Showing papers in "Biophysical Journal in 2015"

TL;DR: MDTraj is a modern, lightweight, and fast software package for analyzing MD simulations that simplifies the analysis of MD data and connects these datasets with the modern interactive data science software ecosystem in Python.

TL;DR: This work provides a high-resolution view of the lipid organization of a plasma membrane at an unprecedented level of complexity, consisting of 63 different lipid species, combining 14 types of headgroups and 11 types of tails asymmetrically distributed across the two leaflets, closely mimicking an idealized mammalian plasma membrane.

TL;DR: It is reported that actomyosin-generated cytoskeletal tension regulates nuclear shape and force transmission through the cytoskeleton and demonstrated the differential short- and long-term response of mesenchymal stem cells to dynamic tensile loading based on the contractility state, the patency of the actin cytos skeleton, and the connections it makes with the nucleus.

TL;DR: In this article, the authors show that when expressed from the same plasmid, the combinations of attainable protein concentrations are constrained by a linear relationship, which can be interpreted as an isocost line, a concept used in microeconomics.

TL;DR: This work disentangle mutual contributions of cell size and cell stiffness to cell deformation by a theoretical analysis in terms of hydrodynamics and linear elasticity theory and demonstrates that the analytical model not only predicts deformed shapes inside the channel but also allows for quantification of cell mechanical parameters.

TL;DR: A light sheet fluorescence microscope that achieves 390 nm isotropic resolution and high optical sectioning strength over large field of views, without the need for structured illumination or deconvolution-based postprocessing is presented.

TL;DR: The coarse-grain Martini force field is extended to include RNA, and the tertiary structure of RNA is constrained using an elastic network, which opens the way to large-scale explicit-solvent molecular dynamics simulations of complex systems involving RNA.

TL;DR: The data show that the ability to overcome the steric hindrance of the matrix cannot be attributed to a single cell property but instead arises from a combination of adhesiveness, nuclear volume, contractility, and cell stiffness.

TL;DR: This work systematically investigates small (dihedral angle flips in a protein), large (nucleosome tail collapse and DNA unwrapping), and mixed (folding of a miniprotein) conformational changes, with nominal simulation times ranging from nanoseconds to microseconds depending on system size.

TL;DR: It is found that the SMA copolymer is a highly efficient membrane-solubilizing agent and that lipid bilayer properties such as fluidity, thickness, lateral pressure profile, and charge density all play distinct roles in the kinetics of solubilization.

TL;DR: A phenomenological model to estimate local mechanical properties of central nervous system (CNS) tissue is developed, which may ultimately help predicting local tissue stiffness, and hence cell behavior in response to mechanical signaling under physiological and pathological conditions, purely based on histological data.

TL;DR: The results indicate that T lymphocytes face different cell rigidities when interacting with myeloid APCs in vivo and that this mechanical landscape changes under inflammation.

TL;DR: The finding that power-law rheology and collapse onto a master curve also applies to cells in suspension provides the foundation for a quantitative high-throughput measurement of cell mechanical properties with microfluidic devices.

TL;DR: All-atom simulation data are presented for ternary mixtures of palmitoyl sphingomyelin (PSM), cholesterol, and either palmitoysl oleoyl phosphatidyl choline or dioleoym phosphatids choline (DOPC) for comparison, and hydrogen bonding between cholesterol and the amide of PSM primes it for more robust hydrogen bonding with other PSM.

TL;DR: It is suggested that targeting intimal stiffening and/or the EC response to intima stiffening clinically may improve vascular health, and matrices mimicking young and healthy blood vessels can promote and augment the atheroprotective signals induced by fluid shear stress.

TL;DR: Exhaustive docking of CL to all known structures of proteins experimentally shown to interact with CL demonstrated the validity of the docking approach, and provides a rich source of information for experimentalists who may wish to validate predictions.

TL;DR: It is shown that the opportunistic pathogen Pseudomonas aeruginosa obeys the incremental rule to achieve cell-length homeostasis during exponential growth but shortens its cells when entering the stationary phase, suggesting that a deficiency in DNA segregation prevents cell division without slowing the exponential elongation rate.

TL;DR: Investigation of the interaction of MP1 with model membranes in the presence and absence of POPS (PS) and DOPE (PE) to understand the role of lipid composition in MP1’s anticancer characteristics finds that PS and PE lipids synergistically combine to enhance membrane poration by MP1, implying that the combined enrichment of both these lipids in the outer leaflet of cancer cells is highly significant for MP1's anticancer action.

TL;DR: Atomic force microscopy time-lapse imaging and mechanical mapping of actin in the cortex of living cells at high lateral and temporal resolution are performed, yielding attuned cortex networks with specific connectivity, mechanical responses, and marked differences in their dynamic behavior.

TL;DR: It is shown that aging takes place in the absence of visible changes in the microtubule wall or tip, as this complex molecular-mechanical system evolves slowly and asymptotically toward the steady-state level of the catastrophe-promoting configurations.

TL;DR: Ca-voltage coupling combined with the nonlinear dynamical behaviors of voltage and Ca cycling play a key role in generating complex EAD and DAD dynamics observed experimentally in cardiac myocytes, whose mechanisms are complex but analyzable.

TL;DR: Density fluctuations at the single- and multicell level are studied, finding that single-cell volumes oscillate with a timescale of 4 h and an amplitude of 20%; the timescale and amplitude are found to depend on cytoskeletal activity.

TL;DR: The results establish a direct connection between discrete and continuum descriptions of cell sheets and can be used to probe a wide range of morphogenetic processes in epithelial tissues.

TL;DR: A method that incorporates solution scattering data as a differentiable energetic restraint into explicit-solvent MD simulations, termed SWAXS-driven MD, with the aim to direct the simulation into conformations satisfying the experimental data is presented.

TL;DR: Computer simulations of a random network comprised of cross-linked biopolymer-like fibers are used to substantiate the notion that this universality lies in the existence of two fundamental stiffening mechanisms and demonstrate how material properties of the constituents, as well as the network microstructure, can affect the transition between the two stiffening mechanism and control the dominant power-law scaling behavior.

TL;DR: A computational model for nuclear and cell mechanics is proposed that shows how frictional transmission of stress from the moving cell boundaries to the nuclear surface shapes the nucleus during early cell spreading, pointing to a surprisingly simple mechanical system in cells for establishing nuclear shapes.

TL;DR: The results establish the importance of myosin II as an active component in modulating suspended cell mechanics, with a functional role distinctly different from that for substrate-adhered cells.

TL;DR: The results indicate that even though membrane tension equilibrates rapidly and mechanically couples local boundary dynamics over cellular scales, steady-state variations in tension can exist in the plasma membranes of moving cells.

TL;DR: In this paper, a combination of functional, structural, and biophysical experiments was performed to investigate the structure and peroxidase activity of cyt-c in its membrane-bound state.

TL;DR: It is shown that inner- and outer-leaflet Lo domains can have significantly different physical properties, and in asymmetric vesicles containing egg SM, outer- and inner-leaflets Lo domains were also depleted in a saturated fluorescent lipid (NBD-DPPE), while inner- leafletLo domains were not.