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The global dispersal of anatomically modern humans over the past 100,000 years has produced patterns of phenotypic variation that have exerted--and continue to exert--powerful influences on the lives of individuals and the experiences of groups. The recency of our common ancestry and continued gene flow among populations have resulted in less genetic differentiation among geographically distributed human populations than is observed in many other mammalian species. Nevertheless, differences in appearance have contributed to the development of ideas about "race" and "ethnicity" that often include the belief that significant inherited differences distinguish humans. The use of racial, ethnic, and ancestral categories in genetics research can imply that group differences arise directly through differing allele frequencies, with little influence from socially mediated mechanisms. At the same time, careful investigations of the biological, environmental, social, and psychological attributes associated with these categories will be an essential component of cross-disciplinary research into the origins, prevention, and treatment of common diseases, including those diseases that differ in prevalence among groups. | [] | The use of racial, ethnic, and ancestral categories in human genetics research. |
Leri-Weill dyschondrosteosis (LWD) is a pseudoautosomal dominant disorder characterized by disproportionate short stature and a characteristic curving of the radius, known as the "Madelung deformity." SHOX mutations resulting in SHOX haploinsufficiency have been found in LWD and in a variable proportion of patients with idiopathic short stature (ISS), whereas homozygous loss of SHOX results in the more severe Langer mesomelic dysplasia (LMD). Defects in SHOX have been identified in approximately 60% of LWD cases, whereas, in the remaining approximately 40%, the molecular basis is unknown. This suggests either genetic heterogeneity or the presence of mutations in unanalyzed regions of SHOX, such as the upstream, intragenic, or downstream regulatory sequences. Therefore, the pseudoautosomal region 1 (PAR1) of 80 patients with LWD, in whom SHOX deletions and mutations had been excluded, was screened for deletions by use of a new panel of microsatellite markers. We identified 12 patients with LWD who presented with a novel class of PAR1 deletions that did not include SHOX. The deletions were of variable size and mapped at least approximately 30-530 kb downstream of SHOX. In our cohort, this type of deletion accounted for 15% of cases. In all cases, the deletions cosegregated with the phenotype. No apparent phenotypic differences were observed between patients with SHOX deletions and those with this new class of PAR1 deletions. Thus, we present here the identification of a second PAR1 region implicated in the etiopathogenesis of LWD. Our findings suggest the presence of distal regulatory elements of SHOX transcription in PAR1 or, alternatively, the existence of an additional locus apparently involved in the control of skeletal development. Deletion analysis of this newly identified region should be included in the mutation screening of patients with LWD, LMD, and ISS. | [
"Benito-Sanz, Sara",
"Thomas, N Simon",
"Huber, Céline",
"Huber, Celine",
"Gorbenko del Blanco, Darya",
"Del Blanco, Darya Gorbenko",
"Aza-Carmona, Miriam",
"Crolla, John A",
"Maloney, Vivienne",
"Rappold, Gudrun",
"Argente, Jesús",
"Argente, Jesus",
"Campos-Barros, Angel",
"Cormier-Daire, Valérie",
"Cormier-Daire, Valerie",
"Heath, Karen E"
] | A novel class of Pseudoautosomal region 1 deletions downstream of SHOX is associated with Leri-Weill dyschondrosteosis. |
Previous evidence suggests that the inheritance of bipolar disorder (BP) may vary depending on the age at onset (AAO). Therefore, we sought to incorporate AAO as a covariate in linkage analyses of BP using two different methods, LODPAL and ordered-subset analysis (OSA), in genomewide scans of 150 multiplex pedigrees with 874 individuals. The LODPAL analysis identified two loci, on chromosomes 21q22.13 (LOD = 3.29; empirical chromosomewide P value = .009) and 18p11.2 (LOD = 2.83; empirical chromosomewide P = .05), with increased linkage among subjects who had early onset (AAO < or = 21 years) and later onset (AAO >21 years), respectively. The finding on 21q22.13 was significant at the chromosomewide level, even after correction for multiple testing. Moreover, a similar finding was observed in an independent sample of 65 pedigrees (LOD = 2.88; empirical chromosomewide P = .025). The finding on 18p11.2 was only nominally significant and was not observed in the independent sample. However, 18p11.2 emerged as one of the strongest regions in the OSA (LOD = 2.92; empirical P = .001), in which it was the only finding to meet chromosomewide levels of significance after correction for multiple testing. These results suggest that 21q22.13 and 18p11.2 may harbor genes that increase the risks for early-onset and later-onset forms of BP, respectively. There have been previous reports of linkage on 21q22.13 and 18p11.2, but the findings have not been consistent. This inconsistency may be due to differences in the AAO characteristics of the samples examined. Future studies to fine map susceptibility genes for BP on chromosomes 21q22.13 and 18p11.2 should take AAO into account. | [
"Lin, Ping-I",
"McInnis, Melvin G",
"Potash, James B",
"Willour, Virginia L",
"Mackinnon, Dean F",
"Miao, Kuangyi",
"Depaulo, J Raymond",
"Zandi, Peter P"
] | Assessment of the effect of age at onset on linkage to bipolar disorder: evidence on chromosomes 18p and 21q. |
The formation of the synaptonemal complex (SC) is a crucial early step in the meiotic process, but relatively little is known about the establishment of the human SC. Accordingly, we recently initiated a study of synapsis in the human male, combining immunofluorescence and fluorescence in situ hybridization methodologies to analyze prophase spermatocytes from a series of control individuals. Our results indicate that synapsis is a tightly regulated process, with relatively little variation among individuals. On nonacrocentric chromosomes, there are two synaptic initiation sites, one on the distal short arm and one on the distal long arm, whereas acrocentric chromosomes exhibit a single site on the distal long arm. For both types of chromosomes, synapsis then proceeds toward the centromere, with little evidence that specific p- or q-arm sequences affect the process. However, the centromere appears to have an inhibitory effect on synapsis--that is, when one arm of a nonacrocentric chromosome is "zippered up" before the other, the centromere acts as a barrier to further movement from that arm. | [
"Brown, Petrice W",
"Judis, Luann",
"Chan, E Ricky",
"Schwartz, Stuart",
"Seftel, Allen",
"Thomas, Anthony",
"Hassold, Terry J"
] | Meiotic synapsis proceeds from a limited number of subtelomeric sites in the human male. |
The minor allele of the R620W missense single-nucleotide polymorphism (SNP) (rs2476601) in the hematopoietic-specific protein tyrosine phosphatase gene, PTPN22, has been associated with multiple autoimmune diseases, including rheumatoid arthritis (RA). These genetic data, combined with biochemical evidence that this SNP affects PTPN22 function, suggest that this phosphatase is a key regulator of autoimmunity. To determine whether other genetic variants in PTPN22 contribute to the development of RA, we sequenced the coding regions of this gene in 48 white North American patients with RA and identified 15 previously unreported SNPs, including 2 coding SNPs in the catalytic domain. We then genotyped 37 SNPs in or near PTPN22 in 475 patients with RA and 475 individually matched controls (sample set 1) and selected a subset of markers for replication in an additional 661 patients with RA and 1,322 individually matched controls (sample set 2). Analyses of these results predict 10 common (frequency >1%) PTPN22 haplotypes in white North Americans. The sole haplotype found to carry the previously identified W620 risk allele was strongly associated with disease in both sample sets, whereas another haplotype, identical at all other SNPs but carrying the R620 allele, showed no association. R620W, however, does not fully explain the association between PTPN22 and RA, since significant differences between cases and controls persisted in both sample sets after the haplotype data were stratified by R620W. Additional analyses identified two SNPs on a single common haplotype that are associated with RA independent of R620W, suggesting that R620W and at least one additional variant in the PTPN22 gene region influence RA susceptibility. | [
"Carlton, Victoria E H",
"Hu, Xiaolan",
"Chokkalingam, Anand P",
"Schrodi, Steven J",
"Brandon, Rhonda",
"Alexander, Heather C",
"Chang, Monica",
"Catanese, Joseph J",
"Leong, Diane U",
"Ardlie, Kristin G",
"Kastner, Daniel L",
"Seldin, Michael F",
"Criswell, Lindsey A",
"Gregersen, Peter K",
"Beasley, Ellen",
"Thomson, Glenys",
"Amos, Christopher I",
"Begovich, Ann B"
] | PTPN22 genetic variation: evidence for multiple variants associated with rheumatoid arthritis. |
Mental retardation (MR) occurs in 2%-3% of the general population. Conventional karyotyping has a resolution of 5-10 million bases and detects chromosomal alterations in approximately 5% of individuals with unexplained MR. The frequency of smaller submicroscopic chromosomal alterations in these patients is unknown. Novel molecular karyotyping methods, such as array-based comparative genomic hybridization (array CGH), can detect submicroscopic chromosome alterations at a resolution of 100 kb. In this study, 100 patients with unexplained MR were analyzed using array CGH for DNA copy-number changes by use of a novel tiling-resolution genomewide microarray containing 32,447 bacterial artificial clones. Alterations were validated by fluorescence in situ hybridization and/or multiplex ligation-dependent probe amplification, and parents were tested to determine de novo occurrence. Reproducible DNA copy-number changes were present in 97% of patients. The majority of these alterations were inherited from phenotypically normal parents, which reflects normal large-scale copy-number variation. In 10% of the patients, de novo alterations considered to be clinically relevant were found: seven deletions and three duplications. These alterations varied in size from 540 kb to 12 Mb and were scattered throughout the genome. Our results indicate that the diagnostic yield of this approach in the general population of patients with MR is at least twice as high as that of standard GTG-banded karyotyping. | [
"de Vries, Bert B A",
"Pfundt, Rolph",
"Leisink, Martijn",
"Koolen, David A",
"Vissers, Lisenka E L M",
"Janssen, Irene M",
"Reijmersdal, Simon van",
"Nillesen, Willy M",
"Huys, Erik H L P G",
"Leeuw, Nicole de",
"Smeets, Dominique",
"Sistermans, Erik A",
"Feuth, Ton",
"van Ravenswaaij-Arts, Conny M A",
"van Kessel, Ad Geurts",
"Schoenmakers, Eric F P M",
"Brunner, Han G",
"Veltman, Joris A"
] | Diagnostic genome profiling in mental retardation. |
Angiotensin I-converting enzyme inhibitors (ACEi), which are used to treat common cardiovascular diseases, are associated with a potentially life-threatening adverse reaction known as angioedema (AE-ACEi). We have previously documented a significant association between AE-ACEi and low plasma aminopeptidase P (APP) activity. With eight large pedigrees, we hereby demonstrate that this quantitative trait is partially regulated by genetic factors. We tested APP activity using a variance-component QTL analysis of a 10-cM genomewide microsatellite scan enriched with seven markers over two candidate regions. We found significant linkage (LOD = 3.75) to a locus that includes the XPNPEP2 candidate gene encoding membrane-bound APP. Mutation screening of this QTL identified a large coding deletion segregating in one pedigree and an upstream single-nucleotide polymorphism (C-2399A SNP), which segregates in the remaining seven pedigrees. Measured genotype analysis strongly suggests that the linkage signal for APP activity at this locus is accounted for predominantly by the SNP association. In a separate case-control study (20 cases and 60 controls), we found significant association of this SNP to ACEi-induced AE (P=.0364). In conclusion, our findings provide supporting evidence that the C-2399A variant in XPNPEP2 is associated with reduced APP activity and a higher incidence of AE-ACEi. | [
"Duan, Qing Ling",
"Nikpoor, Borzoo",
"Dube, Marie-Pierre",
"Molinaro, Giuseppe",
"Meijer, Inge A",
"Dion, Patrick",
"Rochefort, Daniel",
"Saint-Onge, Judith",
"Flury, Leah",
"Brown, Nancy J",
"Gainer, James V",
"Rouleau, Jean L",
"Agostoni, Angelo",
"Cugno, Massimo",
"Simon, Pierre",
"Clavel, Pierre",
"Potier, Jacky",
"Wehbe, Bassem",
"Benarbia, Seddik",
"Marc-Aurele, Julien",
"Chanard, Jacques",
"Foroud, Tatiana",
"Adam, Albert",
"Rouleau, Guy A"
] | A variant in XPNPEP2 is associated with angioedema induced by angiotensin I-converting enzyme inhibitors. |
Recombination is expected to reduce the effect of selection on the extent of linkage disequilibrium (LD), but the impact that recombinational hotspots have on sites linked to selected mutations has not been investigated. We empirically determine chromosomal linkage phase for 5.2 kb spanning the beta -globin gene and hotspot. We estimate that the HbC mutation, which is positively selected because of malaria, originated <5,000 years ago and that selection coefficients are 0.04-0.09. Despite strong selection and the recent origin of the HbC allele, recombination (crossing-over or gene conversion) is observed within 1 kb 5' of the selected site on more than one-third of the HbC chromosomes sampled. The rapid decay in LD upstream of the HbC allele demonstrates the large effect the ss-globin hotspot has in mitigating the effects of positive selection on linked variation. | [
"Wood, Elizabeth T",
"Stover, Daryn A",
"Slatkin, Montgomery",
"Nachman, Michael W",
"Hammer, Michael F"
] | The beta -globin recombinational hotspot reduces the effects of strong selection around HbC, a recently arisen mutation providing resistance to malaria. |
We obtained conclusive linkage of Alzheimer disease (AD) with a candidate region of 19.7 cM at 7q36 in an extended multiplex family, family 1270, ascertained in a population-based study of early-onset AD in the northern Netherlands. Single-nucleotide polymorphism and haplotype association analyses of a Dutch patient-control sample further supported the linkage at 7q36. In addition, we identified a shared haplotype at 7q36 between family 1270 and three of six multiplex AD-affected families from the same geographical region, which is indicative of a founder effect and defines a priority region of 9.3 cM. Mutation analysis of coding exons of 29 candidate genes identified one linked synonymous mutation, g.38030G-->C in exon 10, that affected codon 626 of the PAX transactivation domain interacting protein gene (PAXIP1). It remains to be determined whether PAXIP1 has a functional role in the expression of AD in family 1270 or whether another mutation at this locus explains the observed linkage and sharing. Together, our linkage data from the informative family 1270 and the association data in the population-based early-onset AD patient-control sample strongly support the identification of a novel AD locus at 7q36 and re-emphasize the genetic heterogeneity of AD. | [
"Rademakers, Rosa",
"Cruts, Marc",
"Sleegers, Kristel",
"Dermaut, Bart",
"Theuns, Jessie",
"Aulchenko, Yurii",
"Weckx, Stefan",
"De Pooter, Tim",
"Van den Broeck, Marleen",
"Corsmit, Ellen",
"De Rijk, Peter",
"Del-Favero, Jurgen",
"van Swieten, John",
"van Duijn, Cornelia M",
"Van Broeckhoven, Christine"
] | Linkage and association studies identify a novel locus for Alzheimer disease at 7q36 in a Dutch population-based sample. |
The cytoplasmic plaque protein desmoplakin (DP), which is located in desmosomes, plays a major role in epithelial and muscle cell adhesion by linking the transmembrane cadherins to the cytoplasmic intermediate filament network. Mutations of DP may cause striate palmoplantar keratoderma, arrhythmogenic right ventricular dysplasia, skin fragility/woolly hair syndrome, Naxos-like disease, and Carvajal syndrome. DP must be indispensable, because DP-/- mice are early abortive. Here, we report a patient with severe fragility of skin and mucous membranes caused by genetic truncation of the DP tail. The new phenotype is lethal in the neonatal period because of immense transcutaneous fluid loss. The phenotype also comprised universal alopecia, neonatal teeth, and nail loss. Histology showed suprabasal clefting and acantholysis throughout the spinous layer, mimicking pemphigus. Electron microscopy revealed disconnection of keratin intermediate filaments from desmosomes. Immunofluorescence staining of DP showed a distinct punctate intercellular pattern in the patient's skin. Protein analysis revealed expression of truncated DP polypeptides. Mutational analysis of the patient demonstrated compound heterozygosity for two DP mutations, 6079C-->T (R1934X) and 6370delTT, respectively. Aberrant mRNA transcripts that predict premature termination of translation with loss of the three intermediate filament-binding subdomains in the DP tail were detected by RT-PCR. The new dramatic phenotype, which we named "lethal acantholytic epidermolysis bullosa," underscores the paramount role of DP in epidermal integrity. | [
"Jonkman, Marcel F",
"Pasmooij, Anna M G",
"Pasmans, Suzanne G M A",
"van den Berg, Maarten P",
"Ter Horst, Henk J",
"Timmer, Albertus",
"Pas, Hendri H"
] | Loss of desmoplakin tail causes lethal acantholytic epidermolysis bullosa. |
The principles of linkage disequilibrium mapping of dichotomous diseases can be well applied to the mapping of quantitative-trait loci through the method of selective genotyping. In 1999, M. Slatkin considered a truncation selection (TS) approach. We propose in this report an extended TS approach and an extreme-rank-selection (ERS) approach. The properties of these selection approaches are studied analytically. By using a simulation study, we demonstrate that both the extended TS approach and the ERS approach provide remarkable improvements over Slatkin's original TS approach. | [
"Chen, Zehua",
"Zheng, Gang",
"Ghosh, Kaushik",
"Li, Zhaohai"
] | Linkage disequilibrium mapping of quantitative-trait Loci by selective genotyping. |
Recombination, the precise physical breakage and rejoining of DNA between homologous chromosomes, plays a central role in mediating the orderly segregation of meiotic chromosomes in most eukaryotes. Despite its importance, the factors that control the number and placement of recombination events within a cell remain poorly defined. The rate of recombination exhibits remarkable species specificity, and, within a species, recombination is affected by the physical size of the chromosome, chromosomal location, proximity to other recombination events (i.e., chiasma interference), and, intriguingly, the sex of the transmitting parent. To distinguish between simple genetic and nongenetic explanations of sex-specific recombination differences in mammals, we compared recombination in meiocytes from XY sex-reversed and XO females with that in meiocytes from XX female and XY male mice. The rate and pattern of recombination in XY and XO oocytes were virtually identical to those in normal XX females, indicating that sex, not genotype, is the primary determinant of meiotic recombination patterns in mammals. | [
"Lynn, Audrey",
"Schrump, Stefanie",
"Cherry, Jonathan",
"Hassold, Terry",
"Hunt, Patricia"
] | Sex, not genotype, determines recombination levels in mice. |
The Atlantic slave trade promoted by West European empires (15th-19th centuries) forcibly moved at least 11 million people from Africa, including about one-third from west-central Africa, to European and American destinations. The mitochondrial DNA (mtDNA) genome has retained an imprint of this process, but previous analyses lacked west-central African data. Here, we make use of an African database of 4,860 mtDNAs, which include 948 mtDNA sequences from west-central Africa and a further 154 from the southwest, and compare these for the first time with a publicly available database of 1,148 African Americans from the United States that contains 1,053 mtDNAs of sub-Saharan ancestry. We show that >55% of the U.S. lineages have a West African ancestry, with <41% coming from west-central or southwestern Africa. These results are remarkably similar to the most up-to-date analyses of the historical record. | [
"Salas, Antonio",
"Carracedo, Angel",
"Richards, Martin",
"Macaulay, Vincent"
] | Charting the ancestry of African Americans. |
Dimethylglycine dehydrogenase (DMGDH) (E.C. number 1.5.99.2) is a mitochondrial matrix enzyme involved in the metabolism of choline, converting dimethylglycine to sarcosine. Sarcosine is then transformed to glycine by sarcosine dehydrogenase (E.C. number 1.5.99.1). Both enzymes use flavin adenine dinucleotide and folate in their reaction mechanisms. We have identified a 38-year-old man who has a lifelong condition of fishlike body odor and chronic muscle fatigue, accompanied by elevated levels of the muscle form of creatine kinase in serum. Biochemical analysis of the patient's serum and urine, using (1)H-nuclear magnetic resonance NMR spectroscopy, revealed that his levels of dimethylglycine were much higher than control values. The cDNA and the genomic DNA for human DMGDH (hDMGDH) were then cloned, and a homozygous A-->G substitution (326 A-->G) was identified in both the cDNA and genomic DNA of the patient. This mutation changes a His to an Arg (H109R). Expression analysis of the mutant cDNA indicates that this mutation inactivates the enzyme. We therefore confirm that the patient described here represents the first reported case of a new inborn error of metabolism, DMGDH deficiency. | [
"Binzak, B A",
"Wevers, R A",
"Moolenaar, S H",
"Lee, Y M",
"Hwu, W L",
"Poggi-Bach, J",
"Engelke, U F",
"Hoard, H M",
"Vockley, J G",
"Vockley, J"
] | Cloning of dimethylglycine dehydrogenase and a new human inborn error of metabolism, dimethylglycine dehydrogenase deficiency. |
Deuterium nuclear magnetic resonance spectroscopy was used to investigate the orientations of the indole rings of Trp9 and Trp11 in specific indole-d5-labeled samples of gramicidin A incorporated into dimyristoyl phosphatidylcholine bilayers in the beta 6.3 channel conformation. The magnitudes and signs of the deuterium quadrupolar splittings were fit to the rings and assigned to specific ring bonds, using a full rotation search of the chi 1 and chi 2 angles of each Trp and a least-squares method. Unique assignments were obtained. The data and assignments are in close agreement with four sets of (chi 1, chi 2) angles for each Trp in which the indole N-H is oriented toward the membrane's exterior surface. (Four additional sets of (chi 1, chi 2) angles with the N-H's pointing toward the membrane interior are inconsistent with previous observations.) One of the sets of (chi 1, chi 2) angles for each Trp is consistent with the corresponding Trp orientation found by Arsen'ev et al. (1986. Biol. Membr. 3:1077-1104) for gramicidin in sodium dodecyl sulfate micelles. Together, the 1H and 2H nuclear magnetic resonance methods suggest that the Trp9 and Trp11 side chain orientations could be very similar in dimyristoyl phosphatidylcholine membranes and in sodium dodecyl sulfate micelles. The data for Trp11 could be fit using a static quadrupolar coupling constant of 180 kHz under the assumption that the ring is essentially immobile. By contrast, Trp9 could be fit only under the assumption that the quadrupolar splittings for ring 9 are reduced by approximately 14% due to motional averaging. Such a difference in motional averaging between rings 11 and 9 is also consistent with the 15N data of Hu et al. (1993. Biochemistry. 32:7035-7047). | [
"Koeppe, R E",
"Killian, J A",
"Greathouse, D V"
] | Orientations of the tryptophan 9 and 11 side chains of the gramicidin channel based on deuterium nuclear magnetic resonance spectroscopy. |
Adhesion between patch-clamped lipid membranes and glass micropipettes is measured by high contrast video imaging of the mechanical response to the application of suction pressure across the patch. The free patch of membrane reversibly alters both its contact angle and radius of curvature on pressure changes. The assumption that an adhesive force between the membrane and the pipette can sustain normal tension up to a maximum Ta at the edge of the free patch accounts for the observed mechanical responses. When the normal component of the pressure-induced membrane tension exceeds Ta membrane at the contact point between the free patch and the lipid-glass interface is pulled away from the pipette wall, resulting in a decreased radius of curvature for the patch and an increased contact angle. Measurements of the membrane radius of curvature as a function of the suction pressure and pipette radius determine line adhesion tensions Ta which range from 0.5 to 4.0 dyn/cm. Similar behavior of patch-clamped cell membranes implies similar adhesion mechanics. | [
"Opsahl, L R",
"Webb, W W"
] | Lipid-glass adhesion in giga-sealed patch-clamped membranes. |
The four-way DNA (Holliday) junction is an important postulated intermediate in the process of genetic recombination. Earlier studies have suggested that the junction exists in two alternative conformations, depending upon the salt concentration present. At high salt concentrations the junction folds into a stacked X structure, while at low salt concentrations the data indicate an extended unstacked conformation. The stereochemical conformation of the four-way DNA junction at low salt (low alkali ion concentration and no alkaline earth ions) was established by comparing the efficiency of fluorescence resonance energy transfer (FRET) between donor and acceptor molecules attached pairwise in three permutations to the 5' termini of the duplex arms. A new variation of FRET was implemented based upon a systematic variation of the fraction of donor labeled single strands. The FRET results indicate that the structure of the four-way DNA junction at low salt exists as an unstacked, extended, square arrangement of the four duplex arms. The donor titration measurements made in the presence of magnesium ions clearly show the folding of the junction into the X stacked structure. In addition, the FRET efficiency can be measured. The fluorescence anisotropy of the acceptor in the presence of Mg2+ during donor titrations was also measured; the FRET efficiency can be calculated from the anisotropy data and the results are consistent with the folded, stacked X structure. | [
"Clegg, R M",
"Murchie, A I",
"Lilley, D M"
] | The solution structure of the four-way DNA junction at low-salt conditions: a fluorescence resonance energy transfer analysis. |
We expressed the skeletal muscle chloride channel, ClC-1, in HEK293 cells and investigated it with the patch-clamp technique. Macroscopic properties are similar to those obtained after expression in Xenopus oocytes, except that faster gating kinetics are observed in mammalian cells. Nonstationary noise analysis revealed that both rat and human ClC-1 have a low single channel conductance of about 1 pS. This finding may explain the lack of single-channel data for chloride channels from skeletal muscle despite its high macroscopic chloride conductance. | [
"Pusch, M",
"Steinmeyer, K",
"Jentsch, T J"
] | Low single channel conductance of the major skeletal muscle chloride channel, ClC-1. |
Quantitative patch-clamp analysis based on dwell-time histograms has to deal with the problem of missed events. The correction of the evaluated time constants has to take into account the characteristics of the detector used for the reconstruction of the time series. In previous approaches a simple model of the detector has been used, which is based on the assumption that all events shorter than the temporal resolution tres were missed, irrespective of the preceding events. Rather than the standard assumption of a fixed dead time, we introduce a more realistic model of a detector by a continuous-time version of the Hinkley detector. The combined state of the channel and the detector obeys a Markov model, which is governed by a Fokker-Planck-Kolmogorov partial differential equation. The steady-state solution leads to the determination of the apparent time constants tau o and tau c depending on the true rate constants koc and kco and the temporal resolution tres of the detector. Simulations with different kinds of detectors, including the Bessel filter with half-amplitude threshold detection, are performed. They show that our new equation predicts the dependence of tau c and tau o on koc, kco, and tres better than the standard equation used until now. | [
"Draber, S",
"Schultze, R"
] | Correction for missed events based on a realistic model of a detector. |
Forces acting on the S4 segments of the channel, the voltage-sensing structures, are analyzed. The conformational change in the Na channel is modeled as a helix-coil transition in the four S4 segments, coupled to the membrane voltage by electrical forces. In the model, repulsions between like charges make the S4 segment unstable, but field-dependent forces hold it in an alpha-helix configuration at resting potential. At threshold depolarization, the S4 helices cooperatively expand into random coils, breaking the hydrogen bonds connecting adjacent loops of the alpha helices. Exposed electron pairs left on the carbonyl oxygens constitute sites at which cations can bind selectively. The first hydrogen bond to break is at the channel exterior, then the second breaks, and so on in a zipper-like motion along the entire segment. The Na+ ions hop from one site to the next until all H bonds are broken and all sites are filled with ions. This completes the pathway over which the permeant ions move through the channel, driven by the electrochemical potential difference across the membrane. This microscopic mechanism is consistent with the thermodynamic explanation of ion-channel gating previously formulated as the ferroelectric-superionic transition hypothesis. | [
"Leuchtag, H R"
] | Long-range interactions, voltage sensitivity, and ion conduction in S4 segments of excitable channels. |
Differential scanning calorimetric (DSC) studies of the glassy states of as-received and hydrated lysozyme, hemoglobin, and myoglobin powders, with water contents of < or = 0.25, < or = 0.30, and < or = 0.29 g/g of protein, show that their heat capacity slowly increases with increasing temperature, without showing an abrupt increase characteristic of glass-->liquid transition. Annealing (also referred to as physical aging) of the hydrated proteins causes their DSC scans to show an endothermic region, similar to an overshoot, immediately above the annealing temperature. This annealing effect appears at all temperatures between approximately 150 and 300 K. The area under these peaks increases with increasing annealing time at a fixed temperature. The effects are attributed to the presence of a large number of local structures in which macromolecular segments diffuse at different time scales over a broad range. The lowest time scale corresponds to the > N-H and -O-H group motions which become kinetically unfrozen at approximately 150-170 K on heating at a rate of 30 K min-1 and which have a relaxation time of 5-10 s in this temperature range. The annealing effects confirm that the individual glass transition of the relaxing local regions is spread over a temperature range up to the denaturation temperature region of the proteins. The interpretation is supported by simulation of DSC scans in which the distribution of relaxation times is assumed to be exceptionally broad and in which annealing done at several temperatures over a wide range produces endothermic effects (or regions of DSC scans) qualitatively similar to those observed for the hydrated proteins. | [
"Sartor, G",
"Mayer, E",
"Johari, G P"
] | Calorimetric studies of the kinetic unfreezing of molecular motions in hydrated lysozyme, hemoglobin, and myoglobin. |
We have decorated F-actin with Fab fragments of antibodies to actin residues 1-7. These antibody fragments do not strongly affect the rigor binding of myosin S-1 to actin, but do affect the binding of S-1 to actin in the presence of nucleotide (DasGupta, G., and E. Reisler, 1989. J. Mol. Biol. 207:833-836; 1991. Biochemistry. 30:9961-9966; 1992. Biochemistry. 31:1836-1841). Although the binding constant is rather low, we estimate that we have achieved about 85% occupancy of the actin sites. Three-dimensional reconstructions from electron micrographs of both negatively stained and frozen-hydrated filaments show that the Fab fragment is bound at the location of the NH2 terminus in the model of Holmes et al. (Holmes, K.C., D. Popp, W. Gebhard, and W. Kabsch. 1990. Nature. 347:37-44) for F-actin, excluding very different orientations of the actin subunit in the filament. Most of the mass of the antibody is not visualized, which is due to the large mobility of the NH2 terminus in F-actin, differences in binding angle within the polyclonal antibody population, or a combination of both of these possibilities. | [
"Orlova, A",
"Yu, X",
"Egelman, E H"
] | Three-dimensional reconstruction of a co-complex of F-actin with antibody Fab fragments to actin's NH2 terminus. |
For inorganic crystals such as calcite (CaCO3), Atomic Force Microscopy (AFM) has provided surface structure at atomic resolution (Ohnesorge and Binnig, 1993). As part of a broad effort to obtain high resolution for an individual protein or protein assembly (Binnig et al., 1986; Rugar and Hansma, 1990; Radmacher et al., 1992), we applied AFM to study the ATP-dependent double hexamer of SV40 large T antigen, which assembles around the viral origin of DNA replication. Multimeric mass has been determined in two-dimensional projected images by Scanning Transmission Electron Microscopy (STEM) (Mastrangelo et al., 1989). By AFM, if the DNA-protein preparation has been stained positively by uranyl acetate, the contour at the junction between hexamers is visible as a cleft, 2-4 nm deep. The cleft, whether determined as a fraction of height by AFM or as a fraction of mass thickness by STEM, is of comparable magnitude. On either side of the cleft, hexamers attain a maximum height of 13-16 nm. Monomers found in the absence of ATP show heights of 5-7 nm. Taken together, the z coordinates provide a surface profile of complete and partial replication assemblies consistent with the spatial distribution of recognition pentanucleotides on the DNA, and they contribute direct geometrical evidence for a ring-like hexamer structure. | [
"Mastrangelo, I A",
"Bezanilla, M",
"Hansma, P K",
"Hough, P V",
"Hansma, H G"
] | Structures of large T antigen at the origin of SV40 DNA replication by atomic force microscopy. |
We used digital calcium imaging with Fura-2 in conjunction with the tight-seal whole-cell patch clamp technique to describe a novel cation conductance in olfactory neurons of the clawed toad Xenopus laevis. Substitution of extracellular Ca2+ and Na+ was used as a tool to change [Ca2+]i. When [Ca2+]i was increased to about 450 nM, a conductance gcat activated that was permeable for cations. Upon gcat activation, an increase in [Ca2+]i occurred in the dendritic knob. Once activated, gcat showed no further dependence upon [Ca2+]i. Icat is shown to be different from the current activated by a mixture of the odorants citralva and amyl acetate. We conclude that there are two different cation conductances in the peripheral compartments of olfactory neurons in X. laevis. | [
"Schild, D",
"Lischka, F W"
] | Amiloride-insensitive cation conductance in Xenopus laevis olfactory neurons: a combined patch clamp and calcium imaging analysis. |
This paper presents a Monte Carlo simulation (MCS) method for estimating the parameters that characterize ligand-receptor binding directly from experimentally derived binding isotherms. Binding parameters are estimated by incorporating an MCS algorithm for ligand binding to a two-dimensional receptor array into a nonlinear regression program. The MCS method was tested by analyzing experimental isotherms of avidin binding to biotinylated lipid in Langmuir-Blodgett (LB) monolayers. The MCS-derived cooperativity coefficients and intrinsic association constants for avidin-biotin binding to LB films are correlated strongly (R2 > 0.93) with the binding parameters determined from the same experimental data by a thermodynamic equilibrium binding model (Zhao et al. 1993. Langmuir. 9:3166-3173). This result shows MCS to be an accurate and potentially more versatile method for characterizing biomolecular interactions at surfaces. | [
"Zhao, S",
"Reichert, W M"
] | Analysis of protein binding to receptor-doped lipid monolayers by Monte Carlo simulation. |
A differential equation model with a polynuclear growth mechanism was formulated for a theoretical understanding of protein crystallization. The model equation contains two parameters characterizing nucleation and growth: the number of protein molecules constituting a critical nucleus and the order of growth kinetics. This model was applied successfully to explain the experimental data on the protein concentration changes due to nucleation and crystal growth of tetragonal and orthorhombic hen egg-white lysozyme. It was shown that the critical nucleus most probably consists of three or four molecules. The range and extent of the validity of the present model and analysis are discussed. | [
"Bessho, Y",
"Ataka, M",
"Asai, M",
"Katsura, T"
] | Analysis of the crystallization kinetics of lysozyme using a model with polynuclear growth mechanism. |
Fixed negative charges in many cation channels raise the single-channel conductance, apparently by an electrostatic mechanism: their effects are accentuated in solutions of low ionic strength and attenuated at high ionic strength. The charges of specific amino acids near the ends of the proposed pore-lining M2 segment of the nicotinic acetylcholine receptor, termed the extracellular and cytoplasmic rings, have recently been shown to influence the single-channel K+ conductance (Imoto, K., C. Busch, B. Sakmann, M. Mishina, T. Konno, J. Nakai, H. Bujo, Y. Mori, K. Fukuda and S. Numa. 1988. Nature 335:645-648). We examined whether these charges might act by a direct electrostatic effect on the energy of ions in the pore, rather than indirectly by inducing a structural change. To this end, we measured the conductances of charge mutants over a range of K+ concentrations (ionic strengths). As expected, we found that negative charge mutations raise the conductance, and positive charge mutations lower it. The effects of cytoplasmic-ring mutations are accentuated at low ionic strength, but they are not completely attenuated at high ionic strength. The effects of extracellular-ring mutations are independent of ionic strength. These results are inconsistent with the simplest electrostatic model. We suggest a modified model that qualitatively accounts for the data. | [
"Kienker, P",
"Tomaselli, G",
"Jurman, M",
"Yellen, G"
] | Conductance mutations of the nicotinic acetylcholine receptor do not act by a simple electrostatic mechanism. |
A method for the rational design of locally encoded amino acid sequence features using artificial neural networks and a technique for simulating molecular evolution has been developed. De novo in machine design of Escherichia coli leader peptidase (SP1) cleavage sites serves as an example application. A modular neural network system that employs sequence descriptions in terms of physicochemical properties has been trained on the recognition of characteristic cleavage site features. It is used for sequence qualification in the design cycle, representing the sequence fitness function. Starting from a random sequence several cleavage site sequences were generated by a simulated molecular evolution technique. It is based on a simple genetic algorithm that takes the quality values calculated by the artificial neural network as a heuristic for inductive sequence optimization. Simulated in vivo mutation and selection allows the identification of predominant sequence positions in Escherichia coli signal peptide cleavage site regions (positions -2 and -6). Various amino acid distance maps are used to define metrics for the step size of mutations. Position-specific mutability values indicate sequence positions exposed to high or low selection pressure in the simulations. The use of several distance maps leads to different courses of optimization and to various idealized sequences. It is concluded that amino acid distances are context dependent. Furthermore, a method for identification of local optima during sequence optimization is presented. | [
"Schneider, G",
"Wrede, P"
] | The rational design of amino acid sequences by artificial neural networks and simulated molecular evolution: de novo design of an idealized leader peptidase cleavage site. |
Alamethicin and its analogs from cation selective, multi-conductance channels in lipid bilayers. The conductance levels have been thought to be due to a barrel-stave structure where conducting pores (barrels) are formed by the self-assembly of a variable number of alpha-helical rods (staves). The conductance transitions were then interpreted as the addition or deletion of peptide monomers from the pore-forming complex (Sansom, M.S. 1991. Prog. Biophys. Mol. Biol. 55:139-235). Initially, pore conductances were calculated from that expected of right circular cylinders of "bulk" electrolyte. More recent theories also included the access resistance of the electrolyte outside the pore. However, they all consistently overestimated the observed conductances. The reason for the discrepancy is presented here. Previous theories ignored the effects of ion concentration gradients near the pore. Hence, they only held in the limit of small bilayer potentials (< 25 mV) and so would overestimate measurements that typically used much larger potentials (> 100 mV). This theoretical flaw is corrected by using Läuger's theory of diffusion-limited ion flow (Läuger, P. 1976. Biochim. Biophys. Acta. 455:493-509). Thus, including the effects of ion concentration gradients results in a considerable improvement in predicting pore conductances. It is found that: 1) the effects of ion concentration gradients must be included in the barrel-stave model for it to apply to the available data; 2) previously published explanations for the discrepancy between the model and the data, namely the "distorted bundle" and the "head-to-tail aggregate" hypotheses are not necessary (reviewed by Sansom, 1991). | [
"Laver, D R"
] | The barrel-stave model as applied to alamethicin and its analogs reevaluated. |
Bovine brain phosphatidylserine (BBPS) vesicles were prepared with traces of dioleoylglycerol (18:1, 18:1 DAG) or hexadecane (HD) to determine the influence of changes in headgroup or acyl chain packing on divalent cation-induced lipid mixing rates. A stopped-flow apparatus was used to combine vesicles with 3 mM Ca2+ or Ba2+. Aggregation was monitored by light scattering and lipid mixing by lipid probe dilution. Neither 3-6 mol% 18:1, 18:1 DAG nor up to 10 mol % HD significantly altered the BBPS chain melting temperature, vesicle diameter, or vesicle aggregation rates. Lipid mixing rates doubled by adding either 3 mol % 18:1, 18:1 DAG or 6 mol % HD to BBPS with no change in the Ca2+ concentration threshold. The Arrhenius slopes of the lipid mixing rates for control, 3 mol % 18:1, 18:1 DAG, and 6 mol % HD vesicles were identical. 2H-nuclear magnetic resonance spectra of perdeuterated dipalmitoylglycerol and HD in BBPS in the absence and presence of Ca2+ and Ba2+ showed that the solutes occupied different time-averaged positions in the bilayer under each condition. These data suggest that: 1) the enhanced lipid mixing rate is related to the volume of the added alkyl chains; 2) 18:1, 18:1 DAG and HD may alter the activation entropy or the attempt frequency at one or more steps in the lipid mixing process; 3) 18:1, 18:1 DAG and HD are likely to act at a different spatial or temporal point than the divalent cation; and 4) it is unlikely that the effect of these solutes on lipid mixing is due to their equilibrium time-averaged positions in the bilayer. Others have shown that apolar lipids accelerate fusion in nonbilayer phase-forming systems, but BBPS does not form these phases under these conditions. Therefore, we propose that the effect of very small amounts of apolar substances may be very general, e.g., stabilizing the hydrophobic interstices associated with a variety of proposed intermediate structures. | [
"Walter, A",
"Yeagle, P L",
"Siegel, D P"
] | Diacylglycerol and hexadecane increase divalent cation-induced lipid mixing rates between phosphatidylserine large unilamellar vesicles. |
A neutral area surface can be defined as one whose area remains fixed upon bending. It is assumed that such a surface exists within the amphiphilic monolayers that constitute the bicontinuous cubic mesophases and that it parallels approximately the highly convoluted polar/apolar interface in such systems. Here, we report on how the neutral area surface in the cubic phase (space group Ia3d) of the hydrated monoacylglycerol, monoolein, was determined. It is located at a distance of approximately 8.8 A from the methyl terminus of the acyl chain. At 25 degrees C, the surface area per lipid molecule at the neutral area surface is 35.1 +/- 0.2 A2, which is remarkably similar to the mean cross-sectional area of hydrated monoolein in the lamellar liquid crystalline phase at this same temperature. | [
"Chung, H",
"Caffrey, M"
] | The neutral area surface of the cubic mesophase: location and properties. |
The combined effects of the diacylglycerols (DAGs) with the various acyl chains and Ca2+ on the structure of phosphatidylcholine/phosphatidylserine (4:1 mole/mole) bilayers were studied using 2H- and 31P NMR. The following DAG- and Ca(2+)-induced bilayer perturbations were identified. 1) Increased tendency to form nonbilayer lipid phases was induced by diolein or stearoylarachidonoylglycerol, and was synergistically enhanced by the addition of Ca2+. 2) "Transverse" bilayer perturbation was induced by dioctanoylglycerol. The addition of this DAG caused increased ordering of the phospholipid acyl side chains in the region adjacent to the headgroup, with the concomitant decrease of the order toward the bilayer interior. 3) Separation of the phosphatidylcholine and phosphatidylserine bilayer components was induced by combinations of relatively high (1:5 mole/mole to phosphatidylserine) Ca2+ and 25 mol% (to the phospholipids) of diolein, stearoylarachidonoylglycerol, or oleoylacetylglycerol. 4) Lateral phase separation of the bilayers on the regions of different fluidities was induced by dipalmitin. These physicochemical effects were correlated with the effects of these DAGs and Ca2+ on the activity of protein kinase C. The increased tendency to form nonbilayer lipid phases and the transverse bilayer perturbations correlated with the increased protein kinase C activity, whereas the actual presence of the nonbilayer lipid phases, as well as the separation of the phosphatidylcholine and phosphatidylserine components, was associated with the decrease in the protein kinase C activity. The lateral phase separation of the bilayer on gel-like and liquid crystalline regions did not have an effect on the activity of the enzyme. These results demonstrate the importance of the physicochemical properties of the membranes in the process of activation of protein kinase C. | [
"Goldberg, E M",
"Lester, D S",
"Borchardt, D B",
"Zidovetzki, R"
] | Effects of diacylglycerols and Ca2+ on structure of phosphatidylcholine/phosphatidylserine bilayers. |
In normal lateral diffusion, the mean-square displacement of the diffusing species is proportional to time. But in disordered systems anomalous diffusion may occur, in which the mean-square displacement is proportional to some other power of time. In the presence of moderate concentrations of obstacles, diffusion is anomalous over short distances and normal over long distances. Monte Carlo calculations are used to characterize anomalous diffusion for obstacle concentrations between zero and the percolation threshold. As the obstacle concentration approaches the percolation threshold, diffusion becomes more anomalous over longer distances; the anomalous diffusion exponent and the crossover length both increase. The crossover length and time show whether anomalous diffusion can be observed in a given experiment. | [
"Saxton, M J"
] | Anomalous diffusion due to obstacles: a Monte Carlo study. |
The lamellar/inverted hexagonal (L alpha/HII) phase transition can be very fast, despite the drastic change in the topology of the lipid/water interfaces. The first structures to form in this transition may be similar to those that mediate membrane fusion in many lipid systems. To study the transition mechanism and other dynamic phenomena in membrane dispersions, we constructed an apparatus to rapidly trigger the transition and then vitrify the specimens to preserve the structure of transient intermediates. The apparatus applies millisecond-long temperature jumps of variable size to aqueous dispersions of lipids on electron microscope grids at times 9-16 ms before specimen vitrification. The vitrified specimens are then examined by cryo-transmission electron microscopy. Dispersions of egg phosphatidylethanolamine completed the transition within 9 ms when superheated by 20 K. Similar transition times have been observed in dioleoylphosphatidylethanolamine via time-resolved x-ray diffraction. N-monomethylated dioleoylphosphatidylethanolamine dispersions superheated to lesser extent exhibited slower transitions and more complex morphology. The structure of the first intermediates to form in the transition process could not be determined, probably because the intermediates are labile on the time scale of sample cooling and vitrification (< 1 ms) and because of the poor contrast developed by some of these small structures. However, the results are more compatible with a transition mechanism based on "stalk" intermediates than a mechanism involving inverted micellar intermediates. Temperature-jump cryo-transmission electron microscopy should be useful in studying dynamic phenomena in biomembranes, large protein complexes, and other colloidal dispersions. It should be especially helpful in studying the mechanism of protein-induced membrane fusion. | [
"Siegel, D P",
"Green, W J",
"Talmon, Y"
] | The mechanism of lamellar-to-inverted hexagonal phase transitions: a study using temperature-jump cryo-electron microscopy. |
Kinetic modeling of the exciton migration in the cyanobacterial photosystem I core complex from Synechococcus sp. was performed by an exact solution of the Pauli master equation for exciton motion. A square two-dimensional 10 x 10 pigment lattice and a Förster dipole-dipole coupling between chromophores was assumed. We calculated decay-associated spectra and lifetimes and compared them to the corresponding experimental data from picosecond fluorescence and transient absorption obtained by global analysis. Seven spectral chlorophyll(Chl) forms, identical in shape but shifted in their absorption maximums, were used to describe the non-homogeneous broadening of the PS I-100 particle absorption spectrum. The optimized Chl lattice arrangement best reproducing the experimental decay-associated spectra as well as the steady-state fluorescence spectrum indicated the long-wavelength-absorbing Chls forming a cluster in the corner of the lattice with the reaction center (RC) placed apart at a distance of two lattice constants. The variable parameters, i.e., the charge separation rate in the RC and the lattice constant a, were found to be optimal at kRC = 2.3 ps-1 and a = 1.14 nm, respectively. The surprising conclusions of the simulations is that Chls with absorption maxima as long a 724 nm have to be taken into account to describe the time-resolved spectra of this PS I particle properly. The dependencies of the exciton decay in the model PS I particle on the excitation wavelength and on the temperature are discussed. We also show that the excited state decay of similar PS I particles that lack the long-wavelength absorbing Chls is nearly mono-exponential. Various critical factors that limit the general reliability of the conclusions of such simulations are discussed in detail. | [
"Trinkunas, G",
"Holzwarth, A R"
] | Kinetic modeling of exciton migration in photosynthetic systems. 2. Simulations of excitation dynamics in two-dimensional photosystem I core antenna/reaction center complexes. |
A model is presented that connects the underlying classical thermal transport coefficients to the experimentally determined vibrational temperature of a photoexcited chromophore embedded in a protein matrix that is surrounded by water. Both photo-stationary state heating (e.g., within a 10-ns laser pulse) and transient cooling (e.g., after termination of the laser pulse) are treated. Because only a few thermal transport parameters can be experimentally determined, this simple model provides a practical and efficient method for describing the temperatures of the chromophore, protein, and solvent as functions of time and position. We expect that such a model will be useful in interfacing experimental observations with more elaborate molecular dynamics calculations, which depend upon many variables. In the transient cooling process, which is relevant for ultrafast pulsed laser measurements, the temperature of the chromophore follows a double exponential decay at short times, whereas at longer times the thermal decay "rolls over" to a diffusion limit (t-3/2). For typical 10-ns laser pulses (approximately 0.5 GW/cm2) and chromophore absorption cross-sections (approximately 10(-16) cm2), we find that the biomolecule reaches thermal steady-state on a ps time scale. The role of the various thermal transport coefficients and their independent experimental determination is also discussed. | [
"Li, P",
"Champion, P M"
] | Investigations of the thermal response of laser-excited biomolecules. |
The kinetics of excitation energy transfer and electron transfer processes within the membrane of Heliobacillus mobilis were investigated using femtosecond transient absorption difference spectroscopy at room temperature. The kinetics in the 725- to 865-nm region, upon excitation at 590 and 670 nm, were fit using global analysis. The fits returned three kinetic components with lifetimes of 1-2 ps and 27-30 ps, and a component that does not decay within several nanoseconds. The 1- to 2-ps component is attributed to excitation equilibration to form a thermally relaxed excited state. The 27- to 30-ps phase corresponds to the decay of the relaxed excited state to form a charge-separated state. The intrinsic energy and electron transfer rates were estimated using the experimental results and theoretical models for excitation migration and trapping dynamics. Taking into account the number of antenna pigments and their spectral distribution, an upper limit of 1.2 ps for the intrinsic time constant for charge separation in the reaction center is calculated. This upper limit corresponds with the trapping-limited case for excitation migration and trapping. Reduction of the primary electron acceptor A0 was observed in the 640 to 700 nm region using excitation at 780 nm. An instantaneous absorbance increase followed by a decay of about 30 ps was observed over a broad wavelength region due to the excited state absorption and decay of BChl g molecules in the antenna. In addition, a narrow bleaching band centered at 670 nm grows in with an apparent time constant of about 1.0 ps, superimposed on the 30-ps absorbance increase due to excited state absorption. Measurements on a longer time scale showed that besides the 670 nm pigment a BChl g molecule absorbing near 785 nm may be involved in the primary charge separation, and that this pigment may be in equilibrium with the 670 nm pigment. The bleaching bands at 670 nm and 785nm recovered with a time constant of about 600 ps, due to forward electron transport to a secondary electron acceptor. Energy and electron transfer properties of H. mobilis membranes are compared with Photosystem 1, to which the heliobacteria bear an evolutionary relationship. | [
"Lin, S",
"Chiou, H C",
"Kleinherenbrink, F A",
"Blankenship, R E"
] | Time-resolved spectroscopy of energy and electron transfer processes in the photosynthetic bacterium Heliobacillus mobilis. |
Previous fluorescence studies of horseradish peroxidase conjugated with protoporphyrin IX suggested that the protein behaved hydrodynamically as a prolate ellipsoid of axial ratio 3 to 1. The present study, designed to further investigate the hydrodynamics of this protein, exploits a series of probes, noncovalently bound to the heme binding site of apo-horseradish peroxidase, having different orientations of the excitation and emission transition dipoles with respect to the protein's rotational axes. The probes utilized included protoporphyrin IX and the naphthalene probes 1-anilino-8-naphthalene sulfonate, 2-p-toluidinyl-6-naphthalene sulfonate, and 4,4'-bis(1-anilino-8-naphthalene sulfonate). Time-resolved data were obtained using multifrequency phase fluorometry. The global analysis approach to the determination of molecular shape using multiple probes was evaluated by utilizing all data sets while maintaining a constant molecular shape for the protein. The results indicated that, in such analyses, probes exhibiting a single exponential decay and limited local motion have the major weight in the evaluation of the axial ratio. Probes that show complex decay patterns and local motions, such as the naphthalene derivatives, give rise to significant uncertainties in such global treatments. By explicitly accounting for the effect of such local motion, however, the shape of the protein can be reliably recovered. | [
"Brunet, J E",
"Vargas, V",
"Gratton, E",
"Jameson, D M"
] | Hydrodynamics of horseradish peroxidase revealed by global analysis of multiple fluorescence probes. |
On-lattice simulations of two-dimensional self-avoiding chains subject to homogeneous intramolecular attractive interactions were performed as a model for studying various density regimes in globular proteins. For short chains of less than 15 units, all conformations were generated and classified by density. The range of intramolecular interactions was found to increase uniformly with density, and the average number of topological contacts is directly proportional to density. The uniform interaction energy increases the probability of high density states but does not necessarily lead to dominance of the highest density state. Typically, several large peaks appear in the probability distribution of packing densities, their location and amplitude being determined by the balance between entropic effects enhancing more expanded conformations and attractive interactions favoring compact forms. Also, the homogeneous interaction energy affects the distribution of most probable interacting points in favor of the longer range interactions over the short range ones, but in addition it introduces some more detailed preferences even among short range interactions. There are some implications about the characteristics of the intermediate density states and also for the likelihood that the native state does not correspond completely to the lowest energy conformation. | [
"Bahar, I",
"Jernigan, R L"
] | Stabilization of intermediate density states in globular proteins by homogeneous intramolecular attractive interactions. |
The role played by non-homogeneous interactions in stabilizing cooperative structural changes in proteins was investigated by exhaustive simulations of all compact conformations compatible with several well-defined globule-like shapes in three dimensions. Conformational free energies corresponding to the association of residues i and j were computed both for the unperturbed system, all subject to identical intramolecular interactions, and for the perturbed system in which a single pair of residues is probed by changing its interactions with an attractive or repulsive interaction. The high packing density leads to strong coupling between residues so that specific interactions between a given pair of residues are accompanied by considerable enthalpy changes. Relatively weak, about 1-2 kcal/mol, attractive interactions can exert a dramatic effect on the free energy distribution. Usually, central positions in the sequence most affect the conformational characteristics. Some of these interaction pairs appear to be capable of effecting major conformation transitions because of the high level of cooperativity in the dense state. Effects of repulsive interactions, however, do not depend so strongly on residue pair and cause more localized structural changes. This approach can suggest more, or less, sensitive loci for amino acid substitution. | [
"Bahar, I",
"Jernigan, R L"
] | Cooperative structural transitions induced by non-homogeneous intramolecular interactions in compact globular proteins. |
This article discusses several strategies for the use steady-state and time-resolved fluorescence methods to monitor unfolding transitions in proteins. The assumptions and limitations of several methods are discussed. Simulations are presented to show that certain fluorescence observables directly track the population of states in an unfolding transition, whereas other observables skew the transition toward the dominant fluorescing species. Several examples are given, involving the unfolding of Staphylococcal aureus nuclease A, in which thermodynamic information is obtained for the temperature and denaturant induced transitions in this protein. | [
"Eftink, M R"
] | The use of fluorescence methods to monitor unfolding transitions in proteins. |
Concentration correlation spectroscopy allows the assessment of molecular motions in complex systems. The technique generally monitors concentration fluctuations by means of some method such as the intensity of fluorescent molecules (fluorescence correlation spectroscopy). We describe here the use of scanning confocal laser microscopy to measure correlation functions in both space and time. This methodology offers two major advantages over conventional methods. First, collecting data from different regions of the sample significantly increases the signal-to-noise ratio. Second, molecular motions of colloidal gold can be analyzed by correlation methods with high temporal and spatial resolution. Using a MRC 600 laser scanning system, we collect data from an ensemble of 768 independent subvolumes and determine the space-time correlation function. We demonstrate the technique using two different types of samples, fluorescently labeled DNA molecules in solution and colloidal gold-tagged lipids in a planar bilayer. This approach, which we term "scanning concentration correlation spectroscopy," provides a straightforward means of performing high resolution correlation analysis of molecular motions with available instrumentation. | [
"Koppel, D E",
"Morgan, F",
"Cowan, A E",
"Carson, J H"
] | Scanning concentration correlation spectroscopy using the confocal laser microscope. |
The mucosal immune system actively transports large quantities of antibodies into all mucus secretions, and these secreted antibodies help prevent infectious entry of many pathogens. Mucus is generally thought to protect epithelial cells by forming a diffusional barrier through which only small molecules can pass. However, electron microscopy indicates that the pore size in mucus is approximately 100 nm, which suggests that antibodies as well as other large molecules might also diffuse through mucus. We measured the diffusion coefficients for antibodies and other proteins within human midcycle cervical mucus using two techniques: fluorescence imaging of concentration profiles and fluorescence photobleaching recovery. The two techniques are complementary, since the rates of diffusion are observed over millimeter distances with fluorescence imaging of concentration profiles and micron distances with fluorescence photobleaching recovery. Both methods yielded essentially the same diffusion coefficients. In contrast to previous reports indicating mucus significantly impedes diffusion of small molecules, antibody diffusion in mucus was relatively unimpeded. In our observations IgG, IgG fragments, IgA, and IgM diffused almost as rapidly in cervical mucus as in water (1.0 > Dmucus/Dwater > 0.7). Simple models for diffusion through water-filled pores suggest that the hydrodynamic pore size for cervical mucus is approximately 100 nm, smaller than the approximately 1000 nm pore size of a collagen gel (at 1 mg/ml) and larger than the approximately 10 nm pore size of gelatin (at 100 mg/ml). This estimated pore size is consistent both with electron micrographs and geometric models of interfiber spacing. Based on these results, we predict that particles as large as viruses can diffuse rapidly through human midcycle cervical mucus, provided the particle forms no adhesive interactions with mucus glycoproteins. | [
"Saltzman, W M",
"Radomsky, M L",
"Whaley, K J",
"Cone, R A"
] | Antibody diffusion in human cervical mucus. |
We describe a multidimensional spectrometer that is capable of (nearly) simultaneous measurement of circular dichroism, steady-state fluorescence, and absorbance values on the same sample in a standard 1 x 1 cm cuvette. With a computer controlled thermoelectric cell holder, this instrument is capable of measuring the above types of spectral data at various wavelengths as a function of temperature. We have developed software to control the various acquisition functions and to convert the data files to a format appropriate for use with the nonlinear least squares program, NONLIN (Johnson and Frasier, 1985). We have tested various features of this instrument and we have applied this instrument and data analysis procedure to study the thermal unfolding of ribonuclease A, under conditions were the unfolding of this protein involves an intermediate state. | [
"Ramsay, G",
"Eftink, M R"
] | A multidimensional spectrophotometer for monitoring thermal unfolding transitions of macromolecules. |
A hypothesis of the nature of intracellular ice formation is proposed in which the osmotically driven water efflux that occurs in cells during freezing (caused by the increased osmotic pressure of the extracellular solution in the presence of ice) is viewed as the agent responsible for producing a rupture of the plasma membrane, thus allowing extracellular ice to propagate into the cytoplasm. This hypothesis is developed into a mathematical framework and the forces that are present during freezing are compared to the forces which are required to rupture membranes in circumstances unrelated to low temperatures. The theory is then applied to systems which have been previously studied to test implications of the theory on the nature of intracellular ice formation. The pressure that develops during freezing due to water flux is found to be sufficient to cause a rupture of the plasma membrane and the theory gives an accurate description of the phenomenology of intracellular ice formation. | [
"Muldrew, K",
"McGann, L E"
] | The osmotic rupture hypothesis of intracellular freezing injury. |
The conceptual advances introduced by recent discoveries in the field of active transport have triggered a transition from a "black box" approach to a "mechanistic" approach. At present, treating this subject in the graduate setting requires consideration of equilibrium and kinetic experimentation, protein chemistry, mutational analysis and molecular structure, with the aim of defining the "transport machine." | [
"Inesi, G"
] | Teaching active transport at the turn of the twenty-first century: recent discoveries and conceptual changes. |
A mean-field statistical mechanical theory has been developed to describe molecular distributions in interphases. The excluded volume interaction has been modeled in terms of a reversible work that is required to create a cavity of the solute size against a pressure tensor exerted by the surrounding interphase molecules. The free energy change associated with this compression process includes the configuration entropy as well as the change in conformational energy of the surrounding chain molecules. The lateral pressure profile in a model lipid bilayer (30.5 A2/chain molecule) has been calculated as a function of depth in the bilayer interior by molecular dynamics simulation. The lateral pressure has a plateau value of 309 +/- 48 bar in the highly ordered region and decreases abruptly in the center of the bilayer. Model calculations have shown that for solute molecules with ellipsoidal symmetry, the orientational order increases with the ratio of the long to short molecular axes at a given solute volume and increases with solute volume at a given axial ratio, in accordance with recent experimental data. Increased lateral pressure (p perpendicular) results in higher local order and exclusion of solute from the interphase, in parallel with the effect of surface density on the partitioning and local order. The logarithm of the interphase/water partition coefficient for spherical solutes decreases linearly with solute volume. This is also an excellent approximation for elongated solutes because of the relatively weak dependence of solute partitioning on molecular shape. The slope is equal to (2p perpendicular - p parallel)/3KBT, where p parallel is the normal pressure component, and different from that predicted by the mean-field lattice theory. Finally, the lattice theory has been extended herein to incorporate an additional constraint on chain packing in the interphase and to account for the effect of solute size on partitioning. | [
"Xiang, T X",
"Anderson, B D"
] | Molecular distributions in interphases: statistical mechanical theory combined with molecular dynamics simulation of a model lipid bilayer. |
The temperature-composition phase diagram of monomyristolein in water was constructed using x-ray diffraction. Low- and wide-angle diffraction patterns were collected from samples of fixed hydration as a function of temperature in the heating direction on x-ray-sensitive film and/or image plates. The phases identified in the system include the lamellar crystalline phase, the lamellar liquid crystalline phase, the fluid isotropic phase, and two inverted cubic phases. Particular attention has been devoted to the issues of phase equilibrium and phase boundary verification. Cubic phase undercooling was examined by adjusting the temperature of several samples in the cubic phase to a value where the lamellar liquid crystalline phase represents equilibrium behavior. Cooling-induced structure and phase changes were monitored continuously over a 30-min period by recording low-angle diffraction patterns from the samples using a streak camera. The cubic-to-lamellar transition rate decreased with increasing sample hydration. Additionally, the transition proceeded more rapidly at an incubation temperature of 25 degrees C compared to that at 0 degrees C. A mechanism is proposed that accounts for the hydration and temperature sensitivity of the phase transition under nonequilibrium conditions. | [
"Briggs, J",
"Caffrey, M"
] | The temperature-composition phase diagram of monomyristolein in water: equilibrium and metastability aspects. |
It has been suggested for several years that reactions between ligands and cell surface receptors can be speeded up by nonspecific adsorption of the ligand to the cell surface followed by two-dimensional surface diffusion to the receptor, a mechanism referred to as "reduction-of-dimensionality" (RD) rate enhancement. Most of the theoretical treatments of this and related problems have assumed that the receptor is an irreversibly absorbing perfect sink. Such receptors induce a depletion zone of ligand probability density around themselves. The reaction rate in this case (called "diffusion-limited") is limited only by the time required for ligands to diffuse through this depletion zone. In some cases, however, the receptor may be far from "perfect" such that a collision with a ligand only rarely leads to binding. Receptors then do not create significant local depletion zones of ligand probability density, and the reaction rate becomes strongly affected by the (small) probability of reaction success per diffusive encounter (the "reaction-limited" case). This article presents a simple theory of RD rate enhancement for reaction-limited receptors that are either reversible or irreversible binders. In contrast to the diffusion-limited theories, the reaction-limited theory presented here: (a) differs quantitatively from diffusion-limited models; (b) is simple and algebraic in closed form; (c) exhibits significant rate enhancement in some realistic cases; (d) depends strongly on the actual Brownian rather than pure diffusive nature of the ligand's motion; (e) depends (for irreversibly binding receptors only) on the kinetic rates (not just equilibria) of reversible adsorption to nontarget regions, in contrast to some previous approximate theories of reduction of dimensionality; and (f) is applicable to actual ligand/receptor systems with binding success probabilities at the opposite extreme from the perfect sink/diffusion-limited models. | [
"Axelrod, D",
"Wang, M D"
] | Reduction-of-dimensionality kinetics at reaction-limited cell surface receptors. |
Solutions for transients in arbitrarily branching passive cable neurone models with a soma are extended to models with nonuniform electrical parameters and multiple dendritic shunts. The response to an injected current can again be represented as an infinite series of exponentially decaying components with system time constants obtained from the roots of a recursive transcendental equation. The reciprocity relations and global parameter dependencies are the same as for uniform models. Infinitely many "raw" electro-morphological models map onto a given "core" electrotonic model; local as well as global raw parameter trade-offs are now possible. The solutions are illustrated by means of biologically relevant examples: (i) the effects of nonuniform electrical parameters in a two-cylinder + soma cortical pyramidal cell model, (ii) the errors that can occur when uniformity is incorrectly assumed in a single cylinder model, (iii) nonsumming interactions between cells and electrodes that can dramatically increase the duration of the effective capacitative electrode artefact, and (iv) shunting inhibition and double impalements in a hippocampal CA1 pyramidal cell "cartoon" representation. These solutions should complement compartmental modelling techniques. | [
"Major, G",
"Evans, J D"
] | Solutions for transients in arbitrarily branching cables: IV. Nonuniform electrical parameters. |
Molecular dynamics simulations of oxidized and reduced Clostridium beijerinckii flavodoxin in water have been performed in a sphere of 1.4-nm radius surrounded by a restrained shell of 0.8 nm. The flavin binding site, comprising the active site of the flavodoxin, was in the center of the sphere. No explicit information about protein-bound water molecules was included. An analysis is made of the motional characteristics of residues located in the active site. Positional fluctuations, hydrogen bonding patterns, dihedral angle transitions, solvent behavior, and time-dependent correlations are examined. The 375-ps trajectories show that both oxidized and reduced protein-bound flavins are immobilized within the protein matrix, in agreement with earlier obtained time-resolved fluorescence anisotropy data. The calculated time-correlated behavior of the tryptophan residues reveals significant picosecond mobility of the tryptophan side chain located close to the reduced isoalloxazine part of the flavin. | [
"Leenders, R",
"van Gunsteren, W F",
"Berendsen, H J",
"Visser, A J"
] | Molecular dynamics simulations of oxidized and reduced Clostridium beijerinckii flavodoxin. |
Site-directed mutagenesis was used to mutate alpha Cys418 and beta Cys447 in the M4 domain of Torpedo californica acetylcholine receptor expressed in Xenopus laevis oocytes. The M4 region is a transmembrane domain thought to be located at the lipid-protein interface. By whole-cell voltage clamp analysis, mutation of both alpha subunits to alpha Trp418 increased maximal channel activity approximately threefold, increased the desensitization rate compared with wild-type receptor, and shifted the EC50 for acetylcholine from 32 microM to 13 microM. Patch measurements of single-channel currents revealed that the alpha Trp418 increased channel open times approximately 28-fold at 13 degrees C with no effect on channel conductance. All of our measured functional changes in the alpha Trp418 mutant are consistent with a simple kinetic model of the acetylcholine receptor in which only the channel closing rate is altered by the mutation. Our results show that changes in protein structure at the putative lipid-protein interface can dramatically affect receptor function. | [
"Lee, Y H",
"Li, L",
"Lasalde, J",
"Rojas, L",
"McNamee, M",
"Ortiz-Miranda, S I",
"Pappone, P"
] | Mutations in the M4 domain of Torpedo californica acetylcholine receptor dramatically alter ion channel function. |
Mammalian heart sodium channels inserted into planar bilayers exhibit a distinctive subconductance state when single batrachotoxin-modified channels are exposed to external Zn2+. The current-voltage behavior of the open state and the Zn(2+)-induced substate was characterized in the presence of symmetrical Na+ ranging from 2 to 3000 mM. The unitary conductance of the open state follows a biphasic dependence on [Na+] that can be accounted for by a 3-barrier-2-site model of Na+ permeation that includes double occupancy and Na(+)-Na+ repulsion. The unitary conductance of the Zn2+ substate follows a monophasic dependence on [Na+] that can be explained by a similar 3-barrier-2-site model with low affinity for Na+ and single occupancy due to repulsive interaction with a Zn2+ ion bound near the external entrance to the pore. The apparent association rate of Zn2+ derived from dwell-time analysis of flickering events is strongly reduced as [Na+] is raised from 50 to 500 mM. The apparent dissociation rate of Zn2+ is also enhanced as [Na+] is increased. While not excluding surface charge effects, such behavior is consistent with two types of ion-ion interactions: 1) A competitive binding interaction between Zn2+ and Na+ due to mutual competition for high affinity sites in close proximity. 2) A noncompetitive, destabilizing interaction resulting from simultaneous occupancy by Zn2+ and Na+. The repulsive influence of Zn2+ on Na+ binding in the cardiac Na+ channel is similar to that which has been proposed to occur between Ca2+ and Na+ in structurally related calcium channels. Based on recent mutagenesis data, a schematic model of functionally important residues in the external cation binding sites of calcium channels and cardiac sodium channels is proposed. In this model, the Zn(2+)-induced subconductance state results from Zn2+ binding to a site in the external vestibule that is close to the entrance of the pore but does not occlude it. | [
"Schild, L",
"Moczydlowski, E"
] | Permeation of Na+ through open and Zn(2+)-occupied conductance states of cardiac sodium channels modified by batrachotoxin: exploring ion-ion interactions in a multi-ion channel. |
Fluorescence dipolar resonance energy transfer between a receptor-bound fluorescent agonist, dansyl-C6-choline, and two membrane-partitioned fluorescent probes, C18-rhodamine and C12-eosin, was used to measure the transverse distance between the acetylcholine (ACh) binding sites on the intact Torpedo nicotinic acetylcholine receptor (nAChR) and the surface of the lipid membrane. Control experiments demonstrated that: (1) dansyl-C6-choline binds to cobra-alpha-toxin sensitive sites on the nAChR with a KD approximately 20 nM, (2) the quantum yield of dansyl-C6-choline increases 3.1-fold upon binding, and (3) the receptor-bound dansyl-C6-choline fluorescence is stable for at least 2 h. The calculated transverse distances between receptor-bound dansyl-C6-choline and the membrane-partitioned acceptors, C12-eosin and C18-rhodamine, were 31 and 39 A, respectively. Therefore, given the dimensions of the extracellular domain of the receptor, the ACh binding sites are located significantly below (approximately 25 A) the extracellular apex of the nAChR. These results are in agreement with the recent proposed location for the ACh binding sites in a pocket within each of the two alpha-subunits, approximately 30 A above the membrane surface (Unwin, N. (1993) J. Mol. Biol. 229: 1101-1124). | [
"Valenzuela, C F",
"Weign, P",
"Yguerabide, J",
"Johnson, D A"
] | Transverse distance between the membrane and the agonist binding sites on the Torpedo acetylcholine receptor: a fluorescence study. |
In a previous publication (Shaklai et al., 1977a) the present author developed a theory for evaluating proximity relations and surface densities sigma in biological membranes by measurements of excitation energy transfer from a donor attached to a specific site of a membrane protein and an acceptor attached to a specific carbon on a membrane lipid. It was assumed that the protein and lipid are randomly distributed in the plane of the membrane and that the donor and acceptor groups are confined to different planes in the membrane separated by a distance Rp. In this article several aspects of the theory presented in the previous paper are clarified, especially noting that the previous theoretical expressions for the time-dependent and steady state fluorescence intensities assumed that the labeled protein molecule is cylindrically symmetric with the symmetry axis perpendicular to the plane of the membrane and that the donor is positioned on the symmetry axis of the protein. This assumption is also implicitly or explicitly made in subsequent formulations by other investigators. In this article we generalize the theory to include the case where the donor is not on the symmetry axis of the labeled protein. Equations for calculating the time-dependent and steady state fluorescence intensities for this more general case are presented, and methods for applying these theoretical expressions to the analysis of steady state fluorescence intensity data and evaluation of proximity parameters are discussed. It is also shown in this article that the linear relation l/lo = 1 + Kq sigma previously derived for simple analysis of excitation transfer data for the condition rc/Ro 1 can be modified to apply to almost all practical ranges of rc/Ro without much affecting its simplicity in the analysis of experimental data. | [
"Yguerabide, J"
] | Theory for establishing proximity relations in biological membranes by excitation energy transfer measurements. |
We investigated whether the cysteine residues in Shaker potassium (K+) channels are essential for activation and inactivation gating or for modulation of activation gating by external zinc (Zn2+). Mutants of the Shaker K+ channel were prepared in which all seven cysteine residues were replaced (C-less). These changes were made in both wild-type Shaker H4 channels and in a deletion mutant (delta 6-46) lacking N-type ("fast") inactivation. Replacement of all cysteines left most functional properties of the K+ currents unaltered. The most noticeable difference between the C-less and wild-type currents was the faster C-type inactivation of the C-less channel which could be attributed largely to the mutation of Cys462. This is consistent with the effects of previously reported mutations of nearby residues in the S6 region. There were also small changes in the activation gating of C-less currents. Modulation by external Zn2+ of the voltage dependence and rate of activation gating is preserved in the C-less channels, indicating that none of the cysteines in the Shaker K+ channel plays an important role in Zn2+ modulation. | [
"Boland, L M",
"Jurman, M E",
"Yellen, G"
] | Cysteines in the Shaker K+ channel are not essential for channel activity or zinc modulation. |
An improved voltage clamp with a double vaseline gap chamber was designed to study electroporated skeletal muscle fibers. The new clamp eliminated spike overshock of membrane potential when applying step stimulation occurring in the traditional configuration. It allowed greater consistency in membrane potential distribution. After the intracellular resistances of the fiber segment at the vaseline gap area were compensated, it was possible to change membrane potential more quickly. Using this technique, strong electrical pulses used to mimic the situation of electrical shock can be delivered to the cell membrane by voltage clamp. Transmembrane currents of skeletal muscle cell were simultaneously measured during a high pulsed shock and resolved into different components. Distinct transient changes of the transmembrane current, involving the time courses of the formation of electroporation and their recovery time constants, can be recorded. Because of more even membrane potential distribution and faster response to pulsed membrane potential change, this technique is also suitable for membrane study under physiological conditions. | [
"Chen, W",
"Lee, R C"
] | An improved double vaseline gap voltage clamp to study electroporated skeletal muscle fibers. |
The changes in transmembrane potential during a stimulation pulse in the heart are not known. We have used transmembrane potential sensitive dye fluorescence to measure changes in transmembrane potential along fibers in an anisotropic arterially perfused rabbit epicardial layer. Cathodal or anodal extracellular point stimulation produced changes in transmembrane potential within 60 microns of the electrode that were positive or negative, respectively. The changes in transmembrane potential did not simply decrease to zero with increasing distance, as would occur with a theoretical fiber space constant, but instead became reversed beyond approximately 1 mm from the electrode consistent with a virtual electrode effect. Even stimulation from a line of terminals perpendicular to the fibers produced negative changes in transmembrane potential for cathodal stimulation with the largest negative changes during a 50-ms pulse at 3-4 mm from the electrode terminals. Negative changes as large as the amplitude of the action potential rising phase occurred during a 50-ms pulse for 20-volt cathodal stimulation. Switching to anodal stimulation reversed the directions of changes in transmembrane potential at most recording spots, however for stimulation during the refractory period negative changes in transmembrane potential were significantly larger than positive changes in transmembrane potential. Anodal stimulation during diastole with 3-ms pulses produced excitation in the region of depolarization that accelerated when the stimulation strength was increased to > 3 times the anodal threshold strength. Thus, virtual electrode effects of unipolar stimulation occur in myocardial fibers, and for sufficiently strong stimuli the virtual electrode effects may influence electrical behavior of the myocardium. | [
"Knisley, S B",
"Hill, B C",
"Ideker, R E"
] | Virtual electrode effects in myocardial fibers. |
Interaction of large unilamellar vesicle (LUV) of dipalmitoylphosphatidylcholine (DPPC) with ethanol was investigated by the excimer method developed by Yamazaki et al. (Yamazaki, M., M. Miyazu, and T. Asano. 1992. Biochim. Biophys. Acta. 1106:94-98) and the high-resolution electron cryomicroscope with a new cryostage (top-entry superfluid stage) (HiRECM) developed by Fujiyoshi, Y. et al. (Fujiyoshi, Y., T. Mizusaki, K. Morikawa, H. Aoki, H. Kihara, and Y. Harada. 1991. Ultramicroscopy. 38:241-251). The excimer method is based on the fact that the ratio of excimer to monomer fluorescence intensity (E/M) of pyrene PC is lowered in the membrane in the interdigitated gel structure (L beta I), because structural restriction of L beta I structure largely decreases collisions of pyrene rings of the pyrene PCs in the membrane. E/M of pyrene PC in DPPC LUV decreased largely at high concentrations of ethanol, which indicated the induction of L beta I structures in DPPC LUV. Frozen-hydrated DPPC LUVs in a vitreous ice were observed at 4K with HiRECM, and these images were characterized by a pair of concentric circles. The membrane thickness of DPPC LUV which was estimated from the distance between the two concentric lines decreased largely at high concentration of ethanol. The mean value of membrane thickness of the LUV in the absence of ethanol was 3.8 nm, while at 15% (w/v) ethanol was 3.0 nm. These values were almost same as those obtained from the electron density profile of DPPC MLV by the x-ray diffraction analysis in each structures, L beta' and L beta I structures, respectively. These results indicated directly the induction of L beta 1 structure in DPPC LUV at high concentration of ethanol. | [
"Yamazaki, M",
"Miyazu, M",
"Asano, T",
"Yuba, A",
"Kume, N"
] | Direct evidence of induction of interdigitated gel structure in large unilamellar vesicles of dipalmitoylphosphatidylcholine by ethanol: studies by excimer method and high-resolution electron cryomicroscopy. |
We have investigated the thermotropic phase behavior of aqueous dispersions of the 1,2- and 2,3-di-O-tetradecyl-1(3)-O-(beta-D-galactopyranosyl)-sn- glycerols and their diastereomeric mixture using differential scanning calorimetry and low-angle and wide-angle x-ray diffraction. Upon heating, unannealed aqueous dispersions of these compounds all exhibit a lower temperature, moderately energetic phase transition at approximately 52 degrees C and a higher temperature, weakly energetic phase transition at approximately 63 degrees C, both of which are reversible on cooling. X-ray diffraction measurements identify these events as the L beta (or L' beta)/L alpha and L alpha/HII phase transitions, respectively. The structures of the L beta, L alpha, and HII phases of these lipids, as determined by x-ray diffraction measurements, are identical within the error bars for all of these lipids. On annealing below the L beta/L alpha phase transition temperature, the L beta phase converts to an Lc phase at a rate which is strongly dependent on the chirality of the glycerol backbone (1,2-sn > 1,2-rac > 2,3-sn). The temperature of the phase transition from the Lc phase seen on reheating is also dependent on the glycerol chirality. In addition, the nature of the Lc phase changes on subsequent heating in the 1,2-sn and 1,2-rac lipids, but we have not been able to detect this Lc1/Lc2 phase transition by calorimetry. However, wide-angle x-ray diffraction measurements indicate that these Lc phases differ mostly in their hydrocarbon chain packing modes. The Lc2 phase does not appear to be present in the 2,3-sn compound, suggesting that its formation is not favored in this diastereomeric isomer. These observations are discussed in relation to the effect of glycerol chirality on the molecular packing of these glycolipids, particularly on hydrogen bonding and hydration in the interfacial region of the bilayer. | [
"Mannock, D A",
"McElhaney, R N",
"Harper, P E",
"Gruner, S M"
] | Differential scanning calorimetry and X-ray diffraction studies of the thermotropic phase behavior of the diastereomeric di-tetradecyl-beta-D-galactosyl glycerols and their mixture. |
We have investigated the comparative effects of the incorporation of increasing quantities of androstenol and cholesterol on the thermotropic phase behavior of aqueous dispersions of members of a homologous series of linear saturated diacyl PCs1 using high sensitivity DSC. We have also employed FTIR and 31P-NMR spectroscopy to study the comparative effects of androstenol and cholesterol incorporation on the organization of the host PC bilayer in both the gel and liquid-crystalline states. The effects of androstenol and cholesterol incorporation on the thermotropic phase behavior of shorter chain PCs like 14:0 PC are generally similar but not identical. The incorporation of either sterol progressively decreases the temperature and enthalpy, but not the cooperativity, of the pretransition and completely abolishes it at sterol concentrations above 5 mol%. Moreover, at sterol concentrations of 1 to 20-25 mol%, both androstenol and cholesterol incorporation produce DSC endotherms consisting of superimposed sharp and broad components, the former due to the hydrocarbon chain melting of sterol-poor and the latter to the melting of sterol-rich 14:0 PC domains. The temperature and cooperativity of the sharp component are reduced slightly with increasing concentration of androstenol or cholesterol, and the enthalpy of the sharp component decreases progressively and becomes zero at 20-25 mol% sterol. As well, at cholesterol or androstenol concentrations above 20-25 mol%, the enthalpy of the broad component also decreases linearly with increasing sterol incorporation and becomes zero at sterol levels of about 50 mol%. However, whereas cholesterol incorporation progressively increases the temperature of the broad component of the DSC endotherm, androstenol incorporation decreases the temperature of this component. In contrast, the effects of androstenol and cholesterol incorporation on the thermotropic phase behavior of the intermediate and longer chain PCs studied here are considerably different. Although the incorporation of cholesterol increases the main phase transition temperature of 16:0 PC slightly and decreases the phase transition of 18:0 PC and 21:0 PC, androstenol incorporation decreases the main phase transition temperatures of all three PCs rather markedly. Moreover, androstenol is less effective in reducing the enthalpy and cooperativity of the broad component of the DSC endotherm of 16:0 PC and especially 18:0 PC bilayers in comparison to cholesterol. Androstenol incorporation (> 5 mol%) also results in the appearance of a second, low temperature endotherm in the DSC traces of the intermediate and longer chain PC dispersions that is not observed in similar cholesterol/PC dispersions. FTIR and 31P-NMR results suggest that this endotherm arises from a temperature-induced dissolution of androstenol in the gel phase PC bilayers. This second endotherm occurs at lower androstenol concentrations and increases in area at a given androstenol level as the chain length of the host PC bilayer increases. We ascribe the increasing immiscibility of androstenol in both the gel and liquid-crystalline states of PC bilayers of increasing thickness to an increasing degree of hydrophobic mismatch between the androstenol molecule and the host phospholipid bilayer. | [
"McMullen, T P",
"Lewis, R N",
"McElhaney, R N"
] | Comparative differential scanning calorimetric and FTIR and 31P-NMR spectroscopic studies of the effects of cholesterol and androstenol on the thermotropic phase behavior and organization of phosphatidylcholine bilayers. |
Chronocoulometry was used to characterize the fluidity and lateral diffusion coefficient of supported phospholipid bilayer assemblies. The bilayers were formed on the inner surfaces of the microporous template films of aluminum oxide on gold electrodes. The lipid monolayers were formed by adsorption and fusion of phospholipid vesicles on alkylated oxide surfaces. Octadecyltrichlorosilane (OTS) was used in the initial alkylation step. The surface concentration of the lipids in monolayer assemblies was measured by a radioactive assay method. Surface densities corresponding to 48 +/- 10 A2/molecule (DPPC) and 56 +/- 11 A2/molecule (DMPC) were obtained (for exposure times > 120 min) independent of the temperature of the vesicle's fusion (below or above chain-melting transition). Octadecylviologen (C18MV2+) was used as an electroactive probe species. Its limiting lateral diffusion coefficient in DMPC monolayers was 5 x 10(-8) cm2/s, measured as C18MV2+ mole fraction extrapolated to 0 decreasing linearly from 20 to below 1 mol%. Linear Arrhenius plots for C18MV2+ diffusion in DMPC monolayers were obtained with slopes of approximately 40 kJ/mol between 18 and 45 degrees C, demonstrating homogeneity and fluidity of the lipid monolayers. Chronocoulometry was also used to obtain lateral diffusion coefficient of ubiquinone in DMPC/OTS bilayers. A value of 1.9 x 10(-8) cm2/s at 30 degrees C was obtained. | [
"Torchut, E",
"Laval, J M",
"Bourdillon, C",
"Majda, M"
] | Electrochemical measurements of the lateral diffusion of electroactive amphiphiles in supported phospholipid monolayers. |
The effect of cholesterol on the gel, the liquid-crystalline, and mixed phospholipid phases has been studied using the fluorescence properties of 2-dimethylamino-6-lauroylnaphthalene (Laurdan). Laurdan sensitivity to the polarity and to the dynamics of its environment reveals that cholesterol affects phospholipid bilayers in the gel phase by expelling water and by increasing the amount of dipolar relaxation. In the liquid-crystalline phase, the effect of cholesterol is a reduction of both water concentration and amount of dipolar relaxation. Detailed studies of Laurdan excitation and emission spectral contours as a function of cholesterol concentration show that there are some cholesterol concentrations at which Laurdan spectral properties changes discontinuously. These peculiar cholesterol concentrations are in agreement with recent observations of other workers showing the formation of local order in the liquid-crystalline phase of phospholipids upon addition of phospholipid derivatives of pyrene. A local organization of phospholipids around cholesterol molecule seems to be produced by the presence of peculiar concentrations of cholesterol itself. This local organization is stable enough to be observed during the excited state lifetime of Laurdan of approximately 5-6 ns. | [
"Parasassi, T",
"Di Stefano, M",
"Loiero, M",
"Ravagnan, G",
"Gratton, E"
] | Cholesterol modifies water concentration and dynamics in phospholipid bilayers: a fluorescence study using Laurdan probe. |
Movement of single myosin filaments, synthesized by copolymerization of intact myosin and fluorescently labeled light meromyosin, were observed along a single actin filament suspended in solution by a dual laser trap in a fluorescence microscope. The sliding velocity of the myosin filaments was 11.0 +/- 0.2 micron/s at 27 degrees C. This is similar to that of actin moving toward the center from the tip (the physiological direction) of myosin filaments bound to a glass surface but several times larger than that in the opposite direction (Ishijima and Yanagida, 1991; Yanagida, 1993). This indicates that the movement of myosin filaments is dominated by the myosin heads on one side of the myosin filament, which are correctly oriented relative to the actin filament. The incorrectly oriented myosin heads on the other side do not interfere with the fast movement. The step size (displacement produced during one ATPase cycle) of correctly oriented myosin was estimated from the minimum number of myosin heads necessary to produce the maximum velocity. This was determined by measuring the velocities of various lengths of myosin filaments. The minimum length of the myosin filaments moving near the maximum velocity was 0.30-0.40 microns, which contains 20 +/- 5 correctly oriented myosin heads. This number leads to a myosin step size of 71 +/- 22 nm. This value probably represents the lower limit, because all of the myosin heads on the filament would not always interact with the actin filament. Thus, the myosin step size is considerably larger than the length of a power stroke expected from the physical size of a myosin head, 10-20 nm (Huxley, 1957, 1969). | [
"Saito, K",
"Aoki, T",
"Aoki, T",
"Yanagida, T"
] | Movement of single myosin filaments and myosin step size on an actin filament suspended in solution by a laser trap. |
We describe a model that relates the maximum shortening velocity of a muscle fiber, Vm, to the kinetics of the dissociation of a myosin head from actin. At Vm, the positive work exerted by cross-bridges attached in the powerstroke must be balanced by cross-bridges that have been carried by movement of the filaments into a region where they exert a negative force. This balance allows one to relate Vm and the rate of cross-bridge detachment. Studies of actomyosin kinetics suggest that at high substrate, detachment should be limited by a slow protein isomerization (approximately 50 s-1) that precedes ADP release. This rate is too slow to be easily accommodated in existing models. However, a slow rate for cross-bridge dissociation, similar to that of the isomerization, is predicted if previous models are modified to include rapid detachment of cross-bridges that have been carried so far into the negative force region that their free energy exceeds that of the detached state. The model also explains another aspect of muscle contraction: at high shortening velocities, the observed rate of ATP hydrolysis is low, because a cross-bridge can interact with multiple actin binding sites before releasing the hydrolysis products and binding another ATP. | [
"Cooke, R",
"White, H",
"Pate, E"
] | A model of the release of myosin heads from actin in rapidly contracting muscle fibers. |
A model of oxygen transport in perfused myocardial tissue is presented. Steady-state conditions are assumed in order to mimic the metabolic rate of the arrested heart. The model incorporates Michaelis-Menten dependence of mitochondrial oxygen consumption, oxymyoglobin saturation and oxyhemoglobin saturation on oxygen partial pressure (PO2). The transport equations model both the advective supply of oxygen via the coronary circulation and the diffusive exchange of oxygen between tissues and environment across the epicardial and endocardial surfaces. The left ventricle is approximated by an axisymmetric prolate spheroid and the transport equations solved numerically using finite element techniques. Solution yields the PO2 profile across the heart wall. Integration of this profile yields the simulated rate of metabolic oxygen uptake determined according to the Fick principle. Correction for the diffusive flux of oxygen across the surfaces yields the simulated true metabolic rate of oxygen consumption. Simulated values of oxygen uptake are compared with those measured experimentally according to the Fick principle, using saline-perfused, Langendorff-circulated, K(+)-arrested, guinea pig hearts. Four perfusion variables were manipulated: arterial PO2, environmental PO2, coronary flow and perfusion pressure. In each case agreement between simulated and experimentally determined rates of oxygen consumption gives confidence that the model adequately describes the advective and diffusive transport of oxygen in the isolated, arrested, saline-perfused heart. | [
"Mawson, D A",
"Hunter, P J",
"Kenwright, D N",
"Loiselle, D S"
] | Oxygen exchange in the isolated, arrested guinea pig heart: theoretical and experimental observations. |
To evaluate the contributions of cross-linker dynamics and polymer deformation to the frequency-dependent stiffness of actin filament gels, we compared the rheological properties of actin gels with three types of cross-linkers: a weak one, Acanthamoeba alpha-actinin (dissociation rate constant 5.2 s-1, association rate constant 1.1 x 10(6) M-1 s-1); a strong one, chicken smooth muscle alpha-actinin (dissociation rate constant 0.66 s-1, association rate constant 1.20 x 10(6) M-1 s-1); and an extremely strong one, biotin/avidin (dissociation rate constant approximately zero). The biotin/avidin cross-linked gel, whose behavior is determined by polymer bending alone, behaves like a solid and shows no frequency dependence. The amoeba alpha-actinin cross-linked gel behaves like a viscoelastic fluid, and the frequency dependence of the stiffness can be explained by a mathematical model for dynamically cross-linked gels. The stiffness of the chicken alpha-actinin cross-linked gel is independent of frequency, and has viscoelastic properties intermediate between the two. The two alpha-actinins have similar association rate constants for binding to actin filaments, consistent with a diffusion-limited reaction. Rigid cross-links make the gel stiff, but make it elastic without the ability to deform permanently. Dynamically cross-linked actin filaments should allow the cell to react passively to various outside forces without any sort of signaling. Slower, signal-mediated pathways, such as severing filaments or changing the affinity of cross-linkers, could alter the nature of these passive reactions. | [
"Wachsstock, D H",
"Schwarz, W H",
"Pollard, T D"
] | Cross-linker dynamics determine the mechanical properties of actin gels. |
Highly oriented calf-thymus MgDNA fibers, prepared by a wet spinning method, were studied with a simple mechanochemical set-up. The relative fiber length, L/Lo, was measured with the fibers submerged in ethanol-water solutions. In one type of experiment L/Lo was measured as a function of ethanol concentration at room temperature. No substantial decrease in L/Lo with increasing ethanol concentration was observed, indicating that MgDNA fibers stay in the B form even when the water activity is very low. For low ethanol concentrations the fiber structure is stable and does not dissolve even at very high water activities. In a second type of experiment, the heat-induced helix-coil transition was manifested by a marked contraction of the fibers. The transition temperature decreases linearly with increasing ethanol concentration between 52 and 68% ethanol. At higher ethanol concentrations the helix-coil transition temperature increases due to strong aggregation within the DNA fibers, and above 77% ethanol the fibers do not contract at all, not even at the upper temperature limit of the experiments, approximately 80 degrees C. This behavior is discussed with reference to dried DNA and the P form of DNA. The helix-coil transition temperature of the MgDNA fibers in 70% ethanol does not show any dependence on the MgCl2 concentration. It is shown that the Poisson-Boltzmann cylindrical cell model can account qualitatively for this lack of salt dependence. | [
"Schultz, J",
"Rupprecht, A",
"Song, Z",
"Piskur, J",
"Nordenskiöld, L",
"Lahajnar, G"
] | A mechanochemical study of MgDNA fibers in ethanol-water solutions. |
We calculate room temperature thermal fluctuational base pair opening probability of a daunomycin-poly d(GCAT).poly d(ATGC) complex. This system is constructed at an atomic level of detail based on x-ray analysis of a crystal structure. The base pair opening probabilities are calculated from a modified self-consistent phonon approach of anharmonic lattice dynamics theory. We find that daunomycin binding substantially enhances the thermal stability of one of the base pairs adjacent the drug because of strong hydrogen bonding between the drug and the base. The possible effect of this enhanced stability on the drug inhibition of DNA transcription and replication is discussed. We also calculate the probability of drug dissociation from the helix based on the selfconsistent calculation of the probability of the disruption of drug-base H-bonds and the unstacking probability of the drug. The calculations can be used to determine the equilibrium drug binding constant which is found to be in good agreement with observations on similar daunomycin-DNA systems. | [
"Chen, Y Z",
"Prohofsky, E W"
] | Premelting base pair opening probability and drug binding constant of a daunomycin-poly d(GCAT).poly d(ATGC) complex. |
We discuss the requirement of type II DNA topoisomerase in the process of mitotic chromosome condensation. Using a known model describing the collapse of homopolymers, we propose that the compaction process necessitates a change in the topological state (i.e., a self-knotting) of the chromosomal chain. We argue that the enzymes are necessary to reach the compact metaphase state in a time interval that is much smaller than the time expected in the uncatalyzed process. The folding process is such that the potential entanglement points are localized at particular regions of the chromosome known as the scaffold-associated regions. The concentration of entanglements in the metaphase chromosome is related to the average size of the radial loops. A phantom chain model for the condensation process, in which each potential entanglement point is dealt with by a topoisomerase II molecule, is proposed. | [
"Sikorav, J L",
"Jannink, G"
] | Kinetics of chromosome condensation in the presence of topoisomerases: a phantom chain model. |
Volume changes associated with the primary photochemistry of bacteriorhodopsin (BR) were measured by temperature-dependent laser-induced optoacoustic spectroscopy (LIOAS). Excitation was performed with 8-ns flashes establishing a photoequilibrium between the BR and the K states (BR<-->hvK). The concentration of K at the end of the laser pulse, which is an important parameter for the calculation of the volume change per molecule from the LIOAS data, was determined by flash photolysis with optical detection under the specific conditions (concentration, photon density) of the LIOAS experiment. Temperature-dependent measurements yielded a linear dependency of the ratio of the optoacoustic signals for BR and for a calorimetric reference (CoCl2) with the cubic thermal expansion coefficient beta of water. From the slope of this linear ratio a contraction of 11 cm3/mol was determined. | [
"Schulenberg, P J",
"Rohr, M",
"Gärtner, W",
"Braslavsky, S E"
] | Photoinduced volume changes associated with the early transformations of bacteriorhodopsin: a laser-induced optoacoustic spectroscopy study. |
We present computer simulations of excited state dynamics in models of PS I and PS II which are based upon known structural and spectral properties of the antennae. In particular, these models constrain the pigment binding sites to three-dimensional volumes determined from molecular properties of the antenna complexes. The simulations demonstrate that within a 10-30 ps after light absorption, rapid energy transfer among coupled antenna chlorophylls leads to a quasiequilibrium state in which the fraction of the excited state on any antenna chlorophyll, normalized to the total excited state remaining on the model, remains constant with time. We describe this quasiequilibrium state as a "transfer equilibrium" (TE) state because of its dependence on the rates of processes that couple excited state motion and quenching in the antenna as well as on the individual antenna site energies and temperature. The TE state is not a true equilibrium in that loss of the excited state primarily due to photochemistry (but also due to fluorescence, thermal emission, and intersystem crossing) continues once TE is established. Depending on the dynamics of the system, the normalized distribution of excited state at TE may differ substantially from the Boltzmann distribution (the state of the model at infinite time in the absence of any avenues for decay of excited state). The models predict lifetimes, equilibration times, and photochemical yields that are in agreement with experimental data and affirm trap-limited dynamics in both photosystems. The rapid occurrence of TE states implies that any excited state dynamics that depends on antenna structure and excitation wavelength must occur before the TE state is established. We demonstrate that the excited state distribution of the TE state is central to determining the excited state lifetime and quantum efficiency of photochemistry. | [
"Laible, P D",
"Zipfel, W",
"Owens, T G"
] | Excited state dynamics in chlorophyll-based antennae: the role of transfer equilibrium. |
We have studied diluted bovine eye lens alpha-crystallin solutions by using light scattering. The protein particles were modeled as hard spheres, showing electrostatic repulsion, due to surplus electric charges, and weak attractive interaction. The repulsive potential VR is defined by the radius of the particles, the Debye length kappa-1, and the number of charges at the Gouy layer; the attractive potential has been described by the London-van der Waals potential and is defined by the Hamaker constant A. We have used the diluted gas approximation and the one component macrofluid model to relate the experimental static factor Ki to the theoretical expression of the interaction potential V(x). This resulted in a Hamaker constant A of 0.06 +/- 0.01 KBT and an effective charge q ranging from 18 +/- 1 at low ionic strength (omega = 0.0022 M) to 50 +/- 5 at high ionic strength (omega = 0.1472 M). | [
"Xia, J Z",
"Aerts, T",
"Donceel, K",
"Clauwaert, J"
] | Light scattering by bovine alpha-crystallin proteins in solution: hydrodynamic structure and interparticle interaction. |
During patch clamp recordings, measurement of passive parameters such as access resistance (Ra), membrane resistance (Rm), and membrane capacitance (Cm) often provides useful information regarding physiological changes in the cell. In particular, an increase in capacitance may indicate vesicle fusion events as occurs during exocytosis. Rapid capacitance changes are usually measured with a phase-sensitive detector set to a phase angle that is independent of resistance changes. However, this angle changes over time and may be difficult to determine in cells with a low membrane resistance. The present paper describes a technique for rapidly measuring Ra, Rm, and Cm by simultaneously applying two harmonic frequencies and calculating the passive parameters from the resultant electrode current. Calibration and operation are independent of the compensation circuit settings that may be set to null most of the electrode current. The technique may be implemented on a standard patch clamp setup without other specialized equipment and should be particularly useful for the study of cells that have low Rm or undergo rapid changes in Ra or Rm. | [
"Donnelly, D F"
] | A novel method for rapid measurement of membrane resistance, capacitance, and access resistance. |
Stationary and nonstationary correlation-frequency analysis of heterodyne laser light scattering were utilized to make automated, on-line, objective measurements of tracheal ciliary beat frequency (CBF) in intact, anesthetized canines. The stationary correlation-frequency analysis laser light-scattering technique was used to assess the magnitude of the CBF stimulatory responses induced by aerosolized 10(-5) M fenoterol (sympathomimetic), and 10(-8) M and 10(-6) M methacholine (parasympathomimetic) delivered to the whole lungs of eight barbiturate-anesthetized beagles. The nonstationary correlation-frequency analysis laser light-scattering technique was used to measure the effect on tracheal CBF of increasing the cytosolic calcium ion concentration with a calcium ionophore, A23187. Aerosolized A23187 was delivered to the isolated tracheal lumens of eight beagle dogs in cumulative doses ranging from 10(-9)M to 10(-6) M. Administration of the ionophore synchronized the CBF with a period of 5.3 min. Dose dependencies were observed in both the time to the peak CBF stimulation and the magnitude of the stimulatory response. The magnitude of CBF stimulation was inhibited by prior administration of aerosolized nifedipine (2 mg/ml), a voltage-operated calcium channel blocker. The A23187-induced modulation period of tracheal CBF, was unchanged by nifedipine. These are the first data to demonstrate that the magnitude and periodicity of CBF are two independent coupled processes. The cooperativity of these two processes could be determined in the effectiveness of mucociliary transport. | [
"Chandra, T",
"Yeates, D B",
"Miller, I F",
"Wong, L B"
] | Stationary and nonstationary correlation-frequency analysis of heterodyne mode laser light scattering: magnitude and periodicity of canine tracheal ciliary beat frequency in vivo. |
The time-resolved anisotropy produced in polarized fluorescence photobleaching recovery experiments has been successfully used to measure rotational correlation times in a variety of biological systems, however the magnitudes of the reported initial anisotropies have been much lower than the theoretically predicted maximum values. This small time-zero anisotropy has been attributed to fluorophore motion, wobble and rotation, during the photobleaching pulse. We demonstrate that inclusion of the possibility of saturation of the fluorophore's transition from its ground state to its excited state during the photobleaching pulse leads to the prediction of reduced time-zero anisotropy. This eliminates the need to rely solely on the assumption of fluorophore motion during the photobleaching pulse as the cause of the reduced initial anisotropy. We present theoretical and experimental results which show that the initial anisotropy decreases as both the bleach pulse intensity is increased and bleach pulse duration is decreased so as to keep the total integrated bleach pulse constant. We also show theoretical and experimental results demonstrating that at high excitation intensity the effects of saturation cause the steady state fluorescence polarization to decrease. We estimate that saturation may occur using common photobleaching conditions. | [
"Hellen, E H",
"Burghardt, T P"
] | Saturation effects in polarized fluorescence photobleaching recovery and steady state fluorescence polarization. |
Pre-steady-state transient currents have been investigated in the vegetal pole of Xenopus oocytes using the open-oocyte vaseline-gap technique of Taglialatela, Toro, and Stefani (Biophysical Journal. 61:78-82, 1992). Voltage pulses 40 ms in duration were made from a holding potential of -40 mV to command potentials over the range -160 to +60 mV in increments of 20 mV. Current records (averaged 20X; sampled every 200 microseconds) in the presence of dihydroouabain (DHO) or absence of external Na+ (Nao) were subtracted from current records obtained under Na/Na exchange conditions, i.e. internally perfused with 50 mM Na+, 5 mM ATP, and 5 mM ADP (K(+)-free) and externally superfused with 100 mM Na+,K(+)-free solution. Transient currents were dependent on intracellular Na+ and nucleotides, and diminished by activation of forward pumping; they were also reduced by 10 micrograms ml-1 of oligomycin B applied to the external solution. These properties of the pre-steady state currents are consistent with the Na/K pump operating in its electroneutral Na/Na exchange mode. The voltage dependence of the DHO- and Nao-sensitive transient currents was analyzed using a pseudo two-state model in which only the rate coefficient for Nao-binding/reocclusion is voltage-dependent (Rakowski, R. F. 1993. J. Gen. Physiol. 101:117-144). The apparent valence of the charge moved during the on (zq-on) and off (zq-off) of the pulse were 0.96 +/- 0.05 and 0.95 +/- 0.05 for Nao-sensitive, and 1.10 +/- 0.07 and 0.85 +/- 0.06 for DHO-sensitive transient currents, respectively. The total amount of charge moved (Qtot) and the mid-point voltage of the charge distribution (Vq) were 230 +/- 15 pC and -56.2 +/- 5.1 mV, and 268 +/- 34 pC and -67.0 +/- 7.6 mV for Nao- and DHO-sensitive transient currents, respectively. The apparent valence (zk) and the voltage at which the forward and backward rates are equal (Vk) obtained from the relaxation rates were 0.80 +/- 0.05 and -129.3 +/- 10.0 mV, and 0.86 +/- 0.10 and -135.1 +/- 9.0 mV for the Nao- and DHO-sensitive pre-steady state currents, respectively. The values of the parameters were not statistically significantly different between the Nao- and DHO-sensitive transient currents. Excluding the first 600 microseconds after the onset of a voltage step which was not temporally resolved, transient currents showed no indication of a rising phase. These results support the idea that charge translocation occurs within an external access channel at a rate that is governed by a voltage-dependent binding/reocclusion process and a voltage-independent deocclusion/unbinding process. | [
"Holmgren, M",
"Rakowski, R F"
] | Pre-steady-state transient currents mediated by the Na/K pump in internally perfused Xenopus oocytes. |
The orientation of cholera toxin bound to its cell-surface receptor, ganglioside GM1, in a supporting lipid membrane was determined by electron microscopy of negatively stained toxin-lipid samples. Image analysis of two dimensional crystalline arrays has shown previously that the B-subunits of cholera toxin orient at the membrane surface as a pentameric ring with a central channel (Reed, R. A., J. Mattai, and G.G. Shipley. 1987. Biochemistry. 26:824-832; Ribi, H. O., D. S. Ludwig, K. L. Mercer, G. K. Schoolnik, and R. D. Kornberg. 1988. Science (Wash, DC). 239:1272-1276). We recorded images of negatively stained cholera toxin and isolated B-pentamers oriented perpendicular to the lipid surface so that the pentamer ring is viewed from the side. The pentamer dimensions, estimated from the average of 100 molecules, are approximately 60 by 30 A. Images of side views of whole cholera toxin clearly show density above the pentamer ring away from the lipid layer. On the basis of difference maps between averages of side views of whole toxin and B-pentamers, this density above the pentamer has been identified as a portion of the A-subunit. The A-subunit may also extend into the pore of the pentamer. In addition, Fab fragments from a monoclonal antibody to the A-subunit were mixed with the toxin prior to binding to GM1. Density from the Fab was localized to the region of toxin above the pentamer ring confirming the location of the A-subunit. The structure determined for the homologous heat-labile enterotoxin from Escherichia coli shows that the A-subunit lies mostly on one face of this pentamer with a small region penetrating the pentamer pore (Sixma, T. K., S. E. Pronk, K. H. Kalk, E. S. Wartna, B. A. M. van Zanten, B. Witholt,and W. G. J. Hol. 1991. Nature (Lond.). 351:371-377). The putative GM1 binding sites are located on the opposite face of the B-pentamer. Cholera toxin, therefore appears to bind to a model membrane with its GM1 binding surface adjacent to the membrane. Low resolution density maps were constructed from the x-ray coordinates of the E. coli toxin and compared with the electron microscopy-derived maps. | [
"Cabral-Lilly, D",
"Sosinsky, G E",
"Reed, R A",
"McDermott, M R",
"Shipley, G G"
] | Orientation of cholera toxin bound to model membranes. |
Exploiting the optical sectioning capabilities of laser scanning confocal microscopy and using parameter-specific fluorescent probes, we determined the distribution of pH, free Ca2+, electrical potential, and volume inside cultured adult rabbit cardiac myocytes during ATP depletion and reductive stress with cyanide and 2-deoxyglucose ("chemical hypoxia"). During normoxic incubations, myocytes exhibited a cytosolic pH of 7.1 and a mitochondrial pH of 8.0 (delta pH = 0.9 units). Sarcolemmal membrane potential (delta psi) was -80 mV, and mitochondrial delta psi was as high as -100 mV, yielding a mitochondrial protonmotive force (delta p) of -155 mV (delta P = delta psi - 60 delta pH). After 30 min of chemical hypoxia, mitochondrial delta pH decreased to 0.5 pH units, but mitochondrial delta psi remained essentially unchanged. By 40 min, delta pH was collapsed, and mitochondrial and cytosolic free Ca2+ began to increase. Mitochondrial and sarcolemmal delta psi remained high. as Ca2+ rose, myocytes shortened, hypercontracted, and blebbed with a 30% decrease of cell volume. After hypercontraction, extensive mitochondrial Ca2+ loading occurred. After another few minutes, mitochondrial depolarized completely and released their load of Ca2+. After many more minutes, the sarcolemmal permeability barrier broke down, and viability was lost. These studies demonstrate a sequence of subcellular ionic and electrical changes that may underlie the progression to irreversible hypoxic injury. | [
"Chacon, E",
"Reece, J M",
"Nieminen, A L",
"Zahrebelski, G",
"Herman, B",
"Lemasters, J J"
] | Distribution of electrical potential, pH, free Ca2+, and volume inside cultured adult rabbit cardiac myocytes during chemical hypoxia: a multiparameter digitized confocal microscopic study. |
Directly measured forces between DNA helices in ordered arrays have been reduced to simple force coefficients and mathematical expressions for the interactions between pairs of molecules. The tabulated force parameters and mathematical expressions can be applied to parallel molecules or, by transformation, to skewed molecules of variable separation and mutual angle. This "toolbox" of intermolecular forces is intended for use in modelling molecular interactions, assembly, and conformation. The coefficients characterizing both the exponential hydration and the electrostatic interactions depend strongly on the univalent counterion species in solution, but are only weakly sensitive to anion type and temperature (from 5 to 50 degrees C). Interaction coefficients for the exponentially varying hydration force seen at spacings less than 10 to 15 A between surfaces are extracted directly from pressure versus interaxial distance curves. Electrostatic interactions are only observed at larger spacings and are always coupled with configurational fluctuation forces that result in observed exponential decay lengths that are twice the expected Debye-Huckel length. The extraction of electrostatic force parameters relies on a theoretical expression describing steric forces of molecules "colliding" through soft exponentially varying direct interactions. | [
"Podgornik, R",
"Rau, D C",
"Parsegian, V A"
] | Parametrization of direct and soft steric-undulatory forces between DNA double helical polyelectrolytes in solutions of several different anions and cations. |
GABAA receptor function was studied in outside-out patches from guinea pig hippocampal neurons using a drug application system with an exchange time of under 1.5 ms. Application of GABA to these patches induced a Cl- conductance that desensitized with prolonged exposure. Increasing GABA concentrations induced larger conductance increases that were associated with more complex patterns of desensitization. Smaller GABA responses desensitized with monophasic kinetics, whereas large responses displayed bi- and triphasic kinetics. Desensitization of the response to 1 mM GABA was triphasic in about 70% of the patches (tau = 15.4, 207, and 1370 ms) and biphasic in about 30% of the patches (tau = 44 and 725 ms). All phases of desensitization reversed at the Cl- equilibrium potential. Over the concentration range from 3 microM to 3 mM, both the rate and the extent of desensitization increased; however, complete desensitization was rarely observed. The increase in desensitization rate was due to an increase in the relative contribution of the faster phases with increasing GABA. The time constants of the three phases were independent of concentration. The different phases are not mediated by separate receptor populations, because double pulse experiments demonstrated interconversion among the fastest phase and the two slower phases. We demonstrate the plausibility of a model in which multiphasic desensitization is a consequence of the faster association rate at higher GABA concentrations. | [
"Celentano, J J",
"Wong, R K"
] | Multiphasic desensitization of the GABAA receptor in outside-out patches. |
The interaction of myelin basic protein (MBP) with zinc and phosphate ions has been studied by using the emission properties of the single tryptophan residue of the protein (Trp-115). The studies have been carried out by means of both static and time-resolved fluorescence techniques. The addition of either zinc to MBP in the presence of phosphate or phosphate to MBP in the presence of zinc resulted in an increase of fluorescence intensity and a blue shift of the emission maximum wavelength. Furthermore, a concomitant increase in the scattering was also detected. Anisotropy decay experiments demonstrated that these effects are due to the formation of MBP molecules into large aggregates. A possible physiological role for such interaction is discussed. | [
"Cavatorta, P",
"Giovanelli, S",
"Bobba, A",
"Riccio, P",
"Szabo, A G",
"Quagliariello, E"
] | Myelin basic protein interaction with zinc and phosphate: fluorescence studies on the water-soluble form of the protein. |
The pH dependence of the two-dimensional 1H nuclear magnetic resonance spectra of hen and turkey egg-white lysozymes has been recorded over the pH range 1-7. By monitoring the chemical shifts of the resonances of the various protons of ionizable residues, individual pKa values for the acidic residues have been determined for both proteins. The pKa values are displaced, with the exception of those of the residues in the active site cleft, by an average of 1 unit to low pH compared to model compounds. | [
"Bartik, K",
"Redfield, C",
"Dobson, C M"
] | Measurement of the individual pKa values of acidic residues of hen and turkey lysozymes by two-dimensional 1H NMR. |
The structural dynamics of bovine erythrocyte Cu, Zn superoxide dismutase (BSOD) was studied by time-resolved fluorescence spectroscopy. BSOD is a homodimer containing a single tyrosine residue (and no tryptophan) per subunit. Frequency-domain fluorometry revealed a heterogeneous fluorescence decay that could be described with a Lorentzian distribution of lifetimes. The lifetime distribution parameters (center and width) were markedly dependent on temperature. The distribution center (average lifetime) displayed Arrhenius behavior with an Ea of 4.2 kcal/mol, in contrast with an Ea of 7.4 kcal/mol for the single-exponential decay of L-tyrosine. This indicated that thermal quenching of tyrosine emission was not solely responsible for the effect of temperature on the lifetimes of BSOD. The distribution width was broad (1 ns at 8 degrees C) and decreased significantly at higher temperatures. Furthermore, the width of the lifetime distribution increased in parallel to increasing viscosity of the medium. The combined effects of temperature and viscosity on the fluorescence decay suggest the existence of multiple conformational substrates in BSOD that interconvert during the excited-state lifetime. Denaturation of BSOD by guanidine hydrochloride produced an increase in the lifetime distribution width, indicating a larger number of conformations probed by the tyrosine residue in the denatured state. The rotational mobility of the tyrosine in BSOD was also investigated. Analysis of fluorescence anisotropy decay data enabled resolution of two rotational correlation times. One correlation time corresponded to a fast (picosecond) rotation that contributed 62% of the anisotropy decay and likely reported local mobility of the tyrosine ring. The longer correlation time was 50% of the expected value for rotation of the whole (dimeric) BSOD molecule and appeared to reflect segmental motions in the protein in addition to overall tumbling. Comparison between rotational correlation times and fluorescence lifetimes of BSOD indicates that the heterogeneity in lifetimes does not arise from mobility of the tyrosine per se, but rather from dynamics of the protein matrix surrounding this residue which affect its fluorescence decay. | [
"Ferreira, S T",
"Stella, L",
"Gratton, E"
] | Conformational dynamics of bovine Cu, Zn superoxide dismutase revealed by time-resolved fluorescence spectroscopy of the single tyrosine residue. |
Phosphorylated cystic fibrosis transmembrane conductance regulator (CFTR) Cl- channels require nucleoside triphosphates, such as ATP, to open. As the concentration of intracellular ATP increases, the probability of the channel being open (Po) increases. To better understand how ATP regulates the channel, we studied excised inside-out membrane patches that contained single, phosphorylated CFTR Cl- channels and examined the kinetics of gating at different concentrations of ATP. As the ATP concentration increased from 0.1 to 3 mM the mean closed time decreased, but mean open time did not change. Analysis of the data using histograms of open- and closed-state durations, the maximum likelihood method, and the log-likelihood ratio test suggested that channel behavior could be described by a model containing one open and two closed states (C1<==>C2<==>O). ATP regulated phosphorylated channels at the transition between the closed states C1 and C2: as the concentration of ATP increased, the rate of transition from C1 to C2 (C1-->C2) increased. In contrast, transitions from C2 to C1 and between C2 and the open state (O) were not significantly altered by ATP. Addition of ADP in the presence of ATP decreased the transition rate from C1 to C2 without affecting other transition rates. These data suggest that ATP regulates CFTR Cl- channels through an interaction that increases the rate of transition from the closed state to a bursting state in which the channel flickers back and forth between an open and a closed state (C2). This transition may reflect ATP binding or perhaps a step subsequent to binding. | [
"Winter, M C",
"Sheppard, D N",
"Carson, M R",
"Welsh, M J"
] | Effect of ATP concentration on CFTR Cl- channels: a kinetic analysis of channel regulation. |
Electrical measurements were carried out on planar lipid membranes from thylakoid lipids. The specific capacitance of membranes formed from decane-containing monogalactosyldiacylglycerol (MGDG), which accounts for 57% of the total lipid content of thylakoids, showed that it adopted a bilayer structure. Solvent-free bilayers of MGDG were not formed, with very rare exceptions, indicating that decane is required to stabilize the planar conformation. However, this cone-shaped lipid produces bilayer structures in combination with other cylindrical thylakoid lipids even in the absence of organic solvent. We compared the properties of solvent-free and decane-containing bilayers from MGDG, soybean lecithin, and the quaternary mixture of lipids similar to that found in vivo. The conductance of decane-MGDG was 26 times higher than that of decane-lecithin. The flux through the decane-lecithin bilayer was found to be slightly dependent on pH, whereas the decane-MGDG membrane was not. The specific conductance of bilayers formed from the quaternary mixture of lipids was 5 to 10 times larger than lecithin (with alkane or not). Further experiments with bilayers made in the presence of a KCl gradient showed that decane-MGDG, decane-MGDG/DGDG/SQDG/PG, and solvent-free MGDG/DGDG/SQDG/PG were cation-selective. The permeability coefficient for potassium ranged from 4.9 to 8.3 x 10(-11) cm s-1. The permeability coefficient for protons in galactolipids, however, was determined to be about six orders of magnitude higher than the value for potassium ions. The HCl permeation mechanism through the lipid membranes was determined from diffusion potentials measured in HCl gradients. Our results suggest that HCl was not transported as neutral molecules. The data is discussed with regard to the function of galactolipids in the ion transport through thylakoid membranes. | [
"Fuks, B",
"Homblé, F"
] | Permeability and electrical properties of planar lipid membranes from thylakoid lipids. |
Solid state deuterium NMR was employed on oriented multilamellar dispersions consisting of 1,2-dilauryl-sn-glycero-3-phosphatidylcholine and deuterium (2H) exchange-labeled gramicidin D, at a lipid to protein molar ratio (L/P) of 15:1, in order to study the dynamic structure of the channel conformation of gramicidin in a liquid crystalline phase. The corresponding spectra were used to discriminate between several structural models for the channel structure of gramicidin (based on the left- and right-handed beta 6.3 LD helix) and other models based on a structure obtained from high resolution NMR. The oriented spectrum is complicated by the fact that many of the doublets, corresponding to the 20 exchangeable sites, partially overlap. Furthermore, the asymmetry parameter, eta, of the electric field gradient tensor of the amide deuterons is large (approximately 0.2) and many of the amide groups are involved in hydrogen bonding, which is known to affect the quadrupole coupling constant. In order to account for these complications in simulating the spectra in the fast motional regime, an ab initio program called Gaussian 90 was employed, which permitted us to calculate, by quantum mechanical means, the complete electric field gradient tensor for each residue in gramicidin (using two structural models). Our results indicated that the left-handed helical models were inconsistent with our observed spectra, whereas a model based on the high-resolution structure derived by Arseniev and coworkers, but relaxed by a simple energy minimization procedure, was consistent with our observed spectra. The molecular order parameter was then estimated from the motional narrowing assuming the relaxed (right-handed) Arseniev structure. Our resultant order parameter of SZZ = 0.91 translates into an rms angle of 14 degrees, formed by the helix axis and the local bilayer normal. The strong resemblance between our spectra (and also those reported for gramicidin in 1,2-dipalmitoyl-sn-glycero-3-phosphatidylcholine (DPPC) multilayers) and the spectra of the same peptide incorporated in a lyotropic nematic phase, suggests that the lyotropic nematic phase simulates the local environment of the lipid bilayer. | [
"Prosser, R S",
"Daleman, S I",
"Davis, J H"
] | The structure of an integral membrane peptide: a deuterium NMR study of gramicidin. |
Solid state deuterium (2H) NMR inversion-recovery and Jeener-Broekaert relaxation experiments were performed on oriented multilamellar dispersions consisting of 1,2-dilauroyl-sn-glycero-3-phosphatidylcholine and 2H exchange-labeled gramicidin D, at a lipid to protein molar ratio (L/P) of 15:1, in order to study the dynamics of the channel conformation of the peptide in a liquid crystalline phase. Our dynamic model for the whole body motions of the peptide includes diffusion of the peptide around its helix axis and a wobbling diffusion around a second axis perpendicular to the local bilayer normal in a simple Maier-Saupe mean field potential. This anisotropic diffusion is characterized by the correlation times, tau R parallel and tau R perpendicular. Aligning the bilayer normal perpendicular to the magnetic field and graphing the relaxation rate, 1/T1Z, as a function of (1-S2N-2H), where S2N-2H represents the orientational order parameter, wer were able to estimate the correlation time, tau R parallel, for rotational diffusion. Although in the quadrupolar splitting, which varies as (3 cos2 theta D-1), has in general two possible solutions to theta D in the range 0 < or = theta D < or = 90 degrees, the 1/T1Z vs. (1-S2N-2H) curve can be used to determine a single value of theta D in this range. Thus, the 1/T1Z vs. (1-S2N-2H) profile can be used both to define the axial diffusion rate and to remove potential structural ambiguities in the splittings. The T1Z anisotropy permits us to solve for the two correlation times (tau R parallel = 6.8 x 10(-9) s and tau R perpendicular = 6 x 10(-6) s). The simulated parameters were corroborated by a Jeener-Broekaert experiment where the bilayer normal was parallel to the principal magnetic field. At this orientation the ratio, J2(2 omega 0)/J1(omega 0) was obtained in order to estimate the strength of the restoring potential in a model-independent fashion. This measurement yields the rms angle, <theta 2>1/2 (= 16 +/- 2 degrees at 34 degrees C), formed by the peptide helix axis and the average bilayer normal. | [
"Prosser, R S",
"Davis, J H"
] | Dynamics of an integral membrane peptide: a deuterium NMR relaxation study of gramicidin. |
The first two-dimensional Fourier-transform electron spin resonance (2D-FT-ESR) studies of nitroxide-labeled lipids in membrane vesicles are reported. The considerable enhancement this experiment provides for extracting rotational and translational diffusion rates, as well as orientational ordering parameters by means of ESR spectroscopy, is demonstrated. The 2D spectral analysis is achieved using theoretical simulations that are fit to experiments by an efficient and automated nonlinear least squares approach. These methods are applied to dispersions of 1-palmitoyl-2oleoyl-sn-glycerophosphatidylcholine (POPC) model membranes utilizing spin labels 1-palmitoyl-2-(16-doxyl stearoyl) phosphatidylcholine and the 3-doxyl derivative of cholestan-3-one (CSL). Generally favorable agreement is obtained between the results obtained by 2D-FT-ESR on vesicles with the previous results on similar systems studied by continuous wave (cw) ESR on aligned samples. The precision in determining the dynamic and ordering parameters is significantly better for 2D-FT-ESR, even though the cw ESR spectra from membrane vesicles are resolved more poorly than those from well aligned samples. Some small differences in results by the two methods are discussed in terms of limitations of the methods and/or theoretical models, as well as possible differences between dynamic molecular structure in vesicles versus aligned membranes. An interesting observation with CSL/POPC, that the apparent homogeneous linewidths seem to increase in "real time," is tentatively attributed to the effects of slow director fluctuations in the membrane vesicles. | [
"Crepeau, R H",
"Saxena, S",
"Lee, S",
"Patyal, B",
"Freed, J H"
] | Studies on lipid membranes by two-dimensional Fourier transform ESR: Enhancement of resolution to ordering and dynamics. |
Correlation field splittings of the vibrational modes of methylene chains in lipid bilayers, isolated lipid molecules in perdeuterated lipid bilayers, crystalline lipid, and interdigitated lipid bilayers have been investigated by pressure-tuning Fourier-transform infrared spectroscopy. The correlation field splittings of these modes are originating from the vibrational coupling interactions between the fully extended methylene chains with different site symmetry along each bilayer leaflet. The interchain-interactions of the methylene chains with the same site symmetry only contribute to frequency shift of the vibrational modes. The magnitude of the correlation field splitting is a measure of the strength of the interchain-interactions, and the relative intensities of the correlation field component bands provide information concerning the relative orientation of the zig-zag planes of the interacting methylene chains. It has been demonstrated in the present work that the correlation field splitting of the CH2 bending and rocking modes commonly observed in the vibrational spectra of lipid bilayers is the result of the intermolecular interchain-interactions among the methylene chains of the neighboring molecules. The intramolecular interchain-interactions between the sn-1 and sn-2 methylene chains within each molecule are weak. The correlation field splitting resulting from the intramolecular interchain-interactions exhibits a much smaller magnitude than that from the intermolecular interchain-interactions and is observed only at very high pressure. Interdigitation of the opposing bilayer leaflets disturbs significantly the intermolecular interchain-interactions and results in dramatic changes in the pressure profiles of the correlation field component bands of both the CH2 bending and rocking modes. The relative intensities of the correlation field component bands of these modes and the magnitude of the splitting are also altered significantly. These results provide further evidence that the correlation field splitting of the CH2 bending and rocking modes in the vibrational spectra of lipid bilayers is due to the intermolecular interchain-interactions. The present work has also demonstrated that the correlation field splitting of the vibrational modes in lipid bilayers is mainly contributed by the intermolecular interchain-interactions among the nearest neighboring molecules and that the long-range correlation interactions beyond the second neighboring molecules are insignificant. | [
"Wong, P T"
] | Pressure-induced correlation field splitting of vibrational modes: structural and dynamic properties in lipid bilayers and biomembranes. |
A detailed electron spin resonance (ESR) study of mixtures of 1-palmitoyl-2-oleoyl-phosphatidylcholine (POPC) and phosphatidylserine (POPS) in oriented multilayers in the liquid crystalline phase is reported with the purpose of characterizing the effects of headgroup mixing on the structural and dynamical properties of the acyl chains. These studies were performed over a range of blends of POPC and POPS and temperatures, utilizing the spin-labeled lipids 16-phosphatidylcholine and 5-phosphatidylcholine as well as cholestane (CSL). The ESR spectra were analyzed by nonlinear least-squares fitting using detailed spectral simulations. Whereas CSL shows almost no variation in ordering and rotational dynamics versus mole fraction POPS, (i.e. XPS), and 5-PC shows small effects, the weakly ordered end-chain labeled 16-PC shows large relative effects, such that the orientational order parameter, S is at a minimum for XPS = 0.5 where it is about one-third the value observed for XPS = 0 and 1. This is directly reflected in the ESR spectrum as a substantial variation in the hyperfine splitting with XPS. The least-squares analysis also shows a reduction in rotational diffusion coefficient, R perpendicular by a fractor of 2 for XPS = 0.5 and permits the estimation of S2, the ordering parameter representing deviations from cylindrically symmetric alignment. These results are contrasted with 2H NMR studies which were insensitive to effects of mixing headgroups on the acyl chains. The ESR results are consistent with a somewhat increased disorder in the end-chain region as well as a small amount of chain tilting upon mixing POPC and POPS. They demonstrate the high sensitivity of ESR to subtle effects in chain ordering and dynamics. | [
"Ge, M",
"Budil, D E",
"Freed, J H"
] | An electron spin resonance study of interactions between phosphatidylcholine and phosphatidylserine in oriented membranes. |
Temperature dependence in electronic energy transfer steps within light-harvesting antenna trimers from photosystem II was investigated by studying Chl a pump-probe anisotropy decays at several wavelengths from 675 to 682 nm. The anisotropy lifetime is markedly sensitive to temperature at the longest wavelengths (680-682 nm), increasing by factors of 5 to 6 as the trimers are cooled from room temperature to 13 K. The temperature dependence is muted at 677 and 675 nm. This behavior is modeled using simulations of temperature-broadened Chl a absorption and fluorescence spectra in spectral overlap calculations of Förster energy transfer rates. In this model, the 680 nm anisotropy decays are dominated by uphill energy transfers from 680 nm Chl a pigments at the red edge of the LHC-II spectrum; the 675 nm anisotropy decays reflect a statistical average of uphill and downhill energy transfers from 676-nm pigments. The measured temperature dependence is consistent with essentially uncorrelated inhomogeneous broadening of donor and acceptor Chl a pigments. | [
"Savikhin, S",
"van Amerongen, H",
"Kwa, S L",
"van Grondelle, R",
"Struve, W S"
] | Low-temperature energy transfer in LHC-II trimers from the Chl a/b light-harvesting antenna of photosystem II. |
The structure of a chemically synthesized 25-residue-long functional signal peptide of Escherichia coli ribose binding protein was compared with that of a nonfunctional mutant-signal peptide using circular dichroism and two-dimensional 1H NMR in solvents mimicking the amphiphilic environments. The functional peptide forms an 18-residue-long alpha-helix starting from the NH2-terminal region and reaching to the hydrophobic stretch in a solvent consisting of 10% dimethylsulfoxide, 40% water, and 50% trifluoroethanol (v/v). The nonfunctional mutant peptide, which contains a Pro at position 9 instead of a Leu in the wild-type peptide, does not have any secondary structure in that solvent but forms a 12-residue-long alpha-helix within the hydrophobic stretch in water/trifluoroethanol (50:50, v/v) solvent. It seems that the Pro-9 residue in the nonfunctional peptide disturbs the helix propagation from the hydrophobic stretch to the NH2-terminal region. Because both of these peptides have stable helices within the hydrophobic stretch, it may be concluded that the additional 2 turns of the alpha-helix in the NH2-terminal region of the wild-type signal peptide is important for its function. | [
"Yi, G S",
"Choi, B S",
"Kim, H"
] | Structures of wild-type and mutant signal sequences of Escherichia coli ribose binding protein. |
Surface and subsurface dynamics of Rat Basophilic Leukemia cells, a model system of stimulated secretion, were imaged using Scanning Force Microscopy (SFM) at a rate of 50-60 s/image. Cytoskeletal elements and organelles were tracked within quiescent cells and those activated after IgE receptor crosslinking. In addition, surface waves were observed moving within the plasma membrane. The structures seen in quiescent and activated cells can be correlated with those seen in electron micrographs and topographic SFM images of fixed detergent-extracted cells. Furthermore, images of the detergent-extracted nuclei reveal the presence of numerous nuclear pore complexes. High-magnification images of the nuclear pore complexes show evidence of subunit structure and exhibit dimensions consistent with those reported previously using electron microscopy. The behavior and overall change in morphology of cells observed during activation was consistent with that observed under similar conditions with Differential Interference Contrast microscopy. This study demonstrates that SFM, unlike other techniques, can be used to provide high-resolution information in both fixed and living cells. | [
"Braunstein, D",
"Spudich, A"
] | Structure and activation dynamics of RBL-2H3 cells observed with scanning force microscopy. |
The ability of transmembrane receptor proteins to change their association with the cytoskeleton in response to ligand binding seems to be a key mechanism of signal transduction across membranes. To investigate the molecular features of this mechanism we have used the red cell membrane as a model system to study signal transduction through the integral protein, glycophorin A. In these studies the lateral mobility of integral proteins was measured in situ by fluorescence recovery after photobleaching, and membrane rigidity was characterized by micropipette aspiration technique. We found that binding either a monoclonal antibody or its monovalent Fab to the exoplasmic domain of glycophorin A in normal red cells immobilized the receptor and rigidified the membrane. Further, immobilization and rigidification did not occur when antibodies were bound to Miltenberger V cells containing a mutant form of glycophorin A lacking the cytoplasmic domain. These results imply that the site of the immobilization/rigidification lies within the membrane skeletal structure, not in exofacial receptor crosslinking, and requires the extended cytoplasmic domain of normal glycophorin A. In addition, we found that glycophorin A immobilization and membrane skeletal rigidification were accompanied by immobilization of band 3 receptors. This unexpected result indicates a cooperative coupling between liganded glycophorin A, band 3, and the membrane skeleton. We speculate that cooperation of this type may represent a general mechanism for cytoskeletal linkage and transformation initiated by receptors with short cytoplasmic sequences, such as integrins. | [
"Knowles, D W",
"Chasis, J A",
"Evans, E A",
"Mohandas, N"
] | Cooperative action between band 3 and glycophorin A in human erythrocytes: immobilization of band 3 induced by antibodies to glycophorin A. |
Digital imaging microscopy of fluor-3 fluorescence was used to study the propagation of intracellular Ca2+ waves in isolated adult rat cardiomyocytes from 17 to 37 degrees C. Ca2+ waves spread in both transverse and longitudinal direction of a myocyte. Transverse propagation was pronounced in waves starting from a focus at the edge of a myocyte and in waves following an irregular, curved path (spiral waves). For the former type of waves, propagation velocities were determined. Both transverse and longitudinal wave components propagated at constant velocity ranging from 30 to 125 micron/s. Myocytes were anisotropic with respect to wave propagation: waves propagated faster in the longitudinal than in the transverse direction. The ratio between longitudinal and transverse velocity increased from 1.30 at 17 degrees C to 1.55 at 37 degrees C. Apparent activation energies for transverse and longitudinal wave propagation were estimated to be -20 kJ/mol, suggesting that these processes are limited by diffusion of Ca2+. Direction-dependent propagation velocities are interpreted to result from the highly ordered structure of the myocytes, especially from the anisotropic arrangement of diffusion obstacles such as myofilaments and mitochondria. | [
"Engel, J",
"Fechner, M",
"Sowerby, A J",
"Finch, S A",
"Stier, A"
] | Anisotropic propagation of Ca2+ waves in isolated cardiomyocytes. |
The goal of this work was to analyze an image data set and to detect the structural variability within this set. Two algorithms for pattern recognition based on neural networks are presented, one that performs an unsupervised classification (the self-organizing map) and the other a supervised classification (the learning vector quantization). The approach has a direct impact in current strategies for structural determination from electron microscopic images of biological macromolecules. In this work we performed a classification of both aligned but heterogeneous image data sets as well as basically homogeneous but otherwise rotationally misaligned image populations, in the latter case completely avoiding the typical reference dependency of correlation-based alignment methods. A number of examples on chaperonins are presented. The approach is computationally fast and robust with respect to noise. Programs are available through ftp. | [
"Marabini, R",
"Carazo, J M"
] | Pattern recognition and classification of images of biological macromolecules using artificial neural networks. |
Macroscopic ionic sodium currents and gating currents were studied in voltage-clamped, dialyzed giant axons of the squid Loligo pealei under conditions of regular and inverse sodium gradients. Sodium currents showed regular kinetics but inactivation was incomplete, showing a maintained current for depolarizations lasting 18 ms. The ratio of the maintained current to the peak current increased with depolarization and it did not depend on the direction of the current flow or the sodium gradient. The time constant of inactivation was not affected by the sodium gradient. Double-pulse experiments allowed the separation of a normal inactivating component and a noninactivating component of the sodium currents. In gating current experiments, the results from double-pulse protocols showed that the charge was decreased by the prepulse and that the slow component of the 'on' gating current was preferentially depressed. As expected, charge immobilization was established faster at higher depolarizations than at low depolarizations, however, the amount of immobilized charge was unaffected by the pulse amplitude. This indicates that the incomplete sodium inactivation observed at high depolarizations is not the result of decreased charge immobilization; the maintained current must be due to a conductance that appears after normal charge immobilization and fast inactivation. | [
"Correa, A M",
"Bezanilla, F"
] | Gating of the squid sodium channel at positive potentials. I. Macroscopic ionic and gating currents. |
The alpha 1 subunit of cardiac Ca2+ channel, expressed alone or coexpressed with the corresponding beta subunit in Xenopus laevis oocytes, elicits rapidly inactivating Ca2+ currents. The inactivation has the following properties: 1) It is practically absent in external Ba2+; 2) it increases with Ca2+ current amplitudes; 3) it is faster at more negative potentials for comparable Ca2+ current amplitudes; 4) it is independent of channel density; and 5) it does not require the beta subunit. These findings indicate that the Ca2+ binding site responsible for inactivation is encoded in the alpha 1 subunit and suggest that it is located near the inner channel mouth but outside the membrane electric field. | [
"Neely, A",
"Olcese, R",
"Wei, X",
"Birnbaumer, L",
"Stefani, E"
] | Ca(2+)-dependent inactivation of a cloned cardiac Ca2+ channel alpha 1 subunit (alpha 1C) expressed in Xenopus oocytes. |
Detection of motion and position by the vestibular labyrinth depends on the accumulation of potassium within a central compartment of the inner ear as a source of energy to drive the transduction process. Much circumstantial evidence points to the vestibular dark cell (VDC) epithelium as being responsible for concentrating K+ within the lumen. We have used the vibrating probe technique to directly observe voltage and ion gradients produced by this tissue to put this assumption on a solid experimental footing. Relative current density (Isc,probe) over the apical membrane of VDC epithelium was measured with the vibrating voltage-sensitive probe, and this technique was validated by performing maneuvers known to either stimulate or inhibit the transepithelial equivalent short circuit current. Basolateral bumetanide (5 x 10(-5) M) and ouabain (1 x 10(-3) M) caused a decrease in Isc,probe by 55 +/- 6% and 39 +/- 3%, respectively while raising the basolateral K+ concentration from 4 to 25 mM caused an increase by 35 +/- 8%. A K+ gradient directed toward the apical membrane was detected with the vibrating K(+)-selective electrode, demonstrating that, indeed, the VDC epithelium secretes K+ under control conditions. This secretion was inhibited by bumetanide (by 94 +/- 7%) and ouabain (by 52 +/- 8%). The results substantiate the supposition that dark cells produce a K+ flux and qualitatively support the correlation between this flux and the transepithelial current. | [
"Marcus, D C",
"Shipley, A M"
] | Potassium secretion by vestibular dark cell epithelium demonstrated by vibrating probe. |
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