Related papers: The Role of Structure in the Protein Dynamical Tra…
Combining elastic incoherent neutron scattering experiments at different resolutions with molecular dynamics simulations, we report the observation of a protein-like dynamical transition in linear chains of Poly(N-isopropylacrylamide). We…
Protein folding is analyzed using a replica variational formalism to investigate some free energy landscape characteristics relevant for dynamics. A random contact interaction model that satisfies the minimum frustration principle is used…
We have numerically studied the thermodynamic properties of the spin 1/2 XXZ chain in the presence of a transverse (non commuting) magnetic field. The thermal, field dependence of specific heat and correlation functions for chains up to 20…
Recently described stochastic models of protein evolution have demonstrated that the inclusion of structural information in addition to amino acid sequences leads to a more reliable estimation of evolutionary parameters. We present a…
The incredible thermo-mechanical properties of biological materials arise from the microscopic scale due to a complex hierarchical mechanism, regulated by microinstabilities at the molecular level. The description of such complex structures…
The authors study the short-time dynamics of helix-forming polypeptide chains using an all-atom representation of the molecules and an implicit solvation model to approximate the interaction with the surrounding solvent. The results confirm…
Enhanced dynamical fluctuations of RNAs, facilitated by a network of water molecules with strong interactions with RNA, are suspected to be critical in their ability to respond to a variety of cellular signals. Using atomically detailed…
We investigate the presence of structural collective motions on a picosecond time scale for the heme protein, cytochrome c, as a function of oxidation and hydration, using terahertz (THz) time-domain spectroscopy and molecular dynamics…
Understanding the molecular mechanisms driving the binding between bio-molecules is a crucial challenge in molecular biology. In this respect, characteristics like the preferentially hydrophobic composition of the binding interfaces, the…
Protein motions occur on multiple time and distance scales. Large-scale motions of protein tertiary-structure elements, i.e. domains, are particularly intriguing as they are essential for the catalytic activity of many enzymes and for the…
There is renewed interest in the structure of the essential amino acid Phenylalanine in the solid state. Three new polymorphs were found in the years 2012 to 2014. Here, we investigate the structure, stability, and energetical ordering of…
Proteins, by virtue of their central role in most biological processes, represent one of the key subjects of the study of molecular evolution. Inherent to the indispensability of proteins for living cells is the fact that a given protein…
We have simulated structure and dynamics of water in the grooves of a DNA duplex using moleculear dynamics simulations. We find signatures of a dynamical transition in both translational and orientational dynamics of water molecules in both…
The effect of interactions on dynamics of coupled motor proteins is investigated theoretically. A simple stochastic discrete model, that allows to calculate explicitly the dynamic properties of the system, is developed. It is shown that…
Self Consistent Normal Mode Analysis (SCNMA) is applied to heme c type cytochrome f to study temperature dependent protein motion. Classical Normal Mode Analysis (NMA) assumes harmonic behavior and the protein Mean Square Displacement (MSD)…
We present results from all-atom molecular dynamics simulations for the nonequilibrium dynamics of the collapse and helix-coil transition in polyalanine. In particular, we compare the influence of three different thermostats, viz., the…
We analyze a microscopic RNA model, which includes two widely used models as limiting cases, namely it contains terms for bond as well as for stacking energies. We numerically investigate possible changes in the qualitative and quantitative…
We investigate the transport of proteins inside the proteasome and propose an active transport mechanism based on a spatially asymmetric interaction potential of peptide chains. The transport is driven by fluctuations which are always…
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…
Different aspects of protein folding are illustrated by simplified polymer models. Stressing the diversity of side chains (residues) leads one to view folding as the freezing transition of an heteropolymer. Technically, the most common…