Showing papers in "Biophysical Journal in 2007"

TL;DR: The parmbsc0 force field as mentioned in this paper is a refinement of the AMBER parm99 force field, where emphasis has been made on the correct representation of the a/g concerted rotation in nucleic acids (NAs).

TL;DR: Within a range of stiffness spanning that of soft tissues, fibroblasts tune their internal stiffness to match that of their substrate, and modulation of cellular stiffness by the rigidity of the environment may be a mechanism used to direct cell migration and wound repair.

TL;DR: It is shown that cell-surface attachment is not sensitive to pattern density, whereas the formation of stable focal adhesions and persistent spreading is, and a critical RGD density is essential for the establishment of mature and stable integrin adhesion, which, in turn, induce efficient cell spreading and formation of focal adhesion dynamics.

TL;DR: The recent advances in the prediction of intrinsically disordered proteins and the use of protein disorder prediction in the fields of molecular biology and bioinformatics are reviewed here, especially with regard to protein function.

TL;DR: A significant number of reactions appear to be the first steps in the linear portion of numerous biosynthesis pathways and might be candidates for cell regulation, and it is found that the NAD/NADH and NADP/NadPH ratios maintained in the cell are close to the minimum feasible ratio and maximum feasible ratio, respectively.

TL;DR: The results suggest that one mechanism of cell membrane damage is the increase in membrane permeability due to the presence of oxidized lipids.

TL;DR: The hypothesis that collagen anisotropy is due to the subfibrils being aligned along the fibril axis is supported by nonuniform surface imprints performed by high load nanoindentation.

TL;DR: This study presents a model of electroporation in a spherical cell exposed to an electric field that determines transmembrane potential, number of pores, and distribution of pore radii as functions of time and position on the cell surface.

TL;DR: The results support the hypothesis that direct neural activation with pulsed laser light is induced by a thermal transient, resulting in direct or indirect activation of transmembrane ion channels causing action potential generation.

TL;DR: This study modified the L-type calcium (Ca) current and Ca(i) cycling formulations based on new experimental patch-clamp data obtained in isolated rabbit ventricular myocytes, and developed a minimal seven-state Markovian model of I(Ca,L) that reproduced Ca- and voltage-dependent kinetics.

TL;DR: Overall, the results show that the four silks exhibit a common molecular organization, with mixtures of different amounts of beta-sheets and flexible structures, which are organized with specific orientation levels.

TL;DR: The condensing effect of cholesterol on phospholipid bilayers was systematically investigated for saturated and unsaturated chains, as a function of cholesterol concentration, using X-ray lamellar diffraction to measure the phosphate-to-phosphate distances.

TL;DR: It is concluded that SHG and TPF can characterize differential microscopic features of the collagen hydrogel that are strongly correlated with bulk mechanical properties and may be a useful noninvasive tool to assess tissue mechanics.

TL;DR: This critical review was motivated by the 10th Biophysical Discussions meeting, “Molecular Motors: Point Counterpoint”, held in Asilomar, CA, during October 19–22, 2006, and presents a personal perspective on the current state of kinesin motor mechanics.

TL;DR: A physical model of anomalous subdiffusion due to a combination of binding sites and barriers is translated directly into a plausible biological model testable by single-particle tracking.

TL;DR: The effects of the membrane lateral pressure profile on the conformation or insertion of proteins in membranes are equivalent to the elastic response to the frustrated spontaneous curvature, c(o), of the component lipid monolayer leaflets.

TL;DR: This model provides a quantitative framework to test hypotheses on the biochemical and biomechanical mechanisms that control tumor-induced angiogenesis and shows inhomogeneities in the extravascular tissue lead to sprout branching and anastomosis, phenomena that emerge without any prescribed rules.

TL;DR: N nanoscale resolution in far-field fluorescence microscopy is demonstrated using reversible photoswitching and localization of individual fluorophores at comparatively fast recording speeds and from the interior of intact cells by asynchronously recording the photon bursts of individual molecular switching cycles.

TL;DR: Results of this study indicate that cell transformation and tumorigenicity are associated with a decrease in cell modulus and apparent viscosity, suggesting that cell mechanical properties may provide insight into the metastatic potential and invasiveness of a cell.

TL;DR: The results support recent suggestions that boundary lubrication and wear protection in articular joints are due to the presence of a biological polyelectrolyte on the cartilage surfaces.

TL;DR: This article presents the first simulation to simultaneously consider a large ensemble of red blood cells and the cell deformation, and the numerical results allow us to investigate the variation of apparent blood viscosity along the cross-section of a vessel.

TL;DR: Both the mechanical properties of the cytOSkeleton and cytoskeleton-based processes, including cell motility, coupled MTOC and nucleus dynamics, and cell polarization, depend critically on the integrity of the nuclear lamina, which suggest the existence of a functional mechanical connection between the nucleus and the cytos skeleton.

TL;DR: The control of contour length and therefore the number of amino acids unraveled before reaching the disulfide bond facilitates the test of the chain length dependence on the folding time (tau(F), and both a power law scaling and an exponential scaling fit the data range, in support of different protein-folding scenarios.

TL;DR: It is postulate that the actin cytoskeleton plays a pivotal role in determining the hMSC mechanical properties and modulation of cellular mechanics at the early stage of stem-cell osteodifferentiation.

TL;DR: It is shown that the developed biomolecule-cND complex preserves the original functions of the test protein, and the easily detected natural fluorescent and Raman intrinsic signals, penetration ability, and low cytotoxicity of cNDs render them promising agents in multiple medical applications.

TL;DR: A three-stage mechanism consisting of protein misfolding, nucleation, and fibril elongation is proposed and supported by the features of homogeneous fibrillation responses, and the wide applicability of the model confirms thatfibrillation kinetics may be fairly similar among amyloid proteins and for different environmental factors.

TL;DR: It is proposed, on the basis of the observations, that intracellular fluids are maintained in a state similar to crowded polymer solutions under good solvent conditions to keep the cell viable.

TL;DR: Two-color fluorescence microscopy with nanoscale spatial resolution is demonstrated by applying stimulated emission depletion on fluorophores differing in their absorption and emission spectra and the approximately 5 nm alignment accuracy of the two images establishes the precision with which differently labeled proteins are correlated in space.

TL;DR: To the best of the authors' knowledge, this is the first report of label-free detection of mitochondria inside a somatic mammalian cell using Raman microspectroscopy.

TL;DR: It was found, using atomic force microscopy, that tendon collagen fibrils are composed of subcomponents in a spiral disposition-that is, their structure is similar to that of macroscale ropes.