Related papers: Dissecting Ubiquitin Folding Using the Self-Organi…
We adopt the point of view that analysis of the stability of the protein folding process is central to understanding the underlying physics of folding. Stability of the folding process means that many perturbations do not disrupt the…
Simple two-state folding kinetics of many small single-domain proteins are characterized by chevron plots with linear folding and unfolding arms consistent with a two-state description of equilibrium thermodynamics. This phenomenon is…
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,…
We study folding in 16-monomer heteropolymers on the square lattice. For a given sequence, thermodynamic properties and stability of the native state are unique. However, the kinetics of folding depends on the model of dynamics adopted for…
We present a novel Monte Carlo simulation of protein folding, in which all heavy atoms are represented as interacting hard spheres. This model includes all degrees of freedom relevant to folding - all sidechain and backbone torsions - and…
We solve a two dimensional model for polymer chain folding in the presence of mechanical pulling force ($f$) exactly using equilibrium statistical mechanics. Using analytically derived expression for the partition function we determine 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…
Protein folding cooperativity is defined by the nature of the finite-size thermodynamic transition exhibited upon folding: two-state transitions show a free energy barrier between the folded and unfolded ensembles, while downhill folding is…
Repeat proteins are made with tandem copies of similar amino acid stretches that fold into elongated architectures. Due to their symmetry, these proteins constitute excellent model systems to investigate how evolution relates to structure,…
The conformational change of biological macromolecule is investigated from the point of quantum transition. A quantum theory on protein folding is proposed. Compared with other dynamical variables such as mobile electrons, chemical bonds…
In order to understand the nuclei which develop during the course of protein folding and unfolding, we examine phase segregation of a single heteropolymer chain which occurs in equilibrium. These segregated conformations are characterized…
Understanding how monomeric proteins fold under in vitro conditions is crucial to describing their functions in the cellular context. Significant advances both in theory and experiments have resulted in a conceptual framework for describing…
Single-molecule experiments provide new insights into biological processes hitherto not accessible by measurements performed on bulk systems. We report on a study of the kinetics of a triple-branch DNA molecule with four conformational…
We have used computer simulation to study the collapse of a hydrophobic chain in water. We find that the mechanism of collapse is much like that of a first order phase transition. The evaporation of water in the vicinity of the polymer…
The relevance of various residue positions for the stability and the folding characteristics of the prion protein are investigated by using molecular dynamics simulations of models exploiting the topology of the native state. Highly…
We consider the statistical mechanics of a full set of two-dimensional protein-like heteropolymers, whose thermodynamics is characterized by the coil-to-globular ($T_\theta$) and the folding ($T_f$) transition temperatures. For our model,…
Kinetics of conformational change of a semiflexible polymer under mechanical external field were investigated with Langevin dynamics simulations. It is found that a semiflexible polymer exhibits large hysteresis in mechanical…
We investigate the dynamics and the pathways of the collapse of a single, semiflexible polymer in a poor solvent via 3-D Brownian Dynamics simulations. Earlier work indicates that the condensation of semiflexible polymers generically…
Ultra-cold RbCs molecules in high-lying vibrational levels of the a$^3\Sigma^+$ ground electronic state are confined in an optical trap. Inelastic collision rates of these molecules with both Rb and Cs atoms are determined for individual…
A model which treats the denatured and the native conformers as being confined to harmonic Gibbs energy wells has been used to rationalize the physical basis for the non-Arrhenius behaviour of spontaneously-folding fixed two-state systems.…