Related papers: Cooperativity in Protein Folding: From Lattice Mod…
The quantitative description of model protein folding kinetics using a diffusive collective reaction coordinate is examined. Direct folding kinetics, diffusional coefficients and free energy profiles are determined from Monte Carlo…
Unbiased, label-free proteomics is becoming a powerful technique for measuring protein expression in almost any biological sample. The output of these measurements after preprocessing is a collection of features and their associated…
In simple models side chains are often represented implicitly (e.g., by spin-states) or simplified as one atom. We study side chain effects using square lattice and tetrahedral lattice models, with explicitly side chains of two atoms. We…
A grand canonical Monte Carlo (MC) algorithm is presented for studying the lattice gas model (LGM) of multiple protein sequence alignment, which coherently combines long-range interactions and variable-length insertions. MC simulations are…
Using analytical calculations and computer simulations we consider both the lateral diffusion of a membrane protein and the fluctuation spectrum of the membrane in which the protein is embedded. The membrane protein interacts with the…
A theory is presented for lambda_C, the coefficient of the first-order correction in the density of the collective diffusion coefficient, for protein spheres interacting by electrostatic and adhesive forces. An extensive numerical analysis…
The dynamics of a folded protein is studied in water and glycerol at a series of temperatures below and above their respective dynamical transition. The system is modeled in two distinct states whereby the protein is decoupled from the bulk…
The effect of cooling on a number of observables is calculated in SU(2) lattice gauge theory. The static quark-antiquark potential and spin-dependent interactions are studied, and the topological charge is monitored. The chiral symmetry…
A simple d-dimensional lattice model is proposed, incorporating some degree of frustration and thus capable of describing some aspects of molecular orientation in covalently bound molecular solids. For d=2 the model is shown to be…
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…
The utility of a cooperative length scale for describing the dynamics of small molecule glass-formers is shown. Molecular Dynamics and Monte Carlo simulations reveal a distribution of cooperatively moving fractal events below the…
The coil to globule transition of the polypeptide chain is the physical phenomenon behind the folding of globular proteins. Globular proteins with a single domain usually consist of about 30 to 100 amino acid residues, and this finite size…
We present a solvable model that predicts the folding kinetics of two-state proteins from their native structures. The model is based on conditional chain entropies. It assumes that folding processes are dominated by small-loop closure…
The protein folding problem must ultimately be solved on all length scales from the atomic up through a hierarchy of complicated structures. By analyzing the stability of the folding process using physics and mathematics, this paper shows…
We investigate the interplay between post-translational folding and escape of two small single-domain proteins at the ribosomal exit tunnel by using Langevin dynamics with coarse-grained models. It is shown that at temperatures lower or…
We examine changes in the picosecond structural dynamics with irreversible photobleaching of red fluorescent proteins mCherry, mOrange2 and TagRFP-T. Measurements of the protein dynamical transition using terahertz time-domain spectroscopy…
Fragility index and cooperativity length characterizing the molecular mobility in the amorphous phase are for the first time calculated in drawn polylactide (PLA). The microstructure of the samples is investigated from wide-angle X-ray…
We propose a new statistical mechanics model for the melting transition of DNA. Base pairing and stacking are treated as separate degrees of freedom, and the interplay between pairing and stacking is described by a set of local rules which…
Natural proteins fold to a unique, thermodynamically dominant state. Modeling of the folding process and prediction of the native fold of proteins are two major unsolved problems in biophysics. Here, we show successful all-atom ab initio…
The multiple sequence alignment (MSA) of a protein family provides a wealth of information in terms of the conservation pattern of amino acid residues not only at each alignment site but also between distant sites. In order to statistically…