相关论文: Inherent flexibility determines the transition mec…
Proteins' fuzziness are features for communicating changes in cell signaling instigated by binding with secondary messengers, such as calcium ions, associated with the coordination of muscle contraction, neurotransmitter release, and gene…
Conventional kinesin is a homodimeric motor protein that is capable of walking unidirectionally along a cytoskeletal filament. While previous experiments indicated unyielding unidirectionality against an opposing load up to the so-called…
In this article we use all-atom simulations to elucidate the mechanisms underlying conformational switching and allostery within the coat protein of the bacteriophage MS2. Assembly of most icosahedral virus capsids requires that the capsid…
The process of protein folding from an unfolded state to a biologically active, folded conformation is governed by many parameters e.g the sequence of amino acids, intermolecular interactions, the solvent, temperature and chaperon…
Biological membranes are elastic media in which the presence of a transmembrane protein leads to local bilayer deformation. The energetics of deformation allow two membrane proteins in close proximity to influence each other's equilibrium…
Phagocytosis is a fundamental process of the innate immune system, yet the physical determinants that govern the engulfment of soft, deformable targets remain poorly understood. Existing theoretical models typically approximate targets as…
In the protein sequence space, natural proteins form clusters of families which are characterized by their unique native folds whereas the great majority of random polypeptides are neither clustered nor foldable to unique structures. Since…
Most single-molecule studies derive the kinetic rates of native, intermediate, and unfolded states from equilibrium hopping experiments. Here, we apply Kramers kinetic diffusive model to derive the force-dependent kinetic rates of…
The chromatin fiber is a complex of DNA and specific proteins called histones forming the first structural level of organization of eukaryotic chromosomes. In tightly organized chromatin fibers, the short segments of naked DNA linking the…
Combining simulations and theory I study the interplay between bundle elastic degrees of freedom and crosslink binding propensity. By slowly driving bundles into a deformed configuration, and depending on the mechanical stiffness of the…
Over the years, advances in experimental and computational methods have helped us to understand the role of thermodynamic, kinetic and active (chaperone-aided) effects in coordinating the folding steps required to achieving a knotted native…
We consider a general incompressible finite model protein of size M in its environment, which we represent by a semiflexible copolymer consisting of amino acid residues classified into only two species (H and P, see text) following Lau and…
We investigate the sliding strength of thin filaments in frictional contact with a translating cylinder, perpendicular to the filaments' axes, in knotted (clove hitch) and unknotted (capstan) configurations. Recent work reported superlinear…
For biologically relevant macromolecules such as intrinsically disordered proteins, internal degrees of freedom that allow for shape changes have a large influence on both the motion and function of the compound. A detailed understanding of…
The Extra-Cellular-Matrix (ECM) is a complex interconnected 3D network that provides structural support for the cells and tissues and defines organ architecture key for their healthy functioning. However, the intimate mechanisms by which…
Cooperative action of molecular motors is essential for many cellular processes. One possible regulator of motor coordination is the elasticity-mediated crosstalk (EMC) coupling between myosin II motors whose origin is the tensile stress…
Stretching of a protein by a fluid flow is compared to that in a force-clamp apparatus. The comparison is made within a simple topology-based dynamical model of a protein in which the effects of the flow are implemented using Langevin…
The functionality of protein-protein complexes is closely tied to the strength of their interactions, making the evaluation of binding affinity a central focus in structural biology. However, the molecular determinants underlying binding…
Using numerical simulations, we characterized the behavior of an elastic membrane immersed in an active fluid. Our findings reveal a nontrivial folding and re-expansion of the membrane that is controlled by the interplay of its resistance…
Polymers with active segments constitute prospective future materials and are used as a model for some biological systems such as chromatin. The directions of the active forces are typically introduced with temporal or spatial correlations…