Showing papers in "Biophysical Journal in 1997"

TL;DR: How Brownian dynamics can help bridge the gap between molecular dynamics and probe tests is described, which shows that bond strength progresses through three dynamic regimes of loading rate.

TL;DR: Molecular dynamics simulations were performed on a system consisting of a bilayer of 64 molecules of the lipid dipalmitoylphosphatidylcholine and 23 water molecules per lipid to reproduce the correct density and to give a proper estimate of the area per lipid.

TL;DR: Force-extension (F-x) relationships were measured for single molecules of DNA under a variety of buffer conditions, using an optical trapping interferometer modified to incorporate feedback control, suggesting that the intrinsic persistence length remains close to 40 nm.

TL;DR: The standard heat of solution of a crystalline alkali halide is shown here to be negative (exothermic) only when one ion is a kosmotrope and the ion of opposite charge is a chaotrope, which suggests that inner sphere ion pairs are preferentially formed between oppositely charged ions with matching absolute enthalpies of hydration.

TL;DR: In this article, a derivation of the standard free energy of noncovalent binding has been derived from the underlying statistical thermodynamics of biomolecular systems, which is useful in formulating novel computational methods for predicting binding affinities.

TL;DR: The theoretical and experimental basis for carrying out measurements in a confocal dual-beam fluorescence correlation spectroscopy setup is developed and conditions that are favorable for cross-correlation analysis are discussed.

TL;DR: No single GFP variant is ideal for every application, but each one offers advantages and disadvantages for quantitative imaging in living cells.

TL;DR: This article reviews and extends the connections of some important computational methods with the underlying statistical thermodynamics of noncovalent binding, and a derivation of the standard free energy of binding forms the basis of this review.

TL;DR: It is demonstrated that picosecond to nanosecond simulation of ligand unbinding requires such strong forces that the resulting protein-ligand motion proceeds far from the thermally activated regime of millisecond AFM experiments, and that simulated unbinding cannot be readily extrapolated to the experimentally observed rupture.

TL;DR: Measurements of GFP translation and rotation in aqueous dextran solutions support the view that the primary barrier to GFP diffusion is collisional interactions between GFP and macromolecular solutes.

TL;DR: A new type of analysis for tracking data by making use of the probability distribution of square displacements is presented, which characterizes the so-called immobile fraction often found in FRAP experiments.

TL;DR: In single-particle tracking experiments, the diffusion coefficient D may be measured from the trajectory of an individual particle in the cell membrane and the statistical distribution of single-trajectory diffusion coefficients is examined by Monte Carlo calculations.

TL;DR: The spectroscopic data suggest that reduced pyridine nucleotides, NAD(P)H, are the primary source of the skin autofluorescence at 730 nm excitation, and that this conjecture is confirmed by the observation of the super-quadratic dependence of the fluorescence intensity on the excitation power.

TL;DR: Evidence is presented for a site on the tail of the mSlo subunit that interacts with calcium, a novel calcium-binding motif that includes a string of conserved aspartate residues that suggests that the calcium bowl is sensitive to calcium ion, but insensitive to cadmium ion.

TL;DR: It is reported that cells of a pure culture of a marine magnetotactic coccus, designated strain MC-1, formed microaerophilic bands in capillary tubes and used aerotaxis to migrate to a preferred oxygen concentration in an oxygen gradient.

TL;DR: In this article, a general theoretical framework for studying the adsorption of protein molecules on surfaces with grafted polymers is presented, where the potentials of mean force of the protein with the surface are calculated as a function of polymer surface coverage and amount of protein adsorbed.

TL;DR: Surprisingly, cholesterol effected only a modest increase in the kc of these monolayers, which is much smaller than estimated from its effect on the area compressibility modulus in bilayers.

TL;DR: Based on the observed results, it is hypothesized that decorin facilitates fibrillar slippage during deformation and thereby improves the tensile properties of collagen fibers.

TL;DR: A scaled template technique is implemented within a commercial data analysis application and can be applied to many standard electrophysiological data file formats and was more sensitive than previously described threshold detection techniques.

TL;DR: A scanning ion conductance microscope specially developed for imaging living cells is reported, which maintains the working distance between the probe and the sample such that they do not make direct physical contact with each other.

TL;DR: Multiconformation pH titration gives better agreement with the experimental pKa's for triclinic hen egg lysozyme than conventional rigid protein calculations, making it sensitive to the composition of the local protein structure.

TL;DR: The mitochondrial channel, VDAC, forms large aqueous pores through membranes and is ideally suited to controlling the flow of ATP between the cytosol and the mitochondrial spaces, showing that monovalent ions are still quite permeable, yet ATP flux is almost totally blocked.

TL;DR: Results support the modified stalk mechanism for both membrane fusion and the L alpha/H(II) phase transition, and point out that recent data on the effects of hydrophobic peptides and viral fusion peptide on lipid phase behavior are consistent with an effect of the peptides on TMC stability.

TL;DR: The mixing of cholesterol with PC was found to diminish the in-plane elasticity of the films beyond what was predicted from the additive behavior of the individual lipid components apportioned by mole and area fraction.

TL;DR: A potential energy function for unsaturated hydrocarbons is proposed and is shown to agree well with experiment, using molecular dynamics simulations of a water/octene interface and a dioleoyl phosphatidylcholine (DOPC) bilayer.

TL;DR: It is shown here that specific binding of DNA via its unmodified extremities can be achieved on a great variety of surfaces by a judicious choice of the pH.

TL;DR: The velocity and the unitary steps could be obtained accurately over a wide force range and the force-velocity curves were linear from 0 to a maximum force at 10 microM and 1 mM ATP, and the maximum force was approximately 7 pN, larger by approximately 30% than values previously reported.

TL;DR: The validity of the model is demonstrated with human leukemia (HL-60) cells subjected to a parallel electrode array, and application of the device to separating HL-60 cells from peripheral blood mononuclear cells is shown.

TL;DR: For liposomes containing dimyristoyl phosphatidylcholine (DMPC) or a 10 mol% cholesterol/DMPC mixture, the mechanical property of the membrane, k(c), is shown to be temperature dependent on approaching the main (thermotropic) phase transition temperature T(m).

TL;DR: A novel model for the melittin pore formation was discussed in comparison with other pore-forming peptides, and a new double-labeling method clarified that the pore size increased with the peptide-to-lipid ratio.