Showing papers in "Biophysical Journal in 2010"

TL;DR: A multiscale RBC model is presented that is able to predict RBC mechanics, rheology, and dynamics in agreement with experiments and based on an analytic theory, the modeled membrane properties can be uniquely related to the experimentally established RBC macroscopic properties without any adjustment of parameters.

TL;DR: It is shown here that the unprecedented large statistics obtained by uPAINT on single cells reveal local diffusion properties of specific proteins, either in distinct membrane compartments of adherent cells or in neuronal synapses.

TL;DR: A sequence-based predictor of hydrodynamic radius for IDPs is developed that shows substantial improvement over a simple model based upon chain length alone and observes that polyhistidine tags seem to increase IDP compaction, which suggests that these tags have significant perturbing effects and thus should be removed before any structural characterizations of IDPs.

TL;DR: It is concluded that the velocity field of Madin-Darby canine kidney cells is very coherent in contrast with the NRK cells, which is supported by parallel single-cell tracking experiments.

TL;DR: In this paper, a mathematical framework was presented to study the effect of charge on the diffusive transport of macromolecules and nanoparticles in the extracellular matrix of biological tissues.

TL;DR: Insight is provided into how physical properties of the membrane may modulate interactions of αS with cellular membranes, and Vesicle curvature has a strong effect on the binding affinity, with a >15-fold increase in affinity for small unilamellar vesicles over large unilAMEllarVesicles, suggesting that αS may be a curvature-sensing protein.

TL;DR: The source-sink mismatch in well-coupled cardiac tissue powerfully protects the heart from arrhythmias due to sporadic afterdepolarizations, andStructural and electrophysiological remodeling decrease these numbers significantly but still require synchronization mechanisms for EADs and DADs to overcome the robust protective effects of source-Sink mismatch.

TL;DR: In this paper, the root mean square deviation (RMSD) after roto-translational least-squares fitting is used to measure global structural similarity of macromolecules used commonly.

TL;DR: It is shown that membrane recognition of the N-terminus is essential for the cooperative formation of helical domains in the protein, and the results suggest that the membrane-induced helical folding of the first 25 residues may be driven simultaneously by electrostatic attraction and by a change in lipid ordering.

TL;DR: In this article, the authors analyzed the mobility of microscopic particles in reconstituted mucin hydrogels and showed that electrostatic interactions between diffusing particles and mucin polymers regulate the permeability properties of reconstitized mucin.

TL;DR: In this paper, the authors quantified expression noise from the long terminal repeat (LTR) promoter at different HIV-1 integration sites across the human genome and found that the measured noise levels are inconsistent with constitutive gene expression models, and that each burst generates an average of 2-10 mRNA transcripts before the promoter returned to an inactive state.

TL;DR: A quantitative analysis of the cells adhering on the cadherin-coated surfaces shows that forces are correlated with the formation of Cadherin adhesions, and these findings are consistent with a mechanosensitive regulation of cadher in-mediated intercellular junctions through the cellular contractile machinery.

TL;DR: The motion of swarming Escherichia coli is examined, comparing the motion of individual cells to their motion during swimming, and the swirling that is conspicuous in many swarming systems is observed, probably due to increasingly long-lived correlations among cells that associate into groups.

TL;DR: The mesoscale hydrodynamics simulations in combination with a mechanical sperm model provide a theoretical framework that explains several distinct swimming behaviors of sperm near and far from a wall and suggests a mechanism by which sperm navigate in a chemical gradient via a change of their shape.

TL;DR: It is confirmed that the protein concentration plays an important role on the pH-unfolded BSA state, due to a delicate compromise between interaction forces and crowding effects.

TL;DR: It is found that increasing levels of shear strain induce a succession of distinct elastic responses that reflect stretching processes on different length scales, and a theoretical model is presented that explains these observations in terms of the unique hierarchical architecture of the fibers.

TL;DR: The quasipotential landscape of the stochastic dynamics of a canonical gene circuit that governs branching cell fate commitment is computed and reveals the global dynamics and permits the calculation of potential barriers between cell phenotypes imposed by the circuit architecture.

TL;DR: Fluorescence recovery after photobleaching and numerical modeling are combined to analyze mobility of a set of fluorescent protein fusions in the bacterial cytoplasm, the plasma membrane, and in the nucleoid to predict diffusion rates of proteins in Escherichia coli.

TL;DR: This work proposes and discusses what it believes are new methods to analyze the time series of the particle traces, in particular, for subdiffusion phenomena, and shows that the MME analysis performs better in the determination of the anomalous diffusion exponent.

TL;DR: This comprehensive benchmark based on NMR data applied to many popular MD force fields is presented, finding that for gb3, the force-field AMBER99sb reaches comparable accuracy in back-calculated residual dipolar couplings and J-couplings across hydrogen bonds to ensembles obtained by refinement against N MR data.

TL;DR: The results show that cells can amplify small differences in adhesive cues to large differences in cell adhesion strength, and the weak link between the intra- and extracellular space is at the intracellular side of a focal contact.

TL;DR: It is demonstrated that the analysis of PENs in terms of parameters such as hubs and shortest paths can provide a variety of biologically important information, such as the residues crucial for stabilizing the folded units and the paths of communication between distal residues in the protein.

TL;DR: An interactive software tool for segmentation, tracking, and visualization of individual fibers, using open active contours to quantify cytoskeletal structures imaged by fluorescence microscopy in two and three dimensions, is developed.

TL;DR: It is found that ternary mixtures of DSPC and cholesterol together with either POPC or SOPC, do indeed have regions of Ld + Lo coexistence, however, phase domains are much smaller than the optical resolution limit, likely on the order of the Förster distance for energy transfer.

TL;DR: Here it is shown that microscopy based on ground state depletion followed by individual molecule return (GSDIM) can effectively provide multicolor diffraction-unlimited resolution imaging of immunolabeled fixed and SNAP-tag labeled living cells.

TL;DR: Tracking of fluorescently labeled chromosomal loci in live bacterial cells reveals a robust scaling of the mean square displacement (MSD) as τ(0.39), which is most consistent with fractional Langevin motion and rule out a continuous time random walk model as an explanation for anomalous motion in vivo.

TL;DR: This work paves the way for ultra-high-resolution TIRF-FRET studies on many biomolecules, including DNA processing machinery, the mechanisms of which are often characterized by distance changes on the scale of one DNA basepair.

TL;DR: It is shown that siRNA knockdown of nesprin-1, a protein present in the linker of nucleus to cytoskeleton complex, abolished the reorientation of endothelial cells in response to cyclic strain.

TL;DR: This work uses single-molecule Forster resonance energy transfer to investigate the influence of charged residues on the dimensions of unfolded and intrinsically disordered proteins and finds that IDPs can exhibit a prominent expansion at low ionic strength that correlates with their net charge.

TL;DR: An automated protocol for setting up alchemical free energy calculations for mutations of naturally occurring amino acids (except for proline) that allows an unprecedented, automated screening of large mutant libraries is presented.