Related papers: Rigidity of transmembrane proteins determines thei…
Adsorption of proteins onto membranes can alter the local membrane curvature. This phenomenon has been observed in biological processes such as endocytosis, tubulation and vesiculation. However, it is not clear how the local surface…
By means of extensive replica-exchange simulations of generic coarse-grained models for helical polymers, we systematically investigate the structural transitions into all possible helical phases for flexible and semiflexible elastic…
Under dehydration conditions, amphipathic Late Embryogenesis Abundant (LEA) proteins fold spontaneously from a random conformation into alpha-helical structures and this transition is promoted by the presence of membranes. To gain insight…
The plane of bacterial cell division must be precisely positioned. In the bacterium Myxococcus xanthus, the proteins PomX and PomY form a large cluster, which is tethered to the nucleoid by the ATPase PomZ and moves in a stochastic, but…
We construct a coarse-grained model of parallel actin bundles crosslinked by compact, globular bundling proteins, such as fascin and espin, necessary components of filapodial and mechanosensory bundles. Consistent with structural…
Protein structures in nature often exhibit a high degree of regularity (secondary structures, tertiary symmetries, etc.) absent in random compact conformations. We demonstrate in a simple lattice model of protein folding that structural…
We develop methods for investigating protein drift-diffusion dynamics in heterogeneous cell membranes and the roles played by geometry, diffusion, chemical kinetics, and phase separation. Our hybrid stochastic numerical methods combine…
The sequence of a protein is not only constrained by its physical and biochemical properties under current selection, but also by features of its past evolutionary history. Understanding the extent and the form that these evolutionary…
The interplay of membrane proteins is vital for many biological processes, such as cellular transport, cell division, and signal transduction between nerve cells. Theoretical considerations have led to the idea that the membrane itself…
We investigate the nonequilibrium dynamics of semiflexible polymers driven by motor proteins (MPs) in two-dimensional motility assays under harmonic confinement. Using a coarse-grained agent-based model that incorporates stochastic motor…
Structure-based virtual screening aims to identify high-affinity ligands by estimating binding free energies between proteins and small molecules. However, the conformational flexibility of both proteins and ligands challenges conventional…
The assembly of banana-shaped rodlike proteins on membranes, and the associated membrane shape transformations, are investigated by analytical theory and coarse-grained simulations. The membrane-mediated interactions between two…
The increasing number of protein-based metamaterials demands reliable and efficient theoretical and computational methods to study the physicochemical properties they may display. In this regard, we develop a simulation strategy based on…
Semiflexible polymers form central structures in biological material. Modeling approaches usually neglect influences of polymer-specific molecular features aiming to describe semiflexible polymers universally. Here, we investigate the…
Availability of high-resolution crystal structures of ribosomal subunits of different species opens a route to investigate about molecular interactions between its constituents and stabilization strategy. Structural analysis of the small…
Disordered networks of semiflexible filaments are common support structures in biology. Familiar examples include fibrous matrices in blood clots, bacterial biofilms, and essential components of cells and tissues of plants, animals, and…
We present a model, based on symmetry and geometry, for proteins. Using elementary ideas from mathematics and physics, we derive the geometries of discrete helices and sheets. We postulate a compatible solvent-mediated emergent pairwise…
Confinement is a versatile and well-established tool to study the properties of polymers either to understand biological processes or to develop new nano-biomaterials. We investigate the conformations of a semiflexible polymer ring in weak…
$\alpha$-helices stand out as common and relatively invariant secondary structural elements of proteins. However, $\alpha$-helices are not rigid bodies and their deformations can be significant in protein function ({\it e.g.} coiled coils).…
Whether live cell membranes show miscibility phase transitions (MPTs), and if so, how they fluctuate near the transitions remain outstanding unresolved issues in physics and biology alike. Motivated by these questions we construct a generic…