Exploring the suitability of coarse-grained techniques for the representation of protein dynamics.

TitleExploring the suitability of coarse-grained techniques for the representation of protein dynamics.
Publication TypeJournal Article
Year of Publication2008
AuthorsEmperador, Agustí, Carrillo Oliver, Rueda Manuel, and Orozco Modesto
JournalBiophys J
Volume95
Pagination2127-38
Date Published2008 Sep
ISSN1542-0086
KeywordsAlgorithms, Computer Simulation, Models, Molecular, Protein Conformation
Abstract

A systematic study of two coarse-grained techniques for the description of protein dynamics is presented. The two techniques exploit either Brownian or discrete molecular dynamics algorithms applied in the context of simple C(alpha)-C(alpha) potentials, like those used in coarse-grained normal mode analysis. Coarse-grained simulations of the flexibility of protein metafolds are compared to those computed with fully atomistic molecular dynamics simulations using state-of-the-art physical potentials and explicit solvent. Both coarse-grained models efficiently capture critical features of the protein dynamics.

DOI10.1529/biophysj.107.119115