Conformational sampling of peptides in the presence of protein crowders from AA/CG-multiscale simulations.

ABSTRACT: Macromolecular crowding is recognized as an important factor influencing folding and conformational dynamics of proteins and nucleic acids. Previous views of crowding have focused on the mostly entropic volume exclusion effect of crowding, but recent studies are indicating the importance of enthalpic effects, in particular, changes in electrostatic interactions due to crowding. Here, temperature replica exchange molecular dynamics simulations of trp-cage and melittin in the presence of explicit protein crowders are presented to further examine the effect of protein crowders on peptide dynamics. The simulations involve a three-component multiscale modeling scheme where the peptides are represented at an atomistic level, the crowder proteins at a coarse-grained level, and the surrounding aqu

SUBMITTER: Predeus AV 

PROVIDER: S-EPMC3398202 | biostudies-literature | 2012 Jul

REPOSITORIES: biostudies-literature