Showing papers in "Biophysical Journal in 2004"

TL;DR: A novel statistical approach that quantifies, for the first time, the amount of colocalization of two fluorescent-labeled proteins in an image automatically, removing the bias of visual interpretation is introduced.

TL;DR: A central structural role for the cytoskeleton is hypothesize in driving the membrane outward during spreading whereas adhesion reinforces the spreading.

TL;DR: It is proposed that the anomality of the diffusion can be used as a quantifiable measure for the crowdedness of the cytoplasm at the molecular scale.

TL;DR: The results suggest that the influence of a nonionic polymer or plasma protein on RBC aggregation is simply a consequence of its size in an aqueous environment, and that the specific type of macromolecule is of minor importance.

TL;DR: It is indicated that water and solvent molecules not only influence the 3D structure of proteins in solution but also play a crucial role in their adsorption onto surfaces.

TL;DR: The approach establishes a more general framework to assess the role of diffusion, the number of binding states, and the binding constants underlying a FRAP recovery, and defines constraints on what can be estimated from FRAP data, shows that diffusion should play a key role in many FRAP recoveries, and provides tools to test its contribution.

TL;DR: FRET studies of a series of oligodeoxythymidylates, (dT)N, over a wide range of salt concentrations and chain lengths provide systematic constraints for testing theoretical models and reasonably good agreement could be obtained between the data and the worm-like chain model.

TL;DR: Using Monte Carlo simulations it is shown that estimation algorithms can come close to attaining the limit given in the expression and explicit quantitative results are provided to show how the limit of the localization accuracy is reduced by factors such as pixelation of the detector and noise sources in the detection system.

TL;DR: A search-and-fold mechanism that involves the coupling of protein binding and partial protein folding is proposed that has several important biological implications for search in the presence of other proteins and nucleosomes, simultaneous search by several proteins, etc.

TL;DR: A detailed mathematical model for Ca2+ handling and ionic currents in the rabbit ventricular myocyte is developed, more robust than many previously existing models and reproduces many experimental results using parameters based largely on experimental measurements in myocytes.

TL;DR: A clear connection between statistical thermodynamics and end-point free energy models is presented and a novel method for calculating the association free energy, arising from one molecule's loss of translational and rotational freedom from the standard state concentration, is described.

TL;DR: The results reemphasize the complex phase behavior of cholesterol-containing membranes and provide a framework for interpreting (2)H-NMR experiments in similar membranes.

TL;DR: Results suggest that the spherical AFM tip is large enough to measure the aggregate dynamic elastic modulus of cartilage, whereas the sharp AFMtip depicts the elastic properties of its fine structure.

TL;DR: This AFM-based microrheology allows us to correlate two key parameters of cell motility by relating elastic strength and the Poisson ratio to the adhesive state of a cell, and allows for the decomposition of the elastic modulus into loss and storage modulus.

TL;DR: The results strongly indicate the necessity for the paradigm shift of the concept on the plasma membrane: from the two-dimensional fluid continuum model to the compartmentalized membrane model in which its constituent molecules undergo hop diffusion over the compartments.

TL;DR: Results suggest that a complex of CSQ, triadin 1, and junctin confer RyR luminal Ca sensitivity, whereas CSQ apparently serves as a luminals Ca sensor that inhibits the channel at low luminal [Ca], whereasTriadin 1 and/or junctIn may be required to mediate interactions of CS Q with RyR.

TL;DR: Molecular dynamics simulations of DNA translocation through the nanopore suggest that 20-basepair segments of double-stranded DNA can transit a nanopore of 2.2 x 2.6 nm(2) cross section in a few microseconds at typical electrical fields.

TL;DR: It is demonstrated the existence of several phase transitions in DPPC and DOPC mica-supported bilayers by both atomic force microscopy imaging and force measurements, which provide valuable information on bilayer thickness and phase transitions.

TL;DR: A solid-fluid interface is activated by attaching flagellated bacteria to a solid surface by adsorbing swarmer cells of Serratia marcescens to polydimethylsiloxane or polystyrene, creating flat constructs called "bacterial carpets" that generate both translation and rotation.

TL;DR: E-FRET bridges the gap between the donor recovery after acceptor photobleaching technique, and the sensitized-emission FRET indices, and visualize FRET in terms of true FRET efficiency images, which correlate linearly with the degree of donor interaction.

TL;DR: In this article, the authors show that residues in folded proteins are distributed according to a "small-world" topology, and that the core residues have the same local packing arrangements irrespective of protein size.

TL;DR: The relationship between DNA translocation and blocking current has been established through molecular dynamics simulations and the duration and magnitude of the blocking current transient can be measured to discriminate single-stranded from double-Stranded DNA and resolve the length of the polymer.

TL;DR: It is demonstrated that the pf/pd ratio corresponds to the number of effective steps a water molecule needs to take to permeate a channel, and it is concluded that pF/pd for aquaporin-1 measures approximately 12.1 x 10(-14) cm(3)/s.

TL;DR: Fluorescence correlation spectroscopy promises to be a valuable tool to elucidate lipid raft associations in native cells and to gain deeper insight into the correspondence between model and natural membranes.

TL;DR: The results are in agreement with the approximately logV dependence at high V (where V is the loading rate) observed by other methods, and the extension of these measurements to lower loading rates reveals a much weaker dependence on V.

TL;DR: The single-molecule FRET technique is extended to three colors, using the DNA four-way (Holliday) junction as a model system that undergoes two-state conformational fluctuations and is able to show that the acceptor 1 arm moves away from the donor arm at the same time as theacceptor 2 arm approaches the donor hand, marking the first example of observing correlated movements of two different segments of a single molecule.

TL;DR: A simple geometric analysis for the gating of the mechanosensitive channel MscL suggests that pressure profiles affect its gating through the second moment of the profile in a tension-independent manner.

TL;DR: Theoretical calculations and experimental results suggest that nonspecific electrostatic interactions produce this sequestration of the L-alpha-phosphatidyl-D-myo-inositol 4,5-bisphosphate (PIP2) in model membranes containing physiologically relevant fractions of the monovalent acidic lipid phosph atidylserine.

TL;DR: In the simulations the mechanical threshold tension necessary to cause rupture of the membrane on a nanosecond timescale is much higher in the case of the equilibrated bilayers, as compared with membranes containing preexisting pores.

TL;DR: The data suggest that multiphoton microscopy is a highly sensitive and promising technique for studying the morphometric properties of the microstructure of the blood vessel wall.