2c", ")", "is", "lost.", "Additionally,", "the", "apolar", "moiety", "of", "the", "peptide", "could", "have", "a", "crucial", "role", "in", "peptide", "flip.", "Hydration", "analysis", "(Fig.", "8", ")", "suggests", "peptide", "flip", "results", "in", "peptide", "dehydration", "and", "concomitantly", "enhances", "peptide/lipid", "interaction", "(Fig.", "11", "),", "increasing", "specially", "apolar", "contacts", "(Fig.", "11", ").", "Similar", "behavior", "was", "observed", "in", "a", "study", "of", "the", "interaction", "of", "micelles", "with", "polyatomic", "counterions", "with", "apolar", "and", "polar", "moieties.", "Experimental", "results", "and", "MD", "simulations", "showed", "that", "counterions", "with", "the", "same", "apolar", "groups", "but", "different", "polar", "groups", "resulted", "in", "similar", "ionic", "affinities", "for", "dodecyltrimethylammonium", "micelles,", "and", "the", "simulations", "showed", "that", "counterion", "adsorption", "to", "the", "micelles", "was", "related", "with", "the", "dehydration", "of", "the", "apolar", "group", "of", "the", "counterions", "rather", "than", "by", "the", "polar", "group", "41", "." ]

Original work titled: 'Binding and Flip as Initial Steps for BP-100 Antimicrobial Actions' (Scientific Reports/Nature Publishing Group UK) by the following authors: Peter Park; Leandro R. Franco; Hernan Chaimovich; Kaline Coutinho; Iolanda M. Cuccovia; Filipe S. Lima DOI: 10.1038/s41598-019-45075-5

5388809896c7b2a9adf5d708f6ea4b08

CC-BY

http://creativecommons.org/licenses/by/4.0/

4.0

[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]

[ "The", "5–9", "region", "shows", "high", "stability", "in", "all", "constraint-free", "α-BP100/membranes", "simulations", "and", "has", "the", "overall", "lowest", "energy", "barrier", "in", "the", "helix", "propensity", "scale", "40", ".", "DPPG", "seems", "to", "have", "a", "helix-stabilizing", "effect", "on", "BP100.", "All", "the", "simulations", "with", "α-BP100", "in", "DPPG-containing-membranes", "showed", "high", "alpha-helical", "content,", "including", "the", "region", "of", "residues", "5", "to", "9.", "Our", "helicity", "results", "from", "the", "simulations", "with", "α-BP100", "in", "pure", "DPPG", "(73%)", "and", "in", "PCPG", "(50:50)", "mixed", "bilayers", "(54%)", "are", "remarkably", "close", "to", "those", "reported", "in", "experimental", "studies:", "54%", "in", "POPC:POPG", "(50:50)", "11", "and", "61%", "in", "DMPC/DMPG", "(75:25)", "LUVs", "10", ",", "and", "maximum", "observable", "alpha-helix", "spectrum", "for", "BP100", "in", "pure", "POPG", "vesicles", "11", "proving", "that", "BP100", "alpha-helical", "structure", "is", "dependent", "on", "PG", "content", "11", ".", "For", "L-BP100", "simulations", "with", "DPPG,", "PCPG-R,", "and", "PCPG-NR,", "no", "secondary", "structure", "formation", "was", "detected", "(Fig.", "S3", "),", "with", "the", "peptide", "being", "in", "a", "random", "conformation.", "Non-biased", "random", "peptide", "simulations", "require", "much", "longer", "simulation", "time", "to", "sample", "the", "peptide", "conformational", "potential", "landscape", "or", "might", "dwell", "in", "several", "local", "minimum-energy", "states.", "Peptide", "flip", "BP100", "is", "too", "short", "to", "span", "the", "bilayer", "thickness,", "especially", "in", "the", "alpha-helical", "conformation,", "and", "thus", "single", "molecule", "pore", "formation", "is", "an", "unlikely", "scenario.", "NMR", "data", "of", "BP100", "in", "DMPC:", "DMPG", "(3:1)", "10", "shows", "that", "upon", "binding", "to", "negatively", "charged", "membranes,", "alpha-helical", "BP100", "positions", "parallel", "to", "the", "membrane", "as", "in", "a", "surface-bound", "orientation,", "and", "has", "an", "azimuthal", "rotation", "angle", "close", "to", "160°,", "with", "Lysine", "residues", "facing", "the", "solvent.", "This", "last", "arrangement", "is", "commonly", "observed", "with", "other", "CAMPs", "30", "–", "33", ".", "Peptide/membrane", "simulations", "with", "initially", "alpha-helical", "BP100", "had", "its", "polar", "moiety", "facing", "the", "membrane,", "for", "being", "the", "most", "probable", "scenario", "in", "a", "physical", "environment." ]

Original work titled: 'Binding and Flip as Initial Steps for BP-100 Antimicrobial Actions' (Scientific Reports/Nature Publishing Group UK) by the following authors: Peter Park; Leandro R. Franco; Hernan Chaimovich; Kaline Coutinho; Iolanda M. Cuccovia; Filipe S. Lima DOI: 10.1038/s41598-019-45075-5

5388809896c7b2a9adf5d708f6ea4b08

CC-BY

http://creativecommons.org/licenses/by/4.0/

4.0

[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]

[ "The", "negatively", "charged", "membrane", "interface", "could", "promote", "the", "initial", "peptide", "folding.", "To", "support", "this,", "we", "performed", "three", "600", "ns-long", "simulations", "with", "constrained", "alpha", "helices", "of", "BP100", "on", "three", "regions:", "residues", "1", "to", "5", "(Lys-Lys-Leu-Phe-Lys),", "4", "to", "8", "(Phe-Lys-Lys-Ile-Leu)", "and", "7", "to", "11", "(Ile-Leu-Lys-Tyr-Leu)", "in", "pure", "DPPG", "bilayers.", "The", "secondary", "structure", "analysis", "of", "the", "constrained", "BP100", "simulations", "yielded", "different", "outcomes.", "Constraint", "on", "residues", "1", "to", "5", "rapidly", "induced", "almost", "full", "alpha-helix", "content", "from", "Lys2", "to", "Lys9", "(Fig.", "6A", "),", "reaching", "73%", "of", "helicity,", "similar", "to", "α-BP100", "in", "DPPG", "without", "constraints", "(Fig.", "5B", ").", "Constraint", "on", "residues", "4", "to", "8", "also", "showed", "a", "helix", "formation", "tendency", "(overall", "63%", "helicity,", "5", "out", "of", "11", "residues,", "from", "Phe4", "to", "Lys9).", "In", "sharp", "contrast,", "constraints", "on", "residues", "7", "to", "11", "(36%", "of", "helicity,", "4", "out", "of", "11", "residues,", "from", "Lys7", "to", "Tyr10)", "had", "no", "effects", "on", "the", "secondary", "structure", "formation", "of", "BP100", "during", "600", "ns", "simulation", "(Fig.", "6C", "),", "indicating", "that", "this", "region", "has", "little", "influence", "on", "initial", "peptide", "folding.", "Pace", "and", "Scholtz", "40", ",", "based", "on", "experimental", "studies,", "proposed", "a", "helix", "propensity", "scale", "as", "Δ(ΔG)", "values", "relative", "to", "Alanine", "set", "to", "zero.", "On", "the", "Pace", "and", "Scholtz", "scale,", "the", "5–9", "region", "has", "the", "highest", "helix", "promoting", "residues", "(overall", "helix", "propensity", "of", "1.4", "kcal/mol).", "We", "find", "1.53", "kcal/mol", "for", "residues", "1", "to", "5", "(Lys-Lys-Leu-Phe-Lys),", "1.68", "kcal/mol", "for", "residues", "4", "to", "8", "(Phe-Lys-Lys-Ile-Leu),", "and", "1.62", "kcal/mol", "for", "residues", "7–11", "(Ile-Leu-Lys-Tyr-Leu)." ]

Original work titled: 'Binding and Flip as Initial Steps for BP-100 Antimicrobial Actions' (Scientific Reports/Nature Publishing Group UK) by the following authors: Peter Park; Leandro R. Franco; Hernan Chaimovich; Kaline Coutinho; Iolanda M. Cuccovia; Filipe S. Lima DOI: 10.1038/s41598-019-45075-5

5388809896c7b2a9adf5d708f6ea4b08

CC-BY

http://creativecommons.org/licenses/by/4.0/

4.0

[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]

[ "Also,", "after", "the", "flip,", "apolar", "contacts", "between", "BP100", "and", "DPPG", "were", "more", "frequent", "than", "with", "DPPC", "(Fig.", "11b", ").", "The", "higher", "peptide/DPPG", "apolar", "contact", "frequency", "after", "the", "flip", "is", "also", "observed", "for", "other", "simulations", "with", "peptide", "flip", "(Figs", "S7", "–", "10", ",", "13).", "Discussion", "Peptide", "secondary", "structure", "CD", "spectra", "of", "BP100", "in", "solution", "and", "POPC", "LUVs", "show", "no", "secondary", "structure", "10", ",", "11", ",", "30", "Our", "simulations", "with", "BP100", "in", "solution,", "and", "DPPC", "membrane", "exhibited", "the", "same", "pattern.", "α-BP100", "and", "L-BP100", "in", "solution", "showed", "similar", "behavior,", "with", "a", "prevalence", "of", "random", "conformation", "(Fig.", "4", ").", "In", "a", "related", "MD", "study", "of", "AMPs", "interacting", "with", "membranes", "17", ",", "an", "8", "µs-long", "all-atom", "MD", "simulation", "of", "BP100", "in", "DMPC", "at", "35◽", "the", "authors", "reported", "a", "full", "helix", "length", "during", "1.5", "µs", "and", "a", "subsequent", "unfolding", "event", "of", "Lysines", "at", "positions", "1", "and", "2,", "resulting", "in", "81%", "of", "helicity", "on", "a", "pure", "zwitterionic", "bilayer.", "However,", "as", "reported", "for", "other", "simulated", "peptides", "in", "the", "same", "work,", "the", "forcefield", "used", "could", "result", "in", "an", "over-helical", "artifact", "17", ".", "A", "Brownian", "Dynamics", "simulation", "study", "of", "BP100", "confined", "inside", "an", "implicit", "POPC", "membrane", "reports", "a", "stable", "alpha-helix", "18", ".", "However,", "no", "experimental", "data", "confirms", "that", "BP100", "diffuses", "freely", "in", "the", "membrane", "hydrophobic", "space", "and", "no", "secondary", "structure", "formation", "is", "reported", "for", "pure", "POPC", "vesicles", "11", ".", "In", "our", "simulations", "of", "α-BP100", "and", "L-BP100", "in", "DPPC", "membrane,", "the", "peptide", "quickly", "approached", "the", "membrane", "and", "remained", "on", "the", "surface", "during", "all", "simulation.", "Peptide-lipid", "pair", "analysis", "(Fig.", "S7", ")", "showed", "that", "cationic", "Lysine", "residues", "interacted", "mainly", "with", "phosphate", "groups", "of", "the", "DPPC", "bilayer,", "evidencing", "that", "electrostatic", "interactions", "were", "present.", "In", "the", "case", "of", "L-BP100", "in", "DPPC,", "no", "alpha-helical", "structure", "formation", "was", "observed", "(Fig.", "S3", "),", "and", "for", "α-BP100,", "the", "peptide", "alpha-helix", "conformation", "was", "mostly", "lost,", "although", "one", "helix", "turn", "from", "residues", "5", "to", "9", "remained", "(Fig." ]

Original work titled: 'Binding and Flip as Initial Steps for BP-100 Antimicrobial Actions' (Scientific Reports/Nature Publishing Group UK) by the following authors: Peter Park; Leandro R. Franco; Hernan Chaimovich; Kaline Coutinho; Iolanda M. Cuccovia; Filipe S. Lima DOI: 10.1038/s41598-019-45075-5

5388809896c7b2a9adf5d708f6ea4b08

CC-BY

http://creativecommons.org/licenses/by/4.0/

4.0

[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]

[ "In", "the", "last", "500", "ns", "of", "simulation,", "N(0.5)", "was", "approximately", "178", "±", "11", "in", "DPPC,", "145", "±", "7", "in", "DPPG,", "145", "±", "13", "in", "PCPG-NR,", "and", "148", "±", "3", "in", "PCPG-R.", "No", "peptide", "flip", "was", "detected", "in", "the", "trajectories", "for", "those", "simulations.", "However,", "in", "the", "peptide/membrane", "simulations", "with", "α-BP100", "as", "a", "starting", "configuration", "(Fig.", "8b", "),", "N", "(0.5)", "lowered", "in", "DPPC", "(starting", "at", "~700", "ns),", "DPPG", "(~1500", "ns)", "and", "PCPG-R", "(~390", "ns).", "Alongside", "with", "dehydration,", "a", "peptide-flip", "was", "observed", "in", "DPPG", "and", "PCPG-R.", "For", "the", "α-", "BP100", "in", "DPPC", "simulation,", "we", "observed", "a", "semi-flip,", "as", "the", "peptide", "alpha-helical", "conformation", "was", "only", "38%", "(Fig.", "5a", "),", "suggesting", "that", "the", "peptide", "overall", "polar/apolar", "segregation", "(Fig.", "2c", ")", "was", "lost.", "The", "peptide", "flip", "transition", "time", "varied", "from", "100", "to", "400", "ns.", "During", "the", "peptide-flip,", "in", "the", "simulations", "of", "α-BP100", "in", "DPPG", "and", "PCPG-R,", "the", "mean", "number", "N(0.5)", "was", "reduced", "from", "147", "±", "5", "and", "142", "±", "7", "to", "76", "±", "4", "and", "75", "±", "4,", "respectively.", "These", "represent", "on", "average", "a", "reduction", "of", "approximately", "48%", "in", "the", "number", "of", "water", "molecules", "in", "the", "hydration", "shell", "of", "α-BP100.", "In", "DPPC,", "we", "detected", "a", "smaller", "decrease", "in", "the", "hydration", "of", "α-BP100,", "around", "45%", "(from", "172", "±", "8", "to", "94", "±", "2),", "having", "around", "20", "water", "molecules", "more", "after", "the", "semi-flip.", "Figure", "9", "shows", "the", "density", "profile", "before", "and", "after", "peptide", "flip", "for", "α-BP100", "in", "DPPG", "and", "PCPG-R.", "We", "chose", "residues", "Lys5", "and", "Ile7", "to", "illustrate", "the", "changes", "in", "the", "mean", "position", "of", "hydrophobic", "and", "hydrophilic", "residues", "with", "respect", "to", "the", "membrane", "due", "to", "the", "peptide", "flip.", "These", "residues", "are", "polar", "and", "apolar,", "respectively,", "and", "located", "opposite", "to", "each", "other", "when", "in", "an", "alpha-helix", "conformation", "(Fig.", "2c", ")." ]

Original work titled: 'Binding and Flip as Initial Steps for BP-100 Antimicrobial Actions' (Scientific Reports/Nature Publishing Group UK) by the following authors: Peter Park; Leandro R. Franco; Hernan Chaimovich; Kaline Coutinho; Iolanda M. Cuccovia; Filipe S. Lima DOI: 10.1038/s41598-019-45075-5

5388809896c7b2a9adf5d708f6ea4b08

CC-BY

http://creativecommons.org/licenses/by/4.0/

4.0

[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]

[ "α-BP100", "with", "constraints", "on", "residues", "1–5", "(Lys-Lys-Leu-Phe-Lys)", "acquired", "identical", "helicity", "(73%)", "to", "α-BP100", "with", "no", "constraints", "at", "the", "same", "conditions", "(Fig.", "5b", "),", "after", "50", "ns", "of", "simulation", "(Fig.", "6a", "),", "with", "a", "helix", "spanning", "from", "Lys2", "to", "Lys9", "(Fig.", "6a", ").", "Constraints", "on", "residues", "4–8", "(Phe-Lys-Lys-Ile-Leu)", "showed", "an", "overall", "52%", "of", "helicity", "(Fig.", "6b", "),", "with", "a", "helix", "spanning", "from", "Phe4", "to", "Lys9", "(Fig.", "6b", ").", "Constraints", "on", "residues", "7–11", "(Ile-Leu-Lys-Tyr-Leu)", "did", "not", "affect", "the", "rest", "of", "the", "peptide", "conformation", "(Fig.", "6c", ")", "in", "600", "ns", "of", "simulation.", "Peptide", "flip", "Simulation", "trajectories", "analyses", "(Fig.", "7", ")", "revealed", "that", "the", "peptide", "in", "alpha-helix", "conformation", "initially", "adsorbed", "at", "the", "DPPG-containing", "membranes", "interface", "with", "its", "hydrophilic", "facet", "in", "contact", "with", "the", "membrane,", "leaving", "the", "hydrophobic", "facet", "exposed", "to", "water.", "We", "observed", "that", "the", "alpha-helix", "rotated,", "inserting", "the", "hydrophobic", "facet", "into", "the", "hydrophobic", "region", "of", "the", "membrane.", "We", "define", "this", "dynamic", "phenomenon,", "observed", "in", "our", "simulations,", "as", "peptide", "flip.", "Although", "this", "final", "peptide", "orientation", "is", "known", "31", "–", "34", ",", "no", "MD", "simulation", "on", "peptide", "flip", "has", "been", "reported.", "Figure", "7", "Peptide", "flip", "observed", "from", "above", "in", "α", "-BP100", "in", "DPPG", "set", "after", "circa", "1400", "ns", "of", "simulation.", "In", "blue,", "polar", "facet", "and", "in", "green,", "the", "apolar", "facet.", "Peptide", "flip", "was", "also", "observed", "in", "α", "-BP100", "in", "DPPC,", "α", "-BP100", "in", "PCPG-R,", "and", "α", "-BP100", "res(1–5)", "in", "DPPG", "simulations.", "The", "peptide", "flip", "caused", "dehydration", "(Fig.", "8", ").", "When", "in", "contact", "with", "membranes,", "depending", "on", "the", "secondary", "structure", "of", "the", "peptide", "and", "the", "lipid", "nature,", "the", "hydration", "of", "the", "peptide", "was", "slightly", "different." ]

Original work titled: 'Binding and Flip as Initial Steps for BP-100 Antimicrobial Actions' (Scientific Reports/Nature Publishing Group UK) by the following authors: Peter Park; Leandro R. Franco; Hernan Chaimovich; Kaline Coutinho; Iolanda M. Cuccovia; Filipe S. Lima DOI: 10.1038/s41598-019-45075-5

5388809896c7b2a9adf5d708f6ea4b08

CC-BY

http://creativecommons.org/licenses/by/4.0/

4.0

[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]

[ "In", "all", "cases,", "the", "peptide", "was", "rapidly", "adsorbed", "on", "the", "membranes", "and", "diffused", "laterally.", "Figure", "5", "shows", "that", "the", "BP100", "alpha-helical", "conformation", "was", "proportional", "to", "PG", "content,", "as", "the", "alpha-helix", "percentage", "in", "DPPC", "is", "considerably", "smaller", "than", "that", "observed", "in", "DPPG-containing", "membranes.", "Alpha-helix", "formed", "in", "the", "5", "to", "9", "residues", "region", "(Lys-Lys-Ile-Leu-Lys)", "was", "highly", "stable", "in", "all", "simulations.", "Figure", "5", "Secondary", "structure", "analyses", "of", "α", "-BP100", "in", "DPPC", "(", "a", "),", "DPPG", "(", "b", "),", "PCPG-R", "(", "c", ")", "and", "PCPG-NR", "(", "d", ").", "In", "DPPC,", "α-BP100", "alpha-helix", "conformation", "reached", "a", "plateau", "at", "38%", "helicity", "throughout", "the", "simulation,", "being", "relatively", "less", "stable", "than", "α-BP100", "in", "bilayers", "containing", "DPPG,", "where", "a", "higher", "propensity", "of", "maintaining", "its", "conformation", "was", "observed.", "For", "pure", "DPPG", "(Fig.", "5b", ")", "we", "found", "73%", "(8", "out", "of", "11", "residues),", "and", "for", "both", "PCPG", "(1:1)", "membranes", "we", "report", "54%", "(6", "out", "of", "11)", "of", "helicity", "(Fig.", "5c,d", ").", "No", "alpha-helix", "formation", "was", "detected", "in", "L-BP100", "on", "bilayers", "simulations", "(Fig.", "S3", ").", "Therefore,", "the", "1.8", "µs", "simulation", "was", "not", "enough", "to", "present", "a", "spontaneous", "peptide", "folding.", "The", "alpha-helix", "formed", "in", "the", "region", "of", "the", "residues", "5", "to", "9", "showed", "higher", "stability", "in", "all", "simulations", "with", "α-BP100", "in", "bilayers", "(Fig.", "5", ").", "This", "secondary", "structure", "pattern", "led", "us", "to", "suggest", "that", "the", "residues", "5", "to", "9", "are", "related", "to", "helix", "nucleation,", "in", "which", "the", "formation", "of", "this", "helix", "core", "could", "be", "the", "first", "step", "in", "the", "AMP", "actions.", "Following", "this", "assumption,", "we", "tested", "three", "conformations", "with", "α-BP100", "torsionally", "constrained", "in", "three", "regions:", "res1–5,", "res4–8,", "res7–11", "(Fig.", "3", ")", "and", "simulated", "with", "pure", "DPPG", "membranes.", "Figure", "6", "shows", "the", "evolution", "of", "the", "secondary", "structure", "in", "each", "simulation." ]

Original work titled: 'Binding and Flip as Initial Steps for BP-100 Antimicrobial Actions' (Scientific Reports/Nature Publishing Group UK) by the following authors: Peter Park; Leandro R. Franco; Hernan Chaimovich; Kaline Coutinho; Iolanda M. Cuccovia; Filipe S. Lima DOI: 10.1038/s41598-019-45075-5

5388809896c7b2a9adf5d708f6ea4b08

CC-BY

http://creativecommons.org/licenses/by/4.0/

4.0

[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]

[ "Figure", "4", "shows", "that", "BP100", "conformation", "in", "solution", "was,", "predominantly,", "random", "coil.", "The", "peptide", "lost", "the", "initial", "alpha", "helix", "conformation", "in", "approximately", "40", "ns", "when", "starting", "with", "an", "alpha-helix", "configuration", "and", "occasionally", "formed", "an", "alpha-helix", "turn", "in", "the", "5–9", "residue", "region", "(Fig.", "4a", ").", "For", "L-BP100", "in", "solution,", "we", "observed", "a", "similar", "pattern", "(Fig.", "4b", ").", "Circular", "Dichroism", "(CD)", "shows", "that", "BP100", "is", "random", "in", "solution", "10", ",", "11", ",", "30", ",", "and", "our", "simulations", "reproduced", "these", "data.", "Figure", "4", "Secondary", "structure", "analyses", "graphs", "of", "α", "-BP100", "(", "a", ")", "and", "L", "-BP100", "(", "b", ")", "in", "solution.", "In", "both", "cases,", "the", "peptide", "shows", "predominance", "in", "random", "coil", "structure", "(orange)", "with", "occasional", "formation", "of", "1", "alpha", "helix", "turn", "(blue)", "in", "residues", "5", "to", "9.", "Peptide", "in", "bilayers", "BP100", "conformation,", "antimicrobial", "activity,", "and", "PG", "content", "are", "related", "11", ".", "We", "simulated", "α-BP100", "and", "L-BP100", "on", "DPPC,", "DPPG,", "PCPG-R,", "and", "PCPG-NR", "at", "323", "K,", "above", "DPPG", "and", "DPPC", "transition", "temperatures.", "In", "all", "cases,", "the", "peptide", "was", "rapidly", "adsorbed", "on", "the", "membranes", "and", "diffused", "laterally.", "Figure", "5", "shows", "that", "the", "BP100", "alpha-helical", "conformation", "was", "proportional", "to", "PG", "content,", "as", "the", "alpha-helix", "percentage", "in", "DPPC", "is", "considerably", "smaller", "than", "that", "observed", "in", "DPPG-containing", "membranes.", "Alpha-helix", "formed", "in", "the", "5", "to", "9", "residues", "region", "(Lys-Lys-Ile-Leu-Lys)", "was", "highly", "stable", "in", "all", "simulations.", "Figure", "5", "Secondary", "structure", "analyses", "of", "α", "-BP100", "in", "DPPC", "(", "a", "),", "DPPG", "(", "b", "),", "PCPG-R", "(", "c", ")", "and", "PCPG-NR", "(", "d", ").", "In", "DPPC,", "α-BP100", "alpha-helix", "conformation", "reached", "a", "plateau", "at", "38%", "helicity", "throughout", "the", "simulation,", "being", "relatively", "less", "stable", "than", "α-BP100", "in", "bilayers", "containing", "DPPG,", "where", "a", "higher", "propensity", "of", "maintaining", "its", "conformation", "was", "observed.", "For", "pure", "DPPG", "(Fig." ]

Original work titled: 'Binding and Flip as Initial Steps for BP-100 Antimicrobial Actions' (Scientific Reports/Nature Publishing Group UK) by the following authors: Peter Park; Leandro R. Franco; Hernan Chaimovich; Kaline Coutinho; Iolanda M. Cuccovia; Filipe S. Lima DOI: 10.1038/s41598-019-45075-5

5388809896c7b2a9adf5d708f6ea4b08

CC-BY

http://creativecommons.org/licenses/by/4.0/

4.0

[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]

[ "The", "time", "window", "selected", "for", "computing", "these", "RDFs", "includes", "that", "of", "the", "membrane", "bound", "peptide", "250", "ns-before", "and", "250", "ns-after", "the", "peptide", "flip.", "The", "pairs", "with", "distinguishable", "RDF", "peaks", "and", "following", "minimum", "were", "used", "to", "analyze", "the", "number", "of", "polar", "and", "apolar", "contacts", "between", "lipids", "and", "peptide.", "A", "cutoff", "distance", "for", "each", "pair", "was", "defined", "from", "the", "position", "of", "the", "first", "minimum", "in", "the", "RDF", "curve,", "and", "a", "contact", "was", "defined", "as", "a", "pair", "of", "atoms", "at", "smaller", "distance", "than", "their", "corresponding", "cutoff", "distance.", "The", "simulations", "were", "analyzed", "and", "the", "total", "number", "of", "polar", "and", "apolar", "contacts", "as", "a", "function", "of", "time", "was", "obtained.", "Additionally,", "some", "polar", "and", "apolar", "pairs", "were", "analyzed", "individually.", "Peptide", "hydration", "The", "time", "evolution", "of", "the", "solvent", "shell", "surrounding", "the", "peptide", "in", "its", "α", "and", "L", "conformations", "in", "all", "simulated", "membranes", "was", "analyzed", "using", "the", "minimum", "distance", "distribution", "function", "(MDDF)", "29", "between", "the", "peptide", "and", "the", "water", "molecules,", "as", "well", "as", "the", "average", "number", "of", "water", "molecules", "N(r),", "within", "a", "distance", "r", "=", "0.5", "nm,", "named", "here", "as", "N(0.5).", "For", "comparison", "the", "MDDF", "of", "BP100", "in", "water", "was", "used", "to", "define", "the", "bulk", "water", "hydration", "shell", "at", "the", "same", "distance.", "Results", "The", "17", "sets", "of", "simulations", "(Table", "1", ")", "were", "run", "for", "more", "than", "25", "µs", "of", "simulation", "time,", "and", "each", "unconstrained", "peptide/membrane", "simulation", "had", "at", "least", "1.6", "µs", "of", "simulation.", "After", "comparing", "the", "simulated", "membrane", "properties", "with", "experimental", "and", "other", "computational", "studies", "(Tables", "S1", "and", "S2", "),", "we", "systematically", "analyzed", "the", "peptide", "conformation", "in", "solution", "and", "on", "bilayers,", "peptide", "trajectory,", "and", "dynamics", "on", "membranes", "and", "the", "effect", "of", "BP100", "on", "model", "bilayers.", "In", "the", "following", "sections,", "we", "describe", "our", "results.", "Secondary", "structure", "Peptide", "in", "solution", "To", "study", "BP100", "secondary", "structure", "in", "water,", "we", "did", "simulations", "for", "more", "than", "2", "µs", "with", "both", "α-BP100", "and", "L-BP100", "initial", "conformations.", "Figure", "4", "shows", "that", "BP100", "conformation", "in", "solution", "was,", "predominantly,", "random", "coil.", "The", "peptide", "lost", "the", "initial", "alpha", "helix", "conformation", "in", "approximately", "40", "ns", "when", "starting", "with", "an", "alpha-helix", "configuration", "and", "occasionally", "formed", "an", "alpha-helix", "turn", "in", "the", "5–9", "residue", "region", "(Fig.", "4a", ")." ]

Original work titled: 'Binding and Flip as Initial Steps for BP-100 Antimicrobial Actions' (Scientific Reports/Nature Publishing Group UK) by the following authors: Peter Park; Leandro R. Franco; Hernan Chaimovich; Kaline Coutinho; Iolanda M. Cuccovia; Filipe S. Lima DOI: 10.1038/s41598-019-45075-5

5388809896c7b2a9adf5d708f6ea4b08

CC-BY

http://creativecommons.org/licenses/by/4.0/

4.0

[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]

[ "For", "all", "these", "initial", "conditions,", "we", "obtained", "the", "same", "final", "location", "and", "orientation", "of", "the", "peptide", "that", "will", "be", "discussed", "in", "the", "results", "section.", "To", "investigate", "the", "influence", "of", "small", "core", "alpha-helical", "sequences", "in", "BP100", "to", "its", "stability", "when", "interacting", "with", "bilayers,", "constrained", "simulations", "of", "BP100", "in", "DPPG", "membranes", "were", "performed.", "The", "alpha-helix", "dihedral", "angles", "(ϕ", "=", "−60°;", "ψ", "=", "−40°)", "in", "3", "different", "regions", "were", "fixed:", "1–5", "(Lys-Lys-Leu-Phe-Lys),", "4–8", "(Phe-Lys-Lys-Ile-Leu)", "and", "7–11", "(Ile-Leu-Lys-Tyr-Leu)", "residues", "(Fig.", "3", ").", "We", "maintained", "the", "constrained", "regions", "during", "the", "simulations.", "Figure", "3", "Starting", "structures", "for", "peptides", "with", "permanent", "constrained", "dihedral", "angles.", "Following", "the", "previous", "lipid", "membrane", "systems,", "energy-minimization,", "NVT,", "and", "NPT", "ensembles", "were", "used", "in", "the", "equilibration", "stage", "of", "the", "MD", "simulation.", "Simulation", "details", "MD", "simulations", "were", "carried", "out", "with", "a", "2", "fs", "time-step", "with", "a", "Leap-Frog", "integrator", "24", ",", "in", "isobaric-isothermal", "(NPT)", "ensemble,", "at", "323", "K", "(50", "°C)", "with", "temperature", "coupling", "treated", "separately", "for", "BP100,", "lipids,", "water", "and", "ions", "with", "the", "V-rescale", "thermostat", "25", ".", "Atmospheric", "pressure", "of", "1", "bar", "was", "kept", "with", "the", "Berendsen", "barostat", "26", "and", "semi-isotropic", "pressure", "coupling", "was", "used", "for", "all", "systems.", "All", "bonds", "were", "constrained", "with", "LINCS", "27", "algorithm.", "Long-range", "electrostatic", "correction", "was", "treated", "by", "a", "Particle-mesh-Ewald", "method", "28", "with", "a", "real-space", "cut-off", "of", "1.5", "nm.", "van", "der", "Waals", "interactions", "were", "truncated", "at", "1.5", "nm", "distance", "with", "a", "switch", "function", "from", "1.4", "nm.", "Simulation", "analyses", "Lipid/peptide", "contacts", "For", "the", "computation", "of", "lipid", "contacts", "with", "BP100", "and", "pair", "frequency,", "we", "labeled", "some", "lipid(s)", "and", "BP100", "atoms", "as", "“polar”", "or", "“apolar”,", "based", "on", "charges." ]

Original work titled: 'Binding and Flip as Initial Steps for BP-100 Antimicrobial Actions' (Scientific Reports/Nature Publishing Group UK) by the following authors: Peter Park; Leandro R. Franco; Hernan Chaimovich; Kaline Coutinho; Iolanda M. Cuccovia; Filipe S. Lima DOI: 10.1038/s41598-019-45075-5

5388809896c7b2a9adf5d708f6ea4b08

CC-BY

http://creativecommons.org/licenses/by/4.0/

4.0

[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]

[ "One", "membrane", "was", "composed", "of", "randomly", "distributed", "lipids", "(PCPG-NR)", "on", "both", "leaflets", "and", "the", "other,", "a", "4", "×", "4", "DPPG", "raft", "was", "placed", "in", "the", "center", "of", "both", "monolayers", "(PCPG-R)", "and", "the", "remaining", "48", "lipids", "were", "randomly", "distributed", "(Fig.", "2", ").", "Figure", "2", "Initial", "membrane", "configurations", "membranes.", "TIP3P", "water", "molecules", "were", "used", "to", "solvate", "our", "systems,", "with", "an", "approximately", "53", "water/lipid", "ratio.", "Na", "+", "ions", "(Aqvist", "21", ")", "were", "included", "to", "counter-balance", "charges", "of", "membranes", "containing", "DPPG.", "All", "bilayer", "sets", "were", "minimized", "and", "equilibrated", "for", "20", "ps", "in", "a", "NVT", "ensemble", "and", "thereafter,", "in", "NPT", "conditions", "for", "50", "ns.", "After", "that,", "the", "bilayers", "were", "simulated", "for", "860", "ns", "(DPPC),", "1100", "ns", "(DPPG)", "and", "1200", "ns", "(for", "both", "PCPG-R", "and", "PCPG-NR).", "The", "area", "per", "lipid", "and", "membrane", "thickness", "were", "calculated", "for", "all", "membranes", "and", "thNen", "compared", "with", "experimental", "data", "and", "those", "obtained", "by", "Slipids", "authors", "(Tables", "S1", "and", "S2", ").", "The", "last", "trajectory", "frames", "of", "the", "membrane", "simulations", "were", "used", "to", "build", "our", "peptide-lipid", "systems.", "Peptide-in-solution", "and", "peptide-lipid", "systems", "Following", "a", "study", "by", "Beauchamp", "et", "al.", "22", ",", "ff99sb-ildn-NMR", "force", "field", "was", "chosen", "to", "characterize", "BP100", "in", "our", "modeling", "due", "to", "its", "good", "performance", "in", "simulating", "peptides", "and", "proteins", "structures", "in", "TIP3P", "water", "when", "compared", "with", "NMR", "measurements.", "BP100", "(H-Lys-Lys-Leu-Phe-Lys-Lys-Ile-Leu-Lys-Tyr-Leu-NH", "2", ")", "has", "an", "amidated", "C-terminal", "and", "a", "+6", "charge", "at", "physiological", "pH,", "with", "all", "its", "Lysines", "and", "N-terminal", "amine", "protonated.", "To", "study", "secondary", "structure", "behavior", "of", "BP100", "both", "in", "solution", "and", "in", "bilayers,", "two", "initial", "BP100", "conformations", "were", "used:", "linear", "BP100", "(", "L", "-BP100)", "and", "alpha-helical", "BP100", "(", "α", "-BP100)", "(Fig.", "1", "a,b", ")." ]

Original work titled: 'Binding and Flip as Initial Steps for BP-100 Antimicrobial Actions' (Scientific Reports/Nature Publishing Group UK) by the following authors: Peter Park; Leandro R. Franco; Hernan Chaimovich; Kaline Coutinho; Iolanda M. Cuccovia; Filipe S. Lima DOI: 10.1038/s41598-019-45075-5

5388809896c7b2a9adf5d708f6ea4b08

CC-BY

http://creativecommons.org/licenses/by/4.0/

4.0

[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]

[ "Table", "1", "shows", "all", "simulation", "systems", "and", "its", "simulation", "time.", "The", "program", "used", "to", "analyze", "the", "hydration", "shell", "of", "the", "peptide", "using", "the", "Minimum", "Distance", "Distribution", "Function", "was", "developed", "in", "our", "group.", "Table", "1", "Table", "containing", "all", "MD", "simulation", "sets", "carried", "out", "in", "this", "work.", "For", "bilayers,", "we", "used", "Slipids", "forcefield", "and", "ff99sb-ildn-NMR", "for", "BP100.", "All", "sets", "were", "simulated", "at", "323", "K", "(above", "DPPC", "and", "DPPG", "transition", "temperatures)", "and", "1", "bar.", "L", "-BP100", "indicate", "constraint-free", "simulations", "using", "random", "coil", "BP100", "as", "peptide", "starting", "configuration", "and", "α", "-BP100,", "as", "alpha", "helix.", "Res1–5,", "res4–8", "and", "res7–11", "indicate", "simulations", "with", "BP100", "with", "permanent", "constraints", "on", "the", "referred", "residues.", "Simulation", "sets", "Simulations", "Peptide/Lipid", "Waters/Lipid", "Time", "(ns)", "Bilayers", "DPPC", "0/128", "54", "860", "DPPG", "53", "1100", "PCPG-R", "0/[64/64]", "54", "1200", "PCPG-NR", "52", "1200", "Peptide", "in", "water", "L", "-BP100", "in", "water", "1/0", "—", "2000", "α", "-BP100", "in", "water", "—", "2850", "Peptide", "with", "bilayers", "L", "-BP100", "in", "DPPC", "1/128", "54", "1700", "α", "-BP100", "in", "DPPC", "54", "2000", "L", "-BP100", "in", "DPPG", "1/128", "53", "1700", "α", "-BP100", "in", "DPPG", "53", "2000", "L", "-BP100", "in", "PCPG-R", "1/[64/64]", "54", "1600", "α", "-BP100", "in", "PCPG-R", "54", "2000", "L", "-BP100", "in", "PCPG-NR", "1/[64/64]", "52", "1700", "α", "-BP100", "in", "PCPG-NR", "52", "2000", "Partially", "constrained", "peptide", "in", "DPPG", "α-", "BP100", "(res1–5)", "in", "DPPG", "1/128", "54", "600", "α-", "BP100", "(res4–8)", "in", "DPPG", "54", "600", "α-", "BP100", "(res7–11)", "in", "DPPG", "54", "600", "Lipid", "bilayers", "We", "used", "Slipids", "forcefield", "19", "parameters", "were", "chosen", "to", "simulate", "DPPC,", "DPPG,", "and", "DPPC/DPPG", "mixed", "bilayers." ]

Original work titled: 'Binding and Flip as Initial Steps for BP-100 Antimicrobial Actions' (Scientific Reports/Nature Publishing Group UK) by the following authors: Peter Park; Leandro R. Franco; Hernan Chaimovich; Kaline Coutinho; Iolanda M. Cuccovia; Filipe S. Lima DOI: 10.1038/s41598-019-45075-5

5388809896c7b2a9adf5d708f6ea4b08

CC-BY

http://creativecommons.org/licenses/by/4.0/

4.0

[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]

[ "A", "detailed", "description", "of", "peptide/membrane", "interactions", "at", "the", "atomic", "scale", "may", "help", "to", "gain", "information", "on", "CAMPs", "disruption", "mechanisms,", "permitting", "the", "rational", "design", "of", "new", "derivatives", "and,", "therefore,", "the", "better", "therapeutic", "use", "of", "these", "novel", "antimicrobials.", "Molecular", "Dynamics", "(MD)", "simulations", "provide", "atomic-level", "insights", "and", "have", "been", "widely", "used", "to", "study", "the", "interaction", "of", "AMPs", "with", "membranes", "15", "–", "18", ".", "MD", "simulations", "were", "also", "utilized", "to", "study", "BP100’s", "structure", "and", "activity:", "Wang", "Y.", "et", "al.", "17", "performed", "an", "8", "µs-long", "MD", "simulation", "of", "BP100", "in", "DMPC", "bilayer", "and", "found", "that", "BP100", "remained", "in", "the", "surface-bound-state", "inserting", "through", "its", "C-terminus.", "They", "also", "reported", "the", "unfolding", "of", "BP100", "N-terminus", "(Lys1", "and", "Lys2)", "after", "1.5", "µs,", "resulting", "in", "a", "tilt", "angle", "of", "97°", "and", "81%", "helicity", "10", ",", "17", ".", "In", "a", "study", "with", "Brownian", "Dynamics", "simulations", "with", "a", "coarse-grained", "peptide", "model,", "Alves", "et", "al.", "18", "simulated", "BP100", "confined", "in", "model", "membranes", "at", "293", "K", "for", "1", "µs", "each", "and", "reported", "the", "high", "stability", "of", "BP100", "pre-folded", "alpha", "helix", "and", "a", "threefold", "decrease", "in", "its", "lateral", "diffusion", "in", "POPC:", "POPG", "membranes", "relative", "to", "that", "in", "POPC", "membrane", "18", ".", "In", "this", "work", "we", "report", "simulations,", "in", "solution", "and", "membranes,", "extending", "for", "more", "than", "25", "µs", "of", "BP100", "and", "membranes", "of", "1,2-dipalmitoyl-sn-glycerol-3-phosphocholine", "(DPPC),", "1,2-dipalmitoyl-sn-glycerol-3-phosphoglycerol", "(DPPG),", "and", "DPPC:", "DPPG", "mixtures", "(1:1).", "We", "systematically", "investigated", "the", "dependence", "of", "BP100", "secondary", "structure", "on", "DPPG", "lipids", "which", "agrees", "with", "experimental", "findings", "11", ".", "We", "also", "analyzed", "the", "contribution", "of", "PG-containing", "lipid", "rafts", "on", "BP100", "conformation", "and", "behavior.", "In", "most", "simulations", "containing", "DPPG", "lipids,", "we", "observed", "the", "occurrence", "of", "a", "dynamic", "transition", "of", "the", "peptide", "adsorbed", "at", "the", "membrane", "interface,", "where", "the", "apolar", "facet", "of", "the", "BP100", "(Fig." ]

Original work titled: 'Binding and Flip as Initial Steps for BP-100 Antimicrobial Actions' (Scientific Reports/Nature Publishing Group UK) by the following authors: Peter Park; Leandro R. Franco; Hernan Chaimovich; Kaline Coutinho; Iolanda M. Cuccovia; Filipe S. Lima DOI: 10.1038/s41598-019-45075-5

5388809896c7b2a9adf5d708f6ea4b08

CC-BY

http://creativecommons.org/licenses/by/4.0/

4.0

[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]

[ "Due", "to", "their", "potential", "advantage", "as", "antimicrobials,", "new", "AMPs", "are", "increasingly", "being", "isolated", "or", "synthesized", "and", "their", "properties", "investigated.", "Although", "increasing", "evidence", "shows", "that", "some", "AMPs", "may", "also", "act", "intracellularly,", "inhibiting", "proteins", "1", ",", "nucleic", "acids", "1", "–", "4", "and", "cell-wall", "synthesis", "1", "–", "5", "and", "inducing", "cell", "apoptosis", "1", ",", "3", ",", "5", ",", "most", "of", "them", "kill", "cells", "by", "disturbing", "the", "membrane’s", "integrity", "1", ",", "2", ",", "6", ",", "7", ".", "Several", "CAMPs", "seem", "to", "disturb", "the", "membrane", "of", "cells", "by", "self-aggregation", "on", "the", "membrane", "and", "forming", "pores", "beyond", "a", "peptide/lipid", "(P/L)", "ratio", "threshold", "1", ",", "2", ".", "BP100", "(H-KKLFKKILKYL-NH", "2", "),", "is", "a", "hybrid", "CAMP", "synthesized", "by", "combinatorial", "chemistry", "involving", "parts", "of", "two", "natural", "AMPs,", "melittin,", "and", "cecropin", "A", "8", ".", "BP100", "shows", "high", "antimicrobial", "activity", "and", "selectivity", "against", "some", "Gram-negative", "bacteria,", "with", "a", "promising", "minimal", "inhibitory", "concentration", "ranging", "from", "2.5", "to", "5", "µM", "and", "low", "cytotoxicity", "against", "mammalian", "cells", "making", "this", "peptide", "an", "exciting", "candidate", "for", "therapeutic", "use", "8", ".", "BP100", "conformation", "and", "activity", "on", "model", "membranes", "have", "been", "extensively", "analyzed", "with", "experimental", "techniques", "9", "–", "13", ".", "BP100", "has", "a", "random", "coil", "conformation", "in", "solution", "and", "zwitterionic", "bilayers", "but", "acquires", "predominantly", "alpha-helical", "and", "amphipathic", "conformation", "in", "the", "presence", "of", "negatively", "charged", "membranes.", "BP100", "is", "highly", "mobile", "on", "the", "membrane", "surface", "and", "orients", "parallel", "in", "predominantly", "negatively", "charged", "vesicles", "9", ",", "10", ".", "BP100", "secondary", "structure", "formation", "and", "bacteria", "killing", "performance", "seem", "to", "be", "directly", "related", "to", "negative", "charge", "content", "in", "membranes,", "thus", "explaining", "its", "high", "selectivity", "towards", "negative", "bacterial", "membrane", "and", "low", "cytotoxicity", "against", "predominantly", "less", "negatively", "charged", "mammalian", "cell", "membranes", "11", ",", "14", ".", "Experimental", "approaches", "to", "investigate", "peptide/membrane", "interactions", "mainly", "focus", "macroscopic-averaged", "insight", "on", "a", "mesoscopic", "scale.", "A", "detailed", "description", "of", "peptide/membrane", "interactions", "at", "the", "atomic", "scale", "may", "help", "to", "gain", "information", "on", "CAMPs", "disruption", "mechanisms,", "permitting", "the", "rational", "design", "of", "new", "derivatives", "and,", "therefore,", "the", "better", "therapeutic", "use", "of", "these", "novel", "antimicrobials." ]

Original work titled: 'Gut microbiome associated with chemotherapy-induced diarrhea from the CapeOX regimen as adjuvant chemotherapy in resected stage III colorectal cancer' (Gut Pathogens/BioMed Central) by the following authors: Zuo Fei; Yin Lijuan; Yang Xi; Wu Wei; Zhong Jing; Da Miao; Han Shuwen DOI: 10.1186/s13099-019-0299-4

f7083ca86a7871cc8d04d2500480cbf3

CC-BY

http://creativecommons.org/licenses/by/4.0/

4.0

[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]

[ "How", "to", "effectively", "and", "efficiently", "avoid", "or", "to", "alleviate", "the", "toxicity", "and", "side", "effects", "is", "a", "critical", "clinical", "problem", "that", "should", "be", "solved.", "CID", "is", "a", "common", "side", "effect", "of", "the", "digestive", "system", "in", "the", "antitumor", "treatment", "process", "of", "cytotoxic", "drugs.", "The", "typical", "clinical", "characteristics", "of", "CID", "are", "as", "follows:", "symptoms", "range", "from", "loose", "stool", "without", "pain", "to", "severe,", "watery", "diarrhea", "with", "abdominal", "pain;", "symptoms", "typically", "last", "5", "to", "7", "days", "and", "may", "occur", "during", "or", "after", "chemotherapy;", "and", "patients", "with", "CID", "have", "a", "poor", "treatment", "response", "to", "gentamicin,", "berberine,", "and", "furoxone", "[", "9", "].", "CID", "can", "lead", "to", "weakness,", "electrolyte", "disorders,", "renal", "failure,", "blood", "volume", "reductions,", "shock,", "and", "even", "death", "[", "10", "].", "Its", "occurrence", "can", "result", "in", "delaying", "chemotherapy,", "increasing", "hospitalization", "time", "and", "costs,", "aggravating", "the", "psychological", "stress", "of", "patients,", "reducing", "the", "treatment", "compliance", "of", "patients", "and", "even", "altering", "the", "entire", "chemotherapy", "plan", "[", "11", "].", "A", "unique", "microecosystem", "and", "characteristic", "microbial", "community", "lives", "in", "the", "colorectal", "regions", "owing", "to", "their", "function", "of", "storing", "feces", "[", "12", "].", "Accumulating", "evidence", "points", "to", "the", "gut", "microbiome", "being", "involved", "in", "CRC", "[", "13", "].", "For", "example,", "some", "researchers", "have", "reported", "that", "Streptococcus", "bovis", "[", "14", "]", "and", "Trichophyton", "tonsurans", "[", "15", "]", "are", "specific", "bacteria", "involved", "in", "colorectal", "cancer;", "Castellarin", "et", "al.", "[", "16", "]", "found", "that", "Thanatephorus", "cucumeris", "infection", "is", "prevalent", "in", "CRC", "tissue", "specimens", "and", "Kostic", "et", "al.", "[", "17", "],", "found", "that", "Thanatephorus", "cucumeris", "can", "generate", "a", "proinflammatory", "microenvironment", "that", "is", "conducive", "to", "the", "progression", "of", "CRC", "through", "recruitment", "of", "tumor-infiltrating", "immune", "cells.", "Moreover,", "many", "enzymes,", "peptides", "and", "small", "molecules", "secreted", "by", "the", "intestinal", "gut", "microbiome", "are", "involved", "in", "activating", "and", "regulating", "important", "signaling", "molecules", "and", "signaling", "pathways", "involved", "in", "the", "progression", "of", "CRC", "[", "18", ",", "19", "].", "Diarrhea", "and", "gut", "microbiome", "disorders", "interact", "as", "both", "cause", "and", "effect.", "Diarrhea", "can", "disrupt", "the", "balance", "of", "the", "gut", "microenvironment." ]

Original work titled: 'Gut microbiome associated with chemotherapy-induced diarrhea from the CapeOX regimen as adjuvant chemotherapy in resected stage III colorectal cancer' (Gut Pathogens/BioMed Central) by the following authors: Zuo Fei; Yin Lijuan; Yang Xi; Wu Wei; Zhong Jing; Da Miao; Han Shuwen DOI: 10.1186/s13099-019-0299-4

f7083ca86a7871cc8d04d2500480cbf3

CC-BY

http://creativecommons.org/licenses/by/4.0/

4.0

[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]

[ "Its", "occurrence", "can", "result", "in", "delaying", "chemotherapy,", "increasing", "hospitalization", "time", "and", "costs,", "aggravating", "the", "psychological", "stress", "of", "patients,", "reducing", "the", "treatment", "compliance", "of", "patients", "and", "even", "altering", "the", "entire", "chemotherapy", "plan", "[", "11", "].", "A", "unique", "microecosystem", "and", "characteristic", "microbial", "community", "lives", "in", "the", "colorectal", "regions", "owing", "to", "their", "function", "of", "storing", "feces", "[", "12", "].", "Accumulating", "evidence", "points", "to", "the", "gut", "microbiome", "being", "involved", "in", "CRC", "[", "13", "].", "For", "example,", "some", "researchers", "have", "reported", "that", "Streptococcus", "bovis", "[", "14", "]", "and", "Methanococcus", "voltae", "[", "15", "]", "are", "specific", "bacteria", "involved", "in", "colorectal", "cancer;", "Castellarin", "et", "al.", "[", "16", "]", "found", "that", "Drosophila", "americana", "infection", "is", "prevalent", "in", "CRC", "tissue", "specimens", "and", "Kostic", "et", "al.", "[", "17", "],", "found", "that", "Drosophila", "americana", "can", "generate", "a", "proinflammatory", "microenvironment", "that", "is", "conducive", "to", "the", "progression", "of", "CRC", "through", "recruitment", "of", "tumor-infiltrating", "immune", "cells.", "Moreover,", "many", "enzymes,", "peptides", "and", "small", "molecules", "secreted", "by", "the", "intestinal", "gut", "microbiome", "are", "involved", "in", "activating", "and", "regulating", "important", "signaling", "molecules", "and", "signaling", "pathways", "involved", "in", "the", "progression", "of", "CRC", "[", "18", ",", "19", "].", "Diarrhea", "and", "gut", "microbiome", "disorders", "interact", "as", "both", "cause", "and", "effect.", "Diarrhea", "can", "disrupt", "the", "balance", "of", "the", "gut", "microenvironment.", "Meanwhile,", "the", "invasion", "of", "exogenous", "pathogenic", "microorganisms", "and", "the", "imbalance", "of", "intestinal", "microbes", "can", "lead", "to", "diarrhea", "[", "20", "].", "For", "example,", "the", "invasion", "of", "some", "pathogenic", "bacteria", "including", "Shigella,", "Salmonella", "and", "Klebsiella", "[", "21", ",", "22", "],", "and", "the", "abundance", "changes", "of", "intestinal", "parasitic", "microbes", "include", "Geothlypis", "tolmiei,", "Gratiola", "brevifolia,", "and", "Aeromonas", "can", "induce", "diarrhea", "[", "23", "–", "25", "].", "Chemotherapy", "has", "been", "widely", "used", "in", "the", "clinic", "as", "an", "effective", "therapy", "for", "colorectal", "cancer,", "but", "diarrhea", "caused", "by", "chemotherapeutic", "drugs", "often", "affects", "the", "implementation", "of", "chemotherapy", "regimens", "[", "26", "]." ]

Original work titled: 'Gut microbiome associated with chemotherapy-induced diarrhea from the CapeOX regimen as adjuvant chemotherapy in resected stage III colorectal cancer' (Gut Pathogens/BioMed Central) by the following authors: Zuo Fei; Yin Lijuan; Yang Xi; Wu Wei; Zhong Jing; Da Miao; Han Shuwen DOI: 10.1186/s13099-019-0299-4

f7083ca86a7871cc8d04d2500480cbf3

CC-BY

http://creativecommons.org/licenses/by/4.0/

4.0

[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]

[ "Moreover,", "many", "enzymes,", "peptides", "and", "small", "molecules", "secreted", "by", "the", "intestinal", "gut", "microbiome", "are", "involved", "in", "activating", "and", "regulating", "important", "signaling", "molecules", "and", "signaling", "pathways", "involved", "in", "the", "progression", "of", "CRC", "[", "18", ",", "19", "].", "Diarrhea", "and", "gut", "microbiome", "disorders", "interact", "as", "both", "cause", "and", "effect.", "Diarrhea", "can", "disrupt", "the", "balance", "of", "the", "gut", "microenvironment.", "Meanwhile,", "the", "invasion", "of", "exogenous", "pathogenic", "microorganisms", "and", "the", "imbalance", "of", "intestinal", "microbes", "can", "lead", "to", "diarrhea", "[", "20", "].", "For", "example,", "the", "invasion", "of", "some", "pathogenic", "bacteria", "including", "Shigella,", "Salmonella", "and", "Klebsiella", "[", "21", ",", "22", "],", "and", "the", "abundance", "changes", "of", "intestinal", "parasitic", "microbes", "include", "Pterodroma", "neglecta,", "Banisteriopsis", "caapi,", "and", "Aeromonas", "can", "induce", "diarrhea", "[", "23", "–", "25", "].", "Chemotherapy", "has", "been", "widely", "used", "in", "the", "clinic", "as", "an", "effective", "therapy", "for", "colorectal", "cancer,", "but", "diarrhea", "caused", "by", "chemotherapeutic", "drugs", "often", "affects", "the", "implementation", "of", "chemotherapy", "regimens", "[", "26", "].", "Many", "probiotics", "and", "antibiotics", "play", "a", "positive", "role", "in", "the", "treatment", "of", "infectious", "diarrhea", "by", "regulating", "the", "gut", "microbiome", "[", "27", ",", "28", "].", "The", "study", "of", "relationships", "between", "gut", "microbiome", "and", "CID", "may", "provide", "a", "new", "direction", "for", "solving", "this", "clinical", "problem.", "In", "the", "present", "study,", "we", "aimed", "to", "explore", "the", "association", "between", "the", "gut", "microorganisms", "and", "CID", "of", "the", "CapeOX", "regimen", "in", "resected", "stage", "III", "CRC", "and", "to", "provide", "some", "research", "methods", "and", "research", "ideas", "for", "further", "exploring", "the", "relationship", "between", "intestinal", "microbes", "and", "CID.", "The", "results", "may", "provide", "a", "fresh", "approach", "to", "the", "prevention", "and", "treatment", "of", "CID", "from", "a", "microbiological", "perspective.", "Subjects", "and", "methods", "Subjects", "Patients", "with", "CRC", "treated", "at", "Huzhou", "Central", "Hospital", "from", "January", "2016", "to", "January", "2018", "were", "studied.", "The", "clinical", "protocols", "involving", "the", "patients", "and", "the", "informed", "consent", "form", "were", "approved", "by", "the", "Ethics", "Committee", "of", "Huzhou", "Central", "Hospital", "(No.", "201601023)." ]

Original work titled: 'Gut microbiome associated with chemotherapy-induced diarrhea from the CapeOX regimen as adjuvant chemotherapy in resected stage III colorectal cancer' (Gut Pathogens/BioMed Central) by the following authors: Zuo Fei; Yin Lijuan; Yang Xi; Wu Wei; Zhong Jing; Da Miao; Han Shuwen DOI: 10.1186/s13099-019-0299-4

f7083ca86a7871cc8d04d2500480cbf3

CC-BY

http://creativecommons.org/licenses/by/4.0/

4.0

[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]

[ "②", "Patients", "with", "other", "intestinal", "diseases,", "such", "as", "ulcerative", "colitis", "and", "Crohn’s", "disease.", "③", "Alternation", "of", "chemotherapy", "regimen", "and", "chemotherapeutic", "dosage", "or", "the", "occurrence", "of", "progression", "of", "the", "disease", "(PD)", "during", "the", "8", "cycles", "of", "the", "CapeOX", "regimen.", "④", "Patients", "who", "accepted", "neo-adjuvant", "chemotherapy.", "⑤", "Patients", "with", "a", "history", "of", "the", "use", "of", "oral", "microbial", "agents", "within", "1", "month", "before", "chemotherapy.", "⑥", "Patients", "with", "another", "primary", "cancer.", "⑦", "Patients", "with", "known", "primary", "organ", "failure.", "⑧", "Patients", "who", "could", "not", "obtained", "the", "stool", "samples", "(n", "=", "15)", "or", "obtained", "unqualified", "stool", "samples.", "All", "of", "the", "subjects", "signed", "informed", "consent", "under", "the", "guidelines", "approved", "by", "the", "Ethics", "Committee", "of", "Huzhou", "Central", "Hospital.", "CRC", "patients", "with", "and", "without", "CID", "were", "including", "in", "the", "experimental", "group", "and", "control", "group,", "respectively.", "According", "to", "National", "Cancer", "Institute", "Common", "Toxicity", "Criteria", "(NCI", "CTC)", "V3.0", "[", "30", "]", "CID", "grade", "1", "is", "defined", "as", "the", "number", "of", "defecations", "increased", "to", "less", "than", "4", "times", "a", "day", "and", "an", "excretion", "volume", "slightly", "increased.", "During", "a", "course", "of", "8", "cycles", "of", "chemotherapy", "administered", "over", "nearly", "half", "a", "year,", "there", "are", "many", "factors", "that", "can", "cause", "diarrhea,", "and", "these", "factors", "interfere", "with", "the", "diagnosis", "of", "CID.", "Clinical", "intervention", "measures,", "such", "as", "using", "antibiotics", "and", "antidiarrheal", "drugs,", "may", "be", "performed", "and", "the", "chemotherapy", "regimen", "may", "be", "changed", "in", "patients", "with", "CID", "grade", "3", "and", "grade", "4.", "Therefore,", "we", "did", "not", "include", "patients", "with", "grade", "1,", "grade", "3", "and", "grade", "4", "in", "the", "experimental", "group.", "CID", "grade", "2", "is", "defined", "as", "the", "number", "of", "defecations", "increased", "to", "4–6", "times", "per", "day", "or", "nocturnal", "stools,", "with", "the", "amount", "of", "excretion", "increased", "but", "with", "no", "interference", "in", "daily", "life.", "All", "of", "the", "subjects", "recruited", "into", "the", "experimental", "group", "were", "CID", "grade", "2", "in", "the", "present", "study.", "Collection", "of", "clinical", "data", "and", "stool", "samples", "Basic", "information", "and", "clinical", "serological", "indicators", "were", "obtained", "from", "the", "medical", "record", "management", "system", "of", "Huzhou", "Central", "Hospital", "with", "informed", "consent", "from", "patients.", "Stool", "samples", "of", "the", "patients", "were", "collected", "in", "the", "2", "weeks", "after", "the", "8", "cycles", "of", "chemotherapy.", "Stool", "samples", "were", "collected", "in", "the", "morning", "prior", "to", "breakfast." ]

Original work titled: 'Gut microbiome associated with chemotherapy-induced diarrhea from the CapeOX regimen as adjuvant chemotherapy in resected stage III colorectal cancer' (Gut Pathogens/BioMed Central) by the following authors: Zuo Fei; Yin Lijuan; Yang Xi; Wu Wei; Zhong Jing; Da Miao; Han Shuwen DOI: 10.1186/s13099-019-0299-4

f7083ca86a7871cc8d04d2500480cbf3

CC-BY

http://creativecommons.org/licenses/by/4.0/

4.0

[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]

[ "During", "a", "course", "of", "8", "cycles", "of", "chemotherapy", "administered", "over", "nearly", "half", "a", "year,", "there", "are", "many", "factors", "that", "can", "cause", "diarrhea,", "and", "these", "factors", "interfere", "with", "the", "diagnosis", "of", "CID.", "Clinical", "intervention", "measures,", "such", "as", "using", "antibiotics", "and", "antidiarrheal", "drugs,", "may", "be", "performed", "and", "the", "chemotherapy", "regimen", "may", "be", "changed", "in", "patients", "with", "CID", "grade", "3", "and", "grade", "4.", "Therefore,", "we", "did", "not", "include", "patients", "with", "grade", "1,", "grade", "3", "and", "grade", "4", "in", "the", "experimental", "group.", "CID", "grade", "2", "is", "defined", "as", "the", "number", "of", "defecations", "increased", "to", "4–6", "times", "per", "day", "or", "nocturnal", "stools,", "with", "the", "amount", "of", "excretion", "increased", "but", "with", "no", "interference", "in", "daily", "life.", "All", "of", "the", "subjects", "recruited", "into", "the", "experimental", "group", "were", "CID", "grade", "2", "in", "the", "present", "study.", "Collection", "of", "clinical", "data", "and", "stool", "samples", "Basic", "information", "and", "clinical", "serological", "indicators", "were", "obtained", "from", "the", "medical", "record", "management", "system", "of", "Huzhou", "Central", "Hospital", "with", "informed", "consent", "from", "patients.", "Stool", "samples", "of", "the", "patients", "were", "collected", "in", "the", "2", "weeks", "after", "the", "8", "cycles", "of", "chemotherapy.", "Stool", "samples", "were", "collected", "in", "the", "morning", "prior", "to", "breakfast.", "An", "approximately", "5–10", "g", "stool", "sample", "was", "collected", "after", "defecation", "without", "the", "use", "of", "a", "purgative", "or", "lubricant.", "Within", "half", "an", "hour,", "the", "stool", "samples", "were", "stored", "in", "an", "ultra-low", "temperature", "freezer.", "The", "sample", "preservation", "time", "was", "not", "beyond", "1", "month.", "Finally,", "17", "stool", "samples", "from", "CRC", "patients", "were", "analyzed", "after", "the", "patients", "had", "signed", "informed", "consent", "forms", "and", "the", "unqualified", "specimens", "were", "eliminated.", "Intestinal", "microorganism", "detection", "DNA", "extraction", "and", "PCR", "amplification", "A", "E.Z.N.A.", "®", "Stool", "DNA", "Kit", "(Omega", "Bio-Tek,", "Norcross,", "GA,", "U.S.)", "was", "used", "to", "extract", "total", "DNA", "from", "the", "stool", "samples", "according", "to", "the", "manufacturer’s", "protocols.", "The", "nanodrop", "ND-1000", "spectrophotometer", "(LabTech,", "Washington,", "DC,", "USA)", "with", "the", "absorbances", "at", "260", "nm", "and", "280", "nm", "(A260/A280)", "was", "used", "to", "determine", "the", "quality", "and", "quantity", "of", "the", "purified", "DNA.", "DNA", "integrity", "was", "further", "verified", "by", "electrophoresis", "through", "a", "2.0%", "(w/v)", "agarose", "gel." ]

Original work titled: 'Gut microbiome associated with chemotherapy-induced diarrhea from the CapeOX regimen as adjuvant chemotherapy in resected stage III colorectal cancer' (Gut Pathogens/BioMed Central) by the following authors: Zuo Fei; Yin Lijuan; Yang Xi; Wu Wei; Zhong Jing; Da Miao; Han Shuwen DOI: 10.1186/s13099-019-0299-4

f7083ca86a7871cc8d04d2500480cbf3

CC-BY

http://creativecommons.org/licenses/by/4.0/

4.0

[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]

[ "Intestinal", "microorganism", "detection", "DNA", "extraction", "and", "PCR", "amplification", "A", "E.Z.N.A.", "®", "Stool", "DNA", "Kit", "(Omega", "Bio-Tek,", "Norcross,", "GA,", "U.S.)", "was", "used", "to", "extract", "total", "DNA", "from", "the", "stool", "samples", "according", "to", "the", "manufacturer’s", "protocols.", "The", "nanodrop", "ND-1000", "spectrophotometer", "(LabTech,", "Washington,", "DC,", "USA)", "with", "the", "absorbances", "at", "260", "nm", "and", "280", "nm", "(A260/A280)", "was", "used", "to", "determine", "the", "quality", "and", "quantity", "of", "the", "purified", "DNA.", "DNA", "integrity", "was", "further", "verified", "by", "electrophoresis", "through", "a", "2.0%", "(w/v)", "agarose", "gel.", "PCR", "(95", "°C", "for", "3", "min,", "followed", "by", "25", "cycles", "at", "95", "°C", "for", "30", "s,", "55", "°C", "for", "30", "s,", "and", "72", "°C", "for", "45", "s", "and", "a", "final", "extension", "at", "72", "°C", "for", "5", "min)", "was", "used", "to", "amplify", "the", "V3–V4", "region", "of", "the", "bacterial", "16S", "ribosomal", "RNA", "gene", "(the", "primers", "of", "16S", "V3–V4", "rDNA", "are", "as", "follows:", "forward,", "CCTACGGGNGGCWGCAG", "and", "reverse,", "GACTACHVGGGTATCTAATCC).", "PCR", "amplifications", "were", "performed", "in", "triplicate", "in", "a", "25", "μL", "mixture", "containing", "5", "μL", "of", "DNA", "template,", "2", "μL", "of", "Nextera", "XT", "Index", "Primer", "1", "(10", "M),", "2", "μL", "of", "Nextera", "XT", "Index", "Primer", "2", "(10", "M)", "and", "16", "μL", "ddH", "2", "O.", "Amplicons", "were", "extracted", "from", "2%", "agarose", "gels,", "purified", "using", "the", "AxyPrep", "DNA", "Gel", "Extraction", "Kit", "(Axygen", "Biosciences,", "Union", "City,", "CA,", "USA)", "and", "quantified", "using", "QuantiFluor™-ST", "(Promega,", "U.S.)", "according", "to", "the", "manufacturer’s", "instructions.", "Library", "construction", "and", "sequencing", "The", "MiSeq", "library", "was", "constructed", "as", "follows:", "purified", "PCR", "products", "were", "quantified", "by", "Qubit", "®", "3.0", "(Life", "Technologies,", "Invitrogen).", "PCR", "products", "were", "ligated", "with", "Y", "adapter." ]

Original work titled: 'Gut microbiome associated with chemotherapy-induced diarrhea from the CapeOX regimen as adjuvant chemotherapy in resected stage III colorectal cancer' (Gut Pathogens/BioMed Central) by the following authors: Zuo Fei; Yin Lijuan; Yang Xi; Wu Wei; Zhong Jing; Da Miao; Han Shuwen DOI: 10.1186/s13099-019-0299-4

f7083ca86a7871cc8d04d2500480cbf3

CC-BY

http://creativecommons.org/licenses/by/4.0/

4.0

[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]

[ "An", "Illumina", "Pair-End", "library", "was", "constructed", "using", "pooled", "DNA", "products,", "and", "the", "amplicon", "library", "was", "pair-end", "sequenced", "(2", "×", "250)", "on", "an", "Illumina", "MiSeq", "platform", "(Shanghai", "BIOZERON", "Co.,", "Ltd.)", "according", "to", "standard", "protocols", "(MiSeq", "V3", "or", "V4", "sequencing", "kit,", "Hua", "Ya", "Regenerative", "Medicine", "Biological", "Engineering", "Technology", "CO.,", "LTD,", "Shanghai,", "China).", "Sequencing", "data", "bioinformatics", "analysis", "Sequencing", "data", "processing", "and", "optimization", "were", "performed", "according", "to", "the", "criteria", "at", "http://en.wikipedia.org/wiki/Fastq", ".", "Cutadapt", "(version", "1.11)", "was", "used", "to", "demultiplex", "and", "quality", "filter", "the", "raw", "fastq", "files.", "Pandaseq", "(version", "2.9)", "was", "used", "to", "assemble", "PE", "reads;", "only", "sequences", "that", "overlapped", "longer", "than", "10", "bp", "were", "assembled", "according", "to", "their", "overlap", "sequence.", "Mosaic", "sequences", "and", "sequences", "longer", "than", "300–480", "bp", "were", "discarded.", "In", "addition,", "the", "reads", "that", "receiving", "an", "average", "quality", "score", "<", "20", "were", "discarded.", "The", "Silva", "database", "was", "used", "for", "comparison", "of", "16S", "rRNA", "gene", "sequences", "[", "31", "]", "and", "the", "GeneBank", "database", "was", "used", "to", "analyze", "functional", "genes", "[", "32", "].", "Mothur", "software", "[", "33", "]", "(", "http://www.mothur.org/wiki/Main_Page", ")", "was", "used", "to", "analyze", "the", "microbial", "diversity.", "OTU", "(operational", "taxonomic", "units),", "as", "the", "artificial", "classification", "unit,", "was", "used", "to", "estimate", "the", "number", "of", "species", "in", "each", "sample,", "and", "the", "similarity", "threshold", "was", "97%.", "The", "coverage", "(", "http://www.mothur.org/wiki/Coverage", ")", "was", "used", "as", "the", "sequencing", "depth", "index.", "The", "ACE", "estimator", "(", "http://www.mothur.org/wiki/Ace", ")", "and", "Chao", "estimator", "(", "http://www.mothur.org/wiki/Chao", ")", "were", "used", "to", "estimate", "the", "gut", "microbial", "community", "richness.", "The", "Shannon", "index", "(", "http://www.mothur.org/wiki/Shannon", ")", "and", "Simpson", "index", "(", "http://www.mothur.org/wiki/Simpson", ")", "were", "used", "to", "estimate", "the", "gut", "microbial", "community", "diversity." ]

Original work titled: 'Gut microbiome associated with chemotherapy-induced diarrhea from the CapeOX regimen as adjuvant chemotherapy in resected stage III colorectal cancer' (Gut Pathogens/BioMed Central) by the following authors: Zuo Fei; Yin Lijuan; Yang Xi; Wu Wei; Zhong Jing; Da Miao; Han Shuwen DOI: 10.1186/s13099-019-0299-4

f7083ca86a7871cc8d04d2500480cbf3

CC-BY

http://creativecommons.org/licenses/by/4.0/

4.0

[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]

[ "Mothur", "software", "[", "33", "]", "(", "http://www.mothur.org/wiki/Main_Page", ")", "was", "used", "to", "analyze", "the", "microbial", "diversity.", "OTU", "(operational", "taxonomic", "units),", "as", "the", "artificial", "classification", "unit,", "was", "used", "to", "estimate", "the", "number", "of", "species", "in", "each", "sample,", "and", "the", "similarity", "threshold", "was", "97%.", "The", "coverage", "(", "http://www.mothur.org/wiki/Coverage", ")", "was", "used", "as", "the", "sequencing", "depth", "index.", "The", "ACE", "estimator", "(", "http://www.mothur.org/wiki/Ace", ")", "and", "Chao", "estimator", "(", "http://www.mothur.org/wiki/Chao", ")", "were", "used", "to", "estimate", "the", "gut", "microbial", "community", "richness.", "The", "Shannon", "index", "(", "http://www.mothur.org/wiki/Shannon", ")", "and", "Simpson", "index", "(", "http://www.mothur.org/wiki/Simpson", ")", "were", "used", "to", "estimate", "the", "gut", "microbial", "community", "diversity.", "The", "pie", "charts", "were", "used", "to", "describe", "the", "distribution", "of", "microorganisms", "at", "the", "species", "level.", "Proportions", "less", "than", "1%", "were", "included", "in", "“Others”,", "considering", "the", "best", "visual", "presentation.", "Venn", "diagrams", "were", "implemented", "by", "Venn", "diagram.", "We", "performed", "clustering", "on", "genera", "obtained", "from", "the", "RDP", "Classifier", "by", "means", "of", "the", "complete", "linkage", "hierarchical", "clustering", "technique", "using", "the", "R", "package", "HCLUST", "(", "http://sekhon.berkeley.edu/stats/html/hclust.html", ").", "The", "basic", "process", "of", "LDA", "analysis", "[", "34", "]", "was", "as", "follows:", "First,", "non-parametric", "Kruskal–Wallis", "rank", "sum", "test", "was", "used", "to", "detect", "the", "significant", "difference", "of", "abundance", "among", "species", "between", "the", "two", "groups", "of", "samples.", "Then", "Wilcoxon", "rank", "sum", "test", "was", "used", "to", "analyze", "the", "difference", "between", "groups", "based", "on", "the", "significant", "difference", "species.", "Finally,", "LDA", "was", "used", "to", "reduce", "the", "dimension", "of", "data", "and", "evaluate", "the", "influence", "of", "significantly", "different", "species", "(LDA", "score).", "LDA", "effect", "size", "more", "than", "2", "was", "included", "in", "the", "figure.", "The", "genes", "of", "the", "16S", "corresponding", "species", "and", "their", "copy", "number", "have", "been", "generally", "known,", "and", "these", "genes", "can", "be", "compared", "with", "databases", "(e.g.", "KEGG,", "NOG)", "to", "predict", "the", "possible", "metabolic", "capacity", "of", "these", "species." ]

Original work titled: 'Gut microbiome associated with chemotherapy-induced diarrhea from the CapeOX regimen as adjuvant chemotherapy in resected stage III colorectal cancer' (Gut Pathogens/BioMed Central) by the following authors: Zuo Fei; Yin Lijuan; Yang Xi; Wu Wei; Zhong Jing; Da Miao; Han Shuwen DOI: 10.1186/s13099-019-0299-4

f7083ca86a7871cc8d04d2500480cbf3

CC-BY

http://creativecommons.org/licenses/by/4.0/

4.0

[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]

[ "According", "to", "the", "NCCN", "guidelines,", "the", "CapeOX", "regimen", "for", "resected", "stage", "III", "CRC", "has", "been", "defined", "as", "8", "cycles", "of", "capecitabine", "(1000", "mg/m", "2", "twice", "daily)", "combined", "with", "oxaliplatin", "(130", "mg/m", "2", "every", "3", "weeks)", "[", "36", "].", "CID", "is", "one", "of", "the", "most", "common", "side", "effects", "of", "the", "CapeOX", "regimen", "[", "37", "].", "The", "degree", "of", "diarrhea", "caused", "by", "different", "chemotherapeutic", "agents", "varies.", "Among", "the", "chemotherapeutic", "drugs", "for", "colorectal", "cancer,", "the", "most", "common", "drugs", "that", "cause", "diarrhea", "are", "fluorouracil,", "irinotecan", "and", "platinum,", "and", "the", "incidence", "of", "diarrhea", "associated", "with", "these", "drugs", "can", "be", "as", "high", "as", "50–80%", "[", "38", "].", "Our", "previous", "clinical", "investigation", "found", "that", "the", "probability", "of", "CID", "increased", "with", "an", "increase", "of", "chemotherapeutic", "frequency", "and", "chemotherapeutic", "dosage", "and", "most", "cases", "of", "CID", "occur", "within", "2", "weeks", "after", "chemotherapy.", "Therefore,", "in", "the", "present", "study,", "stool", "samples", "from", "the", "patients", "were", "collected", "in", "2", "weeks", "after", "the", "8", "cycles", "of", "chemotherapy", "of", "the", "CapeOX", "regimen", "were", "completed.", "Studies", "of", "Carroll", "et", "al.", "[", "39", "]", "suggested", "that", "the", "richness", "of", "16S", "rRNA", "sequences", "was", "significantly", "decreased", "in", "patients", "with", "diarrhea-predominant", "irritable", "bowel", "syndrome.", "Lee", "[", "40", "]", "has", "reported", "the", "community", "diversity", "of", "gut", "microbiome", "is", "lower", "in", "patients", "with", "kidney", "posttransplant", "diarrhea.", "Similar", "results", "have", "been", "reported", "in", "dogs", "with", "acute", "diarrhea", "[", "41", "].", "The", "research", "on", "these", "diarrhea", "diseases", "is", "consistent", "with", "our", "findings.", "We", "found", "that", "the", "gut", "microbial", "community", "richness", "and", "community", "diversity", "was", "lower", "in", "CRC", "patients", "with", "CID", "in", "the", "present", "study.", "The", "decrease", "of", "microbial", "diversity", "may", "be", "related", "to", "the", "imbalance", "of", "gut", "microbiome.", "The", "dominant", "pathogenic", "bacteria", "leads", "to", "the", "reduction", "of", "the", "resident", "normal", "microbiota", "through", "the", "plunder", "of", "nutrients", "or", "the", "killing", "effect", "of", "bacterial", "toxic", "metabolites.", "Our", "results", "from", "the", "microbial", "community", "structure", "analysis", "showed", "Caridina", "spongicola", "occupied", "the", "highest", "proportion", "(31.22%)", "of", "gut", "microbiome", "in", "CRC", "patients", "with", "CID." ]

Original work titled: 'Gut microbiome associated with chemotherapy-induced diarrhea from the CapeOX regimen as adjuvant chemotherapy in resected stage III colorectal cancer' (Gut Pathogens/BioMed Central) by the following authors: Zuo Fei; Yin Lijuan; Yang Xi; Wu Wei; Zhong Jing; Da Miao; Han Shuwen DOI: 10.1186/s13099-019-0299-4

f7083ca86a7871cc8d04d2500480cbf3

CC-BY

http://creativecommons.org/licenses/by/4.0/

4.0

[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]

[ "Our", "previous", "clinical", "investigation", "found", "that", "the", "probability", "of", "CID", "increased", "with", "an", "increase", "of", "chemotherapeutic", "frequency", "and", "chemotherapeutic", "dosage", "and", "most", "cases", "of", "CID", "occur", "within", "2", "weeks", "after", "chemotherapy.", "Therefore,", "in", "the", "present", "study,", "stool", "samples", "from", "the", "patients", "were", "collected", "in", "2", "weeks", "after", "the", "8", "cycles", "of", "chemotherapy", "of", "the", "CapeOX", "regimen", "were", "completed.", "Studies", "of", "Carroll", "et", "al.", "[", "39", "]", "suggested", "that", "the", "richness", "of", "16S", "rRNA", "sequences", "was", "significantly", "decreased", "in", "patients", "with", "diarrhea-predominant", "irritable", "bowel", "syndrome.", "Lee", "[", "40", "]", "has", "reported", "the", "community", "diversity", "of", "gut", "microbiome", "is", "lower", "in", "patients", "with", "kidney", "posttransplant", "diarrhea.", "Similar", "results", "have", "been", "reported", "in", "dogs", "with", "acute", "diarrhea", "[", "41", "].", "The", "research", "on", "these", "diarrhea", "diseases", "is", "consistent", "with", "our", "findings.", "We", "found", "that", "the", "gut", "microbial", "community", "richness", "and", "community", "diversity", "was", "lower", "in", "CRC", "patients", "with", "CID", "in", "the", "present", "study.", "The", "decrease", "of", "microbial", "diversity", "may", "be", "related", "to", "the", "imbalance", "of", "gut", "microbiome.", "The", "dominant", "pathogenic", "bacteria", "leads", "to", "the", "reduction", "of", "the", "resident", "normal", "microbiota", "through", "the", "plunder", "of", "nutrients", "or", "the", "killing", "effect", "of", "bacterial", "toxic", "metabolites.", "Our", "results", "from", "the", "microbial", "community", "structure", "analysis", "showed", "Paxillus", "involutus", "occupied", "the", "highest", "proportion", "(31.22%)", "of", "gut", "microbiome", "in", "CRC", "patients", "with", "CID.", "Lu", "et", "al.", "[", "42", "]", "reported", "that", "the", "rate", "of", "Paxillus", "involutus", "was", "approximately", "0.5%", "in", "Beijing", "by", "culturing", "the", "stool", "pathogens", "from", "outpatients", "with", "diarrhea", "syndromes", "using", "the", "Vitek2", "Compact", "instrument.", "Zhang", "et", "al.", "[", "22", "]", "only", "isolated", "43", "Paxillus", "involutus", "strains", "from", "551", "stool", "specimens", "from", "diarrhea", "patients.", "Although", "the", "study", "may", "have", "be", "interfered", "by", "other", "factors", "such", "as", "geographical", "location,", "nosocomial", "infection,", "or", "pollution", "contamination", "in", "the", "fecal", "collection", "process.", "The", "increased", "proportion", "of", "Paxillus", "involutus", "in", "patients", "with", "CID", "remains", "a", "phenomenon", "of", "concern.", "Microorganisms", "can", "adjust", "and", "modify", "their", "surroundings", "due", "to", "their", "metabolic", "products.", "A", "series", "of", "enzymes", "and", "genes", "participate", "in", "the", "process", "of", "metabolism", "[", "12", "]." ]

Original work titled: 'Gut microbiome associated with chemotherapy-induced diarrhea from the CapeOX regimen as adjuvant chemotherapy in resected stage III colorectal cancer' (Gut Pathogens/BioMed Central) by the following authors: Zuo Fei; Yin Lijuan; Yang Xi; Wu Wei; Zhong Jing; Da Miao; Han Shuwen DOI: 10.1186/s13099-019-0299-4

f7083ca86a7871cc8d04d2500480cbf3

CC-BY

http://creativecommons.org/licenses/by/4.0/

4.0

[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]

[ "Fig.", "4", "Functional", "analysis.", "The", "Picrust", "software", "was", "used", "to", "analyze", "the", "pathway", "based", "on", "the", "KEGG", "database.", "The", "significant", "differences", "in", "functional", "metabolism", "are", "shown", "in", "the", "figure", "Discussion", "The", "CapeOX", "regimen", "is", "recommended", "as", "the", "postoperative", "adjuvant", "chemotherapy", "regimen", "in", "resected", "CRC", "patients", "with", "stage", "III", "or", "high-risk", "stage", "II", "[", "35", "].", "The", "high-risk", "factors", "in", "stage", "II", "may", "affect", "the", "accuracy", "of", "experimental", "results,", "Thus,", "CRC", "patients", "with", "stage", "III", "were", "recruited", "in", "the", "present", "study.", "According", "to", "the", "NCCN", "guidelines,", "the", "CapeOX", "regimen", "for", "resected", "stage", "III", "CRC", "has", "been", "defined", "as", "8", "cycles", "of", "capecitabine", "(1000", "mg/m", "2", "twice", "daily)", "combined", "with", "oxaliplatin", "(130", "mg/m", "2", "every", "3", "weeks)", "[", "36", "].", "CID", "is", "one", "of", "the", "most", "common", "side", "effects", "of", "the", "CapeOX", "regimen", "[", "37", "].", "The", "degree", "of", "diarrhea", "caused", "by", "different", "chemotherapeutic", "agents", "varies.", "Among", "the", "chemotherapeutic", "drugs", "for", "colorectal", "cancer,", "the", "most", "common", "drugs", "that", "cause", "diarrhea", "are", "fluorouracil,", "irinotecan", "and", "platinum,", "and", "the", "incidence", "of", "diarrhea", "associated", "with", "these", "drugs", "can", "be", "as", "high", "as", "50–80%", "[", "38", "].", "Our", "previous", "clinical", "investigation", "found", "that", "the", "probability", "of", "CID", "increased", "with", "an", "increase", "of", "chemotherapeutic", "frequency", "and", "chemotherapeutic", "dosage", "and", "most", "cases", "of", "CID", "occur", "within", "2", "weeks", "after", "chemotherapy.", "Therefore,", "in", "the", "present", "study,", "stool", "samples", "from", "the", "patients", "were", "collected", "in", "2", "weeks", "after", "the", "8", "cycles", "of", "chemotherapy", "of", "the", "CapeOX", "regimen", "were", "completed.", "Studies", "of", "Carroll", "et", "al.", "[", "39", "]", "suggested", "that", "the", "richness", "of", "16S", "rRNA", "sequences", "was", "significantly", "decreased", "in", "patients", "with", "diarrhea-predominant", "irritable", "bowel", "syndrome.", "Lee", "[", "40", "]", "has", "reported", "the", "community", "diversity", "of", "gut", "microbiome", "is", "lower", "in", "patients", "with", "kidney", "posttransplant", "diarrhea.", "Similar", "results", "have", "been", "reported", "in", "dogs", "with", "acute", "diarrhea", "[", "41", "].", "The", "research", "on", "these", "diarrhea", "diseases", "is", "consistent", "with", "our", "findings." ]

Original work titled: 'Gut microbiome associated with chemotherapy-induced diarrhea from the CapeOX regimen as adjuvant chemotherapy in resected stage III colorectal cancer' (Gut Pathogens/BioMed Central) by the following authors: Zuo Fei; Yin Lijuan; Yang Xi; Wu Wei; Zhong Jing; Da Miao; Han Shuwen DOI: 10.1186/s13099-019-0299-4

f7083ca86a7871cc8d04d2500480cbf3

CC-BY

http://creativecommons.org/licenses/by/4.0/

4.0

[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]

[ "The", "increased", "proportion", "of", "Petroica", "boodang", "in", "patients", "with", "CID", "remains", "a", "phenomenon", "of", "concern.", "Microorganisms", "can", "adjust", "and", "modify", "their", "surroundings", "due", "to", "their", "metabolic", "products.", "A", "series", "of", "enzymes", "and", "genes", "participate", "in", "the", "process", "of", "metabolism", "[", "12", "].", "Functional", "analysis", "of", "these", "enzymes", "and", "genes", "would", "be", "conducive", "to", "understand", "the", "whole", "microecological", "environment.", "In", "the", "present", "study,", "we", "screened", "75", "differentiated", "microorganisms", "at", "the", "species", "level", "by", "using", "LDA", "effect", "size", "analysis", "as", "well", "as", "23", "pathways", "associated", "with", "differential", "microorganisms", "by", "using", "KEGG", "databases.", "These", "differential", "pathways", "are", "related", "to", "microbial", "metabolites,", "cell", "proliferation", "and", "death,", "immune", "system,", "and", "many", "other", "aspects.", "These", "differentiated", "microorganisms,", "their", "metabolic", "products", "and", "the", "relevant", "pathways", "make", "up", "the", "intestinal", "microecosystem", "that", "causes", "CID.", "These", "results", "may", "provide", "characteristic", "microorganisms", "or", "potential", "molecular", "targets", "for", "the", "treatment", "and", "prevention", "of", "CID.", "It", "must", "be", "emphasized", "that", "small", "sample", "size", "and", "potential", "sample", "contamination", "may", "affect", "the", "accuracy", "of", "the", "present", "study.", "Strict", "inclusion", "and", "exclusion", "criteria", "was", "performed", "in", "this", "study.", "Subjects", "in", "the", "experimental", "group", "were", "only", "included", "the", "resected", "stage", "III", "colorectal", "cancer", "(CRC)", "patients", "who", "voluntarily", "accepted", "and", "completed", "8", "cycles", "of", "the", "CapeOX", "regimen", "and", "accompanied", "with", "grade", "2", "of", "CID.", "Thus,", "the", "small", "sample", "size", "limits", "the", "applicability", "of", "the", "findings.", "A", "multi-center,", "large", "study", "will", "provide", "more", "powerful", "data", "to", "support", "the", "clarification", "of", "the", "microbial", "differences", "in", "CRC", "patients", "with", "CID.", "Conclusion", "Chemotherapy", "induced", "diarrhea", "(CID)", "is", "a", "common", "side", "effect", "in", "patients", "receiving", "chemotherapy", "for", "cancer.", "In", "the", "present", "study,", "We", "found", "that", "the", "gut", "microbial", "community", "structure", "and", "community", "diversity", "have", "changed", "in", "CRC", "patients", "with", "CID.", "The", "gut", "microbial", "community", "richness", "and", "community", "diversity", "were", "lower", "in", "CID.", "Petroica", "boodang", "was", "the", "most", "predominant", "species", "among", "the", "gut", "microbiome", "in", "CRC", "patients", "with", "CID.", "It", "may", "provide", "novel", "insights", "into", "the", "prevention", "and", "treatment", "of", "patients", "with", "CID", "to", "improve", "patients’", "quality", "of", "life", "and", "chemotherapy", "tolerance." ]

Original work titled: 'Gut microbiome associated with chemotherapy-induced diarrhea from the CapeOX regimen as adjuvant chemotherapy in resected stage III colorectal cancer' (Gut Pathogens/BioMed Central) by the following authors: Zuo Fei; Yin Lijuan; Yang Xi; Wu Wei; Zhong Jing; Da Miao; Han Shuwen DOI: 10.1186/s13099-019-0299-4

f7083ca86a7871cc8d04d2500480cbf3

CC-BY

http://creativecommons.org/licenses/by/4.0/

4.0

[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]

[ "Lee", "[", "40", "]", "has", "reported", "the", "community", "diversity", "of", "gut", "microbiome", "is", "lower", "in", "patients", "with", "kidney", "posttransplant", "diarrhea.", "Similar", "results", "have", "been", "reported", "in", "dogs", "with", "acute", "diarrhea", "[", "41", "].", "The", "research", "on", "these", "diarrhea", "diseases", "is", "consistent", "with", "our", "findings.", "We", "found", "that", "the", "gut", "microbial", "community", "richness", "and", "community", "diversity", "was", "lower", "in", "CRC", "patients", "with", "CID", "in", "the", "present", "study.", "The", "decrease", "of", "microbial", "diversity", "may", "be", "related", "to", "the", "imbalance", "of", "gut", "microbiome.", "The", "dominant", "pathogenic", "bacteria", "leads", "to", "the", "reduction", "of", "the", "resident", "normal", "microbiota", "through", "the", "plunder", "of", "nutrients", "or", "the", "killing", "effect", "of", "bacterial", "toxic", "metabolites.", "Our", "results", "from", "the", "microbial", "community", "structure", "analysis", "showed", "Porphyromonas", "endodontalis", "occupied", "the", "highest", "proportion", "(31.22%)", "of", "gut", "microbiome", "in", "CRC", "patients", "with", "CID.", "Lu", "et", "al.", "[", "42", "]", "reported", "that", "the", "rate", "of", "Porphyromonas", "endodontalis", "was", "approximately", "0.5%", "in", "Beijing", "by", "culturing", "the", "stool", "pathogens", "from", "outpatients", "with", "diarrhea", "syndromes", "using", "the", "Vitek2", "Compact", "instrument.", "Zhang", "et", "al.", "[", "22", "]", "only", "isolated", "43", "Porphyromonas", "endodontalis", "strains", "from", "551", "stool", "specimens", "from", "diarrhea", "patients.", "Although", "the", "study", "may", "have", "be", "interfered", "by", "other", "factors", "such", "as", "geographical", "location,", "nosocomial", "infection,", "or", "pollution", "contamination", "in", "the", "fecal", "collection", "process.", "The", "increased", "proportion", "of", "Porphyromonas", "endodontalis", "in", "patients", "with", "CID", "remains", "a", "phenomenon", "of", "concern.", "Microorganisms", "can", "adjust", "and", "modify", "their", "surroundings", "due", "to", "their", "metabolic", "products.", "A", "series", "of", "enzymes", "and", "genes", "participate", "in", "the", "process", "of", "metabolism", "[", "12", "].", "Functional", "analysis", "of", "these", "enzymes", "and", "genes", "would", "be", "conducive", "to", "understand", "the", "whole", "microecological", "environment.", "In", "the", "present", "study,", "we", "screened", "75", "differentiated", "microorganisms", "at", "the", "species", "level", "by", "using", "LDA", "effect", "size", "analysis", "as", "well", "as", "23", "pathways", "associated", "with", "differential", "microorganisms", "by", "using", "KEGG", "databases.", "These", "differential", "pathways", "are", "related", "to", "microbial", "metabolites,", "cell", "proliferation", "and", "death,", "immune", "system,", "and", "many", "other", "aspects.", "These", "differentiated", "microorganisms,", "their", "metabolic", "products", "and", "the", "relevant", "pathways", "make", "up", "the", "intestinal", "microecosystem", "that", "causes", "CID." ]

Original work titled: 'Gut microbiome associated with chemotherapy-induced diarrhea from the CapeOX regimen as adjuvant chemotherapy in resected stage III colorectal cancer' (Gut Pathogens/BioMed Central) by the following authors: Zuo Fei; Yin Lijuan; Yang Xi; Wu Wei; Zhong Jing; Da Miao; Han Shuwen DOI: 10.1186/s13099-019-0299-4

f7083ca86a7871cc8d04d2500480cbf3

CC-BY

http://creativecommons.org/licenses/by/4.0/

4.0

[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]

[ "The", "innermost", "layer", "shows", "the", "taxonomic", "tree.", "The", "circle", "from", "the", "inside", "to", "the", "outside", "represents", "different", "taxon", "levels", "from", "phylum", "to", "genus.", "Yellow", "circles", "represent", "no", "statistical", "difference", "in", "species", "between", "the", "two", "groups,", "and", "red", "circles", "and", "green", "circles", "represent", "the", "higher", "abundance", "of", "genus", "in", "the", "control", "group", "and", "the", "chemotherapy-induced", "diarrhea", "group,", "respectively.", "The", "lowercase", "English", "letters", "corresponding", "to", "the", "different", "bacteria", "are", "shown", "in", "the", "legends", "The", "functional", "analysis", "of", "16S", "rRNA", "genes", "associated", "with", "CID", "during", "the", "CapeOX", "regimen", "for", "CRC", "It", "has", "been", "confirmed", "that", "many", "gene", "function", "annotation", "databases", "are", "associated", "with", "corresponding", "16S", "rRNA", "gene", "sequences.", "Functional", "analysis", "of", "enzymes", "and", "genes", "would", "be", "conducive", "to", "understand", "the", "whole", "microecological", "environment.", "As", "shown", "in", "Fig.", "4", ",", "the", "figure", "shows", "the", "results", "of", "the", "functional", "analysis.", "Overall,", "23", "pathways", "(p", "<", "0.001)", "associated", "with", "statistically", "significant", "differences", "might", "be", "involved", "in", "CID", "during", "the", "CapeOX", "regimen", "for", "adjuvant", "chemotherapy", "in", "resected", "stage", "III", "colorectal", "cancer.", "These", "differential", "pathways", "are", "related", "to", "microbial", "metabolites,", "cell", "proliferation", "and", "death,", "immune", "system,", "and", "many", "other", "aspects.", "Fig.", "4", "Functional", "analysis.", "The", "Picrust", "software", "was", "used", "to", "analyze", "the", "pathway", "based", "on", "the", "KEGG", "database.", "The", "significant", "differences", "in", "functional", "metabolism", "are", "shown", "in", "the", "figure", "Discussion", "The", "CapeOX", "regimen", "is", "recommended", "as", "the", "postoperative", "adjuvant", "chemotherapy", "regimen", "in", "resected", "CRC", "patients", "with", "stage", "III", "or", "high-risk", "stage", "II", "[", "35", "].", "The", "high-risk", "factors", "in", "stage", "II", "may", "affect", "the", "accuracy", "of", "experimental", "results,", "Thus,", "CRC", "patients", "with", "stage", "III", "were", "recruited", "in", "the", "present", "study.", "According", "to", "the", "NCCN", "guidelines,", "the", "CapeOX", "regimen", "for", "resected", "stage", "III", "CRC", "has", "been", "defined", "as", "8", "cycles", "of", "capecitabine", "(1000", "mg/m", "2", "twice", "daily)", "combined", "with", "oxaliplatin", "(130", "mg/m", "2", "every", "3", "weeks)", "[", "36", "].", "CID", "is", "one", "of", "the", "most", "common", "side", "effects", "of", "the", "CapeOX", "regimen", "[", "37", "].", "The", "degree", "of", "diarrhea", "caused", "by", "different", "chemotherapeutic", "agents", "varies." ]

Original work titled: 'Gut microbiome associated with chemotherapy-induced diarrhea from the CapeOX regimen as adjuvant chemotherapy in resected stage III colorectal cancer' (Gut Pathogens/BioMed Central) by the following authors: Zuo Fei; Yin Lijuan; Yang Xi; Wu Wei; Zhong Jing; Da Miao; Han Shuwen DOI: 10.1186/s13099-019-0299-4

f7083ca86a7871cc8d04d2500480cbf3

CC-BY

http://creativecommons.org/licenses/by/4.0/

4.0

[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]

[ "The", "cladogram", "in", "Fig.", "3", "c", "displays", "the", "composition", "and", "proportion", "of", "microorganisms", "at", "different", "taxonomic", "levels.", "The", "cladogram", "showed", "that", "the", "abundance", "of", "these", "bacteria", "including", "Actinomycetaceae,", "Micrococcaceae,", "Bacteroidaceae,", "Porphyromonadaceae,", "Ruminococcaceae,", "Erysipelotrichaceae,", "Leptotrichiaceae,", "Enterobacteriaceae", "(Klebsiella", "belongs", "to", "Enterobacteriaceae)", "and", "Synergistaceae", "had", "significant", "differences", "at", "family", "level", "between", "the", "two", "groups.", "Fig.", "3", "Differential", "microbes", "analysis.", "The", "samples", "were", "divided", "into", "two", "groups", "according", "to", "patients", "with", "or", "without", "CID.", "The", "number", "of", "OTUs", "that", "were", "exclusive", "or", "shared", "by", "the", "two", "groups", "were", "visualized", "by", "a", "Venn", "Chart", "(", "a", ").", "The", "strip", "figure", "in", "b", "displays", "the", "LDA", "effect", "size", "analysis.", "LDA", "effect", "size", "analysis", "was", "used", "to", "compare", "the", "differences", "in", "microbial", "abundance", "between", "the", "two", "groups", "(", "b", ").", "LDA", "scores", "over", "2", "mean", "that", "the", "differences", "are", "statistically", "significant", "(p", "<", "0.05).", "The", "cladogram", "in", "c", "displays", "the", "composition", "and", "proportion", "of", "microorganisms", "at", "different", "taxonomic", "levels.", "The", "innermost", "layer", "shows", "the", "taxonomic", "tree.", "The", "circle", "from", "the", "inside", "to", "the", "outside", "represents", "different", "taxon", "levels", "from", "phylum", "to", "genus.", "Yellow", "circles", "represent", "no", "statistical", "difference", "in", "species", "between", "the", "two", "groups,", "and", "red", "circles", "and", "green", "circles", "represent", "the", "higher", "abundance", "of", "genus", "in", "the", "control", "group", "and", "the", "chemotherapy-induced", "diarrhea", "group,", "respectively.", "The", "lowercase", "English", "letters", "corresponding", "to", "the", "different", "bacteria", "are", "shown", "in", "the", "legends", "The", "functional", "analysis", "of", "16S", "rRNA", "genes", "associated", "with", "CID", "during", "the", "CapeOX", "regimen", "for", "CRC", "It", "has", "been", "confirmed", "that", "many", "gene", "function", "annotation", "databases", "are", "associated", "with", "corresponding", "16S", "rRNA", "gene", "sequences.", "Functional", "analysis", "of", "enzymes", "and", "genes", "would", "be", "conducive", "to", "understand", "the", "whole", "microecological", "environment.", "As", "shown", "in", "Fig.", "4", ",", "the", "figure", "shows", "the", "results", "of", "the", "functional", "analysis." ]

Datasets:

tznurmin
/

tea_curated

Dataset Summary

Licensing

Usage

For development or regenerating augmentations, you can use the dyn-aug branch:

Clone the dataset repository

Install dependencies

Usage

More information