相关论文: Excluded volume, local structural cooperativity,an…

We present a simple model of protein folding dynamics that captures key qualitative elements recently seen in all-atom simulations. The goals of this theory are to serve as a simple formalism for gaining deeper insight into the physical…

Folding kinetics of a lattice model of protein is studied. It uses the Random Energy Model for the intrachain couplings and a temperature dependent free energy of solvation derived from a realistic hydration model of apolar solutes. The…

A variety of experimental and theoretical studies have established that the folding process of monomeric proteins is strongly influenced by the topology of the native state. In particular, folding times have been shown to correlate well…

We describe the results obtained from an improved model for protein folding. We find that a good agreement with the native structure of a 46 residue long, five-letter protein segment is obtained by carefully tuning the parameters of the…

The folding kinetics of a number of sequences for off-lattice continuum model of proteins is studied using Langevin simulations at two values of the friction coefficient. We show that there is a remarkable correlation between folding times,…

Polymer networks formed by cross linking flexible polymer chains are ubiquitous in many natural and synthetic soft-matter systems. Current micromechanics models generally do not account for excluded volume interactions except, for instance,…

Chromatin and associated proteins constitute the highly folded structure of chromosomes. We consider a self-avoiding polymer model of the chromatin, segments of which may get cross-linked via protein binders that repel each other. The…

Novel numerical techniques, validated by an analysis of barnase and chymotrypsin inhibitor, are used to elucidate the paramount role played by the geometry of the protein backbone in steering the folding to the correct native state. It is…

Based on the wormlike chain model, a coarse-grained description of the nonlinear dynamics of a weakly bending semiflexible polymer is developed. By means of a multiple scale perturbation analysis, a length-scale separation inherent to the…

Applying multicanonical simulations we investigated folding properties of off-lattice heteropolymers employing a mesoscopic hydrophobic-polar model. We study for various sequences folding channels in the free-energy landscape by comparing…

We develop a theoretical approach to the protein folding problem based on out-of-equilibrium stochastic dynamics. Within this framework, the computational difficulties related to the existence of large time scale gaps in the protein folding…

The thermodynamic properties for three different types of off-lattice four-strand beta-sheet protein models interacting via a hybrid Go-type potential have been investigated. Discontinuous molecular dynamic simulations have been performed…

We present a theoretical study of the folding of small proteins inside confining potentials. Proteins are described in the framework of an effective potential model which contains the Ramachandran angles as degrees of freedom and does not…

Natural protein sequences somehow encode the structural forms that these molecules adopt. Recent developments in structure-prediction are agnostic to the mechanisms by which proteins fold and represent them as static objects. However, the…

Scaling of folding times in Go models of proteins and of decoy structures with the Lennard-Jones potentials in the native contacts reveal %robust power law trends when studied under optimal folding conditions. The power law exponent depends…

Extensive Monte Carlo folding simulations for four proteins of various structural classes are carried out, using a single atomistic potential. In all cases, collapse occurs at a very early stage, and proteins fold into their native-like…

In spite of decades of research, much remains to be discovered about folding: the detailed structure of the initial (unfolded) state, vestigial folding instructions remaining only in the unfolded state, the interaction of the molecule with…

Many biological processes are supported by special molecules, called motor proteins or molecular motors, that transport cellular cargoes along linear protein filaments and can reversibly associate to their tracks. Stimulated by these…

Molecular dynamics simulation methods are used to study the folding of polymer chains into packed cubic states. The polymer model, based on a chain of linked sites moving in the continuum, includes both excluded volume and torsional…

Molecular dynamics studies of Go models of proteins with the 10-12 contact potential and the bond and dihedral angle terms indicate statistical similarities to other Go models, e.g. with the Lennard-Jones contact potentials. The folding…