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| 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. | description |
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| Trinkunas, G, Holzwarth, A R | authors |
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| Investigations of the thermal response of laser-excited biomolecules. | name |
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| 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. | description |
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| Li, P, Champion, P M | authors |
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| Time-resolved spectroscopy of energy and electron transfer processes in the photosynthetic bacterium Heliobacillus mobilis. | name |
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| 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. | description |
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| Lin, S, Chiou, H C, Kleinherenbrink, F A, Blankenship, R E | authors |
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| Hydrodynamics of horseradish peroxidase revealed by global analysis of multiple fluorescence probes. | name |
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| 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. | description |
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| Brunet, J E, Vargas, V, Gratton, E, Jameson, D M | authors |
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| Stabilization of intermediate density states in globular proteins by homogeneous intramolecular attractive interactions. | name |
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| 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. | description |
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| Bahar, I, Jernigan, R L | authors |
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| Cooperative structural transitions induced by non-homogeneous intramolecular interactions in compact globular proteins. | name |
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| 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. | description |
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| Bahar, I, Jernigan, R L | authors |
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| The use of fluorescence methods to monitor unfolding transitions in proteins. | name |
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| 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. | description |
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| Eftink, M R | authors |
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| Scanning concentration correlation spectroscopy using the confocal laser microscope. | name |
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| 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. | description |
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| Koppel, D E, Morgan, F, Cowan, A E, Carson, J H | authors |
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| Antibody diffusion in human cervical mucus. | name |
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| 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. | description |
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| Saltzman, W M, Radomsky, M L, Whaley, K J, Cone, R A | authors |
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| A multidimensional spectrophotometer for monitoring thermal unfolding transitions of macromolecules. | name |
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| 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. | description |
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| Ramsay, G, Eftink, M R | authors |
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| The osmotic rupture hypothesis of intracellular freezing injury. | name |
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| 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. | description |
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| Muldrew, K, McGann, L E | authors |
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| Teaching active transport at the turn of the twenty-first century: recent discoveries and conceptual changes. | name |
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| 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." | description |
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| Inesi, G | authors |
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| Molecular distributions in interphases: statistical mechanical theory combined with molecular dynamics simulation of a model lipid bilayer. | name |
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| 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. | description |
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| Xiang, T X, Anderson, B D | authors |
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| The temperature-composition phase diagram of monomyristolein in water: equilibrium and metastability aspects. | name |
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| 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. | description |
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| Briggs, J, Caffrey, M | authors |
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| Reduction-of-dimensionality kinetics at reaction-limited cell surface receptors. | name |
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| 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. | description |
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| Axelrod, D, Wang, M D | authors |
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| Solutions for transients in arbitrarily branching cables: IV. Nonuniform electrical parameters. | name |
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| 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. | description |
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| Major, G, Evans, J D | authors |
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| Molecular dynamics simulations of oxidized and reduced Clostridium beijerinckii flavodoxin. | name |
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| 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. | description |
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| Leenders, R, van Gunsteren, W F, Berendsen, H J, Visser, A J | authors |
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| Mutations in the M4 domain of Torpedo californica acetylcholine receptor dramatically alter ion channel function. | name |
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| 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. | description |
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| Lee, Y H, Li, L, Lasalde, J, Rojas, L, McNamee, M, Ortiz-Miranda, S I, Pappone, P | authors |
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| 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. | name |
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| 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. | description |
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| Schild, L, Moczydlowski, E | authors |
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| Transverse distance between the membrane and the agonist binding sites on the Torpedo acetylcholine receptor: a fluorescence study. | name |
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| 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). | description |
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| Valenzuela, C F, Weign, P, Yguerabide, J, Johnson, D A | authors |
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| Theory for establishing proximity relations in biological membranes by excitation energy transfer measurements. | name |
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| 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. | description |
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| Yguerabide, J | authors |
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| Cysteines in the Shaker K+ channel are not essential for channel activity or zinc modulation. | name |
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| 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. | description |
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| Boland, L M, Jurman, M E, Yellen, G | authors |
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| An improved double vaseline gap voltage clamp to study electroporated skeletal muscle fibers. | name |
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| 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. | description |
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| Chen, W, Lee, R C | authors |
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| Virtual electrode effects in myocardial fibers. | name |
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| 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. | description |
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| Knisley, S B, Hill, B C, Ideker, R E | authors |
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| 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. | name |
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| 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. | description |
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| Yamazaki, M, Miyazu, M, Asano, T, Yuba, A, Kume, N | authors |
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| 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. | name |
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| 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. | description |
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| Mannock, D A, McElhaney, R N, Harper, P E, Gruner, S M | authors |
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| 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. | name |
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| 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. | description |
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| McMullen, T P, Lewis, R N, McElhaney, R N | authors |
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| Electrochemical measurements of the lateral diffusion of electroactive amphiphiles in supported phospholipid monolayers. | name |
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| 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. | description |
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| Torchut, E, Laval, J M, Bourdillon, C, Majda, M | authors |
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| Cholesterol modifies water concentration and dynamics in phospholipid bilayers: a fluorescence study using Laurdan probe. | name |
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| 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. | description |
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| Parasassi, T, Di Stefano, M, Loiero, M, Ravagnan, G, Gratton, E | authors |
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| Movement of single myosin filaments and myosin step size on an actin filament suspended in solution by a laser trap. | name |
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| 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). | description |
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| Saito, K, Aoki, T, Aoki, T, Yanagida, T | authors |
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| A model of the release of myosin heads from actin in rapidly contracting muscle fibers. | name |
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| 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. | description |
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| Cooke, R, White, H, Pate, E | authors |
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| Oxygen exchange in the isolated, arrested guinea pig heart: theoretical and experimental observations. | name |
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| 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. | description |
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| Mawson, D A, Hunter, P J, Kenwright, D N, Loiselle, D S | authors |
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| Cross-linker dynamics determine the mechanical properties of actin gels. | name |
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| 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. | description |
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| Wachsstock, D H, Schwarz, W H, Pollard, T D | authors |
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| A mechanochemical study of MgDNA fibers in ethanol-water solutions. | name |
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| 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. | description |
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