Related papers: Three-helix-bundle Protein in a Ramachandran Model
First shells of hydration and bulk solvent plays a crucial role in the folding of proteins. Here, the role of water in the dynamics of proteins has been investigated using a theoretical protein-solvent model and a statistical physics…
Atomic-scale helices exist as motifs for several material lattices. We examine a tight-binding model for a single one-dimensional monatomic chain with a p-orbital basis coiled into a helix. A topologically nontrivial phase emerging from…
A microscopic theory of the free energy barriers and folding routes for minimally frustrated proteins is presented, greatly expanding on the presentation of the variational approach outlined previously [J. J. Portman, S. Takada, P. G.…
Supercooled water exhibits remarkably slow dynamics similar to the behavior observed for various glass-forming liquids. The local order of tetrahedral structures due to hydrogen-bonds (H-bonds) increases with decreasing temperature. Thus,…
The native state structures of globular proteins are stable and well-packed indicating that self-interactions are favored over protein-solvent interactions under folding conditions. We use this as a guiding principle to derive the geometry…
Triangular lattice models for pattern formation by hard-core soft-shell particles at interfaces are introduced and studied in order to determine the effect of the shell thickness and structure. In model I, we consider particles with…
We have performed a multicanonical molecular dynamics simulation on a simple model protein.We have studied a model protein composed of charged, hydrophobic, and neutral spherical bead monomers.Since the hydrophobic interaction is considered…
We present the results of a self-consistent, unified molecular dynamics study of simple model heteropolymers in the continuum with emphasis on folding, sequence design and the determination of the interaction parameters of the effective…
The dynamic behavior of bundles of actin filaments growing against a loaded obstacle is investigated through a generalized version of the standard multi filaments Brownian Ratchet model in which the (de)polymerizing filaments are treated…
One of the most puzzling and unsolved challenges in molecular biology is understanding how proteins fold. Despite having advanced predictive tools that can accurately estimate the native structures of proteins, we still lack a comprehensive…
The triaxial nature of low-lying rotational bands of $^{166}$Er is presented from the viewpoint of the Bohr Hamiltonian and from that of many-fermion calculations by the Monte Carlo shell model and the constrained Hartree-Fock method with…
Exchanging hydrophobic alkyl-based side chains to hydrophilic glycol-based side chains is a widely adopted method for improving mixed-transport device performance, despite the impact on solid state packing and polymer-electrolyte…
Stable bound quantum states are ubiquitous in nature. Mostly, they result from the interaction of only pairs of particles, so called two-body interactions, even when large complex many-particle structures are formed. We show that…
Using Wang-Landau sampling with suitable Monte Carlo trial moves (pull moves and bond-rebridging moves combined) we have determined the density of states and thermodynamic properties for a short sequence of the HP protein model. For free…
The prediction of the three-dimensional structures of the native state of proteins from the sequences of their amino acids is one of the most important challenges in molecular biology. An essential ingredient to solve this problem within…
Protein sequences serve as a natural record of the evolutionary constraints that shape their functional structures. We show that it is possible to use only sequence information to go beyond predicting native structures and global stability…
Molecular dynamics simulations are performed to study the temperature-dependent dynamics and structures of the hydration shells of elastin-like and collagen-like peptides. For both model peptides, it is consistently observed that, upon…
Exploring and understanding the protein-folding problem has been a long-standing challenge in molecular biology. Here, using molecular dynamics simulation, we reveal how parallel distributed adjacent planar peptide groups of unfolded…
Three-dimensional protein structures usually contain regions of local order, called secondary structure, such as $\alpha$-helices and $\beta$-sheets. Secondary structure is characterized by the local rotational state of the protein…
We consider a model of an extensible semiflexible filament moving in two dimensions on a motility assay of motor proteins represented explicitly as active harmonic linkers. Their heads bind stochastically to polymer segments within a…