Coarse-Grained Peptide Modeling Using a Systematic Multiscale Approach

TitleCoarse-Grained Peptide Modeling Using a Systematic Multiscale Approach
Publication TypeJournal Article
Year of Publication2007
AuthorsZhou, J, Thorpe, IF, Izvekov, S, Voth, GA
JournalBiophys J
Keywords*Algorithms Computer Simulation *Models, Chemical *Models, Molecular Peptides/*chemistry Protein Conformation

A systematic new approach to derive multiscale coarse-grained (MS-CG) models has been recently developed. The approach employs information from atomistically detailed simulations to derive CG forces and associated effective potentials. In this work, the MS-CG methodology is extended to study two peptides representing distinct structural motifs, alpha-helical polyalanine and the beta-hairpin V(5)PGV(5). These studies represent the first known application of this approach to peptide systems. Good agreement between the MS-CG and atomistic models is achieved for several structural properties including radial distribution functions, root mean-square deviation, and radius of gyration. The new MS-CG models are able to preserve the native states of these peptides within approximately 1 A backbone root mean-square deviation during CG simulations. The MS-CG approach, as with most coarse-grained models, has the potential to increase the length and timescales accessible to molecular simulations. However, it is also able to maintain a clear connection to the underlying atomistic-scale interactions.