Showing papers in "Biophysical Journal in 2018"

TL;DR: A historical account of the development of ensemble docking is given and some pertinent methodological advances in conformational sampling are discussed.

TL;DR: Two phase separation mechanisms can explain that chromatin bodies are dynamic spherical structures, which can coalesce and are in constant and rapid exchange with the surrounding nucleoplasm, however, they make distinct predictions about how the size, density, and stability of Chromatin bodies depends on the concentration and interaction behavior of the molecules involved.

TL;DR: In this article, it was shown that Drosophila HP1a protein undergoes liquid-liquid demixing in vitro, and nucleates into foci that display liquid properties during the early stages of heterochromatin domain formation in early Drosphila embryos, suggesting that the repressive action of H1 may be mediated in part by emergent properties of phase separation.

TL;DR: In this article, a non-catalytic domain within CRISPR-Cas9, REC3, recognizes target mismatches and governs the HNH nuclease to regulate overall catalytic competence.

TL;DR: The results reveal that both the binding pose and residue substitutions within PETase favor proximity between the catalytic residues and the labile carbonyl of the substrate at room temperature, suggesting a more favorable hydrolytic reaction.

TL;DR: This work identifies the local coordination number (or connectivity) 〈z〉 as a key architectural parameter that governs the elastic response of collagen and shows that the initial stress-stiffening response of collagen networks is controlled by the negative normal stress that builds up under shear.

TL;DR: The presented work constitutes the first step toward an in vivo assessment of spinal cord tissue mechanics during regeneration, provides a methodical basis to identify key determinants of mechanical tissue properties, and allows us to test their relative importance in combination with biochemical and genetic factors during developmental and regenerative processes.

TL;DR: In this article, a model with differential attraction between euchromatin and heterochromatin leads to phase separation and reproduces compartmentalization as observed in Hi-C. The results suggest that chromatin organization on the megabase scale emerges from competition of nonequilibrium active loop extrusion and epigenetically defined compartment structure.

TL;DR: This method uses a convex hull model to estimate the hydrodynamic volume of the molecule and is orders of magnitude faster than common methods and works well for both folded proteins and ensembles of conformationally heterogeneous proteins and for nucleic acids.

TL;DR: A coarse-grained model for plastic deformation of collagen networks that can be employed to simulate multicellular interactions in processes such as morphogenesis, cancer invasion, and fibrosis is developed.

TL;DR: PAM (pulsed interleaved excitation analysis with MATLAB), an open-source software package written in MATLAB that offers a simple and efficient workflow through its graphical user interface, is presented.

TL;DR: Study of the active diffusion of vesicles in mouse oocytes reveals that measuring in vivo active fluctuations allows extraction of the molecular-scale activity in agreement with single-molecule studies and demonstrates a mesoscopic framework to access force kinetics.

TL;DR: Here, a general theory is reported to determine the true Young's moduli of a single cell from a force-indentation curve and the influence of the solid support on the measurements is reduced by using sharp and high aspect ratio tips.

TL;DR: The recent discovery of a new -taxis phenomenon, the topotaxis, which mediates directional cell migration in response to the gradients of such topographic features as the density of extracellular matrix fibers is highlighted.

TL;DR: It is shown that the mean DOL of the cell-bound antibody fraction is lower than that of the stock using single molecule fluorescence measurements, showing multiple effects of fluorophore conjugation, which must not be overlooked in quantitative cell biological measurements.

TL;DR: An integrative modeling approach is reported to simultaneously determine structure and dynamics of macromolecular systems from cryo-electron microscopy density maps and provide insights into the mechanisms by which the integral membrane receptor STRA6 interacts with retinol binding protein and translocatesretinol across the membrane.

TL;DR: It is found that both Aβ40 and Aβ42 populate an ensemble of rapidly reconfiguring unfolded states, with no long-lived conformational state distinguishable from that of the disordered ensemble, giving rise to very similar ensemble-averaged FRET efficiencies.

TL;DR: A sphere-with-skirt surface reveals that nonzero Gaussian curvature not only affects the positioning of cells and alignment of stress fiber subpopulations but also directs migration in a manner fundamentally distinct from that of migration on planar surfaces.

TL;DR: It is found that DNA local flexibility, not simply charge density, determines the LLPS and a role of local DNA flexibility, encoded in the sequence, in the regulation and selectivity of multicomponent LLPS in membraneless intracellular organization is pointed toward.

TL;DR: Self-assembling polypeptide coacervates are employed to explore the partitioning of the ubiquitous cytoskeletal protein actin into liquid polymer-rich droplets and suggest that coacerville can serve as a versatile platform in which to localize and enrich biomolecules to study their reactivity in physiological environments.

TL;DR: This work reconstituted the LD formation topology by embedding artificial LDs into the intermonolayer space of bilayer vesicles and determined that slight tension asymmetries between the membrane monolayers regulate the droplet budding side.

TL;DR: Results from a comprehensive series of experiments using fluorescence correlation spectroscopy and single-molecule tracking indicate that full-length K-Ras4B lacks intrinsic dimerization capability, suggesting that any lateral organization of Ras in living cell membranes likely stems from interactions with other factors.

TL;DR: A tool called CONtact ANalysis (CONAN) is proposed that, from molecular dynamics (MD) trajectories, analyzes interresidue contacts, creates videos of time-resolved contact maps, and performs correlation, principal component, and cluster analysis, revealing how specific contacts relate to functionally relevant states sampled by MD.

TL;DR: Recent advances in microdroplet chemistry that accelerate reaction rates by many orders of magnitude as compared to bulk are highlighted and it is suggested that similar mechanisms may also affect reaction kinetics in cellular condensates.

TL;DR: A mechanical explanation for the early cell shrinkage event induced by melittin and a variety of other cationic peptides is proposed, based on curvature stress concepts derived from model bilayer studies.

TL;DR: PyContact, an easy-to-use, highly flexible, and intuitive graphical user interface-based application, designed to provide a toolkit to investigate biomolecular interactions in MD trajectories, analyzes and visualizes the noncovalent interactions underlying the ion permeation pathway of the human P2X3 receptor.

TL;DR: The data show that the force-sensitive dynamics of vinculin impact force transmission and enable the mechanical integration of subcellular processes, suggesting that the regulation of force- sensitive protein dynamics may have an underappreciated role in many cellular processes.

TL;DR: Self-assembly experiments show that small nanodisks are the thermodynamically preferred end state, which can be an important step toward the design of optimized extraction tools for membrane protein research.

TL;DR: The results are consistent with the energetically preferred location of POPE residing in the inner leaflet, where it also resides in natural membranes, most likely causing the coupling of both leaflets, and no evidence for transbilayer structural coupling above the melting temperature of either sample preparation is found.