Related papers: Structure fluctuations and conformational changes …
The copy number of any protein fluctuates among cells in a population; characterizing and understanding these fluctuations is a fundamental problem in biophysics. We show here that protein distributions measured under a broad range of…
We study the dynamics of hydration water/protein association in folded proteins, using lysozyme and myoglobin as examples. Extensive molecular dynamics simulations are performed to identify underlying mechanisms of the dynamical transition…
Geometric and structural constraints greatly restrict the selection of folds adapted by protein backbones, and yet, folded proteins show an astounding diversity in functionality. For structure to have any bearing on function, it is thus…
Globular proteins are expected to assume folds with fixed secondary structures, alpha-helices and beta-sheets. Fold-switching proteins challenge this expectation by remodeling their secondary and/or tertiary structures in response to…
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…
Changes in the extent of local concavity along with changes in surface roughness of binding sites of proteins have long been considered as useful markers to identify functional sites of proteins. However, an algorithm that describes the…
What are the molecular mechanisms that dictate protein-protein binding stability and whether those are related to the ones behind protein fold stability are still largely open questions. Indeed, despite many past efforts, we still lack…
We investigate proteins within heterogeneous cell membranes where non-equilibrium phenomena arises from spatial variations in concentration and temperature. We develop simulation methods building on non-equilibrium statistical mechanics to…
Sequentially-built random sphere-packings have been numerically studied in the packing fraction interval $0.329 < \gamma < 0.586$. For that purpose fast running geometrical algorithms have been designed in order to build about 300…
Understanding of the evolutionary origins of protein structures represents a key component of the understanding of molecular evolution as a whole. Here we seek to elucidate how the features of an underlying protein structural "space" might…
We study the geometrical features of the order parameter's fluctuations near the critical point of mixed-order phase transitions in randomly interdependent spatial networks. In contrast to continuous transitions, where the structure of the…
Availability of high-resolution crystal structures of ribosomal subunits of different species opens a route to investigate about molecular interactions between its constituents and stabilization strategy. Structural analysis of the small…
A growing number of experimental evidence shows that it is general for a ligand binding protein to have a potential for allosteric regulation and for further evolution. In addition, such proteins generically change their conformation upon…
For biologically relevant macromolecules such as intrinsically disordered proteins, internal degrees of freedom that allow for shape changes have a large influence on both the motion and function of the compound. A detailed understanding of…
Due to the time-scale limitations of all-atom simulation of proteins, there has been substantial interest in coarse-grained approaches. Some methods, like "Resolution Exchange," [E. Lyman et al., Phys. Rev. Lett. 96, 028105 (2006)] can…
Conformation of a protein (CorA) is examined in a matrix with mobile solute constituents as a function of solute-residue interaction strength (f) by a coarse-grained model with a Monte Carlo simulation. Solute particles are found to reach…
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 new statistical mechanics formulation of characterizing the structural fluctuation of protein correlated with that of water is presented based on the generalized Langevin equation and the 3D-RISM/RISM theory of molecular liquids. The…
Sidechain rotamer libraries of the common amino acids of a protein are useful for folded protein structure determination and for generating ensembles of intrinsically disordered proteins (IDPs). However much of protein function is modulated…
The past decade has witnessed the development and success of coarse-grained network models of proteins for predicting many equilibrium properties related to collective modes of motion. Curiously, the results are usually robust towards the…