Related papers: Soliton driven relaxation dynamics and universalit…
In this paper we show that a dynamical description of the protein folding process provides an effective representation of equilibrium properties and it allows for a direct investigation of the mechanisms ruling the approach towards the…
A geometric analysis of protein folding, which complements many of the models in the literature, is presented. We examine the process from unfolded strand to the point where the strand becomes self-interacting. A central question is how it…
We propose that protein loops can be interpreted as topological domain-wall solitons. They interpolate between ground states that are the secondary structures like alpha-helices and beta-strands. Entire proteins can then be folded simply by…
Here we review the development of protein scaling theory, starting from backgrounds in mathematics and statistical mechanics, and leading to biomedical applications. Evolution has organized each protein family in different ways, but scaling…
The folding dynamics of small single-domain proteins is a current focus of simulations and experiments. Many of these proteins are 'two-state folders', i.e. proteins that fold rather directly from the denatured state to the native state,…
Developing accurate and efficient coarse-grained representations of proteins is crucial for understanding their folding, function, and interactions over extended timescales. Our methodology involves simulating proteins with molecular…
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,…
A reduced model, which can fold both helix and sheet structures, is proposed to study the problem of protein folding. The goal of this model is to find an unbiased effective potential that has included the effects of water and at the same…
To address the large gap between time scales that can be easily reached by molecular simulations and those required to understand protein dynamics, we propose a rapid self-consistent approximation of the side chain free energy at every…
Protein folding is one of the age-old biological problems that refers to the mechanism of understanding and predicting how a protein's linear sequence of amino acids folds into its specific three dimensional structure.This structure is…
The determination of the folding mechanisms of proteins is critical to understand the topological change that can propagate Alzheimer and Creutzfeld-Jakobs diseases, among others. The computational community has paid considerable attention…
The folding mechanism of the Villin headpiece (HP36) is studied by means of a novel approach which entails an initial coarse-grained Monte Carlo (MC) scheme followed by all-atom molecular dynamics (MD) simulations in explicit solvent. The…
Understanding the protein folding process is an outstanding issue in biophysics; recent developments in molecular dynamics simulation have provided insights into this phenomenon. However, the large freedom of atomic motion hinders the…
Single molecule force spectroscopy methods can be used to generate folding trajectories of biopolymers from arbitrary regions of the folding landscape. We illustrate the complexity of the folding kinetics and generic aspects of the collapse…
The motion involved in barrier crossing for protein folding are investigated in terms of the chain dynamics of the polymer backbone, completing the microscopic description of protein folding presented in the previous paper. Local reaction…
We discuss recent theoretical developments in the study of simple lattice models of proteins. Such models are designed to understand general features of protein structures and mechanism of folding. Among the topics covered are (i) the use…
Coarse-grained (lattice-) models have a long tradition in aiding efforts to decipher the physical or biological complexity of proteins. Despite the simplicity of these models, however, numerical simulations are often computationally very…
Using Monte Carlo dynamics and the Monte Carlo Histogram Method, the simple three-dimensional 27 monomer lattice copolymer is examined in depth. The thermodynamic properties of various sequences are examined contrasting the behavior of good…
A generalized computational method for folding proteins with a fully transferable potential and geometrically realistic all-atom model is presented and tested on seven different helix bundle proteins. The protocol, which includes…
The enterobacteria lambda phage is a paradigm temperate bacteriophage. Its lysogenic and lytic life cycles echo competition between the DNA binding $\lambda$-repressor (CI) and CRO proteins. Here we scrutinize the structure, stability and…