Evaluation of a fast implicit solvent model for molecular dynamics simulations.

TitleEvaluation of a fast implicit solvent model for molecular dynamics simulations.
Publication TypeJournal Article
Year of Publication2002
AuthorsFerrara P., Apostolakis J., Caflisch A.
JournalProteins: Structure, Function, and Bioinformatics
Volume46
Issue1
Pagination24-33
Date Published2002 Jan 1
Type of ArticleResearch Article
ISSN0887-3585
KeywordsComputer Simulation, Hydrogen Bonding, Models, Chemical, Protein Conformation, Protein Structure, Secondary, Proteins, Solvents, Surface Properties
Abstract

A solvation term based on the solvent accessible surface area (SASA) is combined with the CHARMM polar hydrogen force field for the efficient simulation of peptides and small proteins in aqueous solution. Only two atomic solvation parameters are used: one is negative for favoring the direct solvation of polar groups and the other positive for taking into account the hydrophobic effect on apolar groups. To approximate the water screening effects on the intrasolute electrostatic interactions, a distance-dependent dielectric function is used and ionic side chains are neutralized. The use of an analytical approximation of the SASA renders the model extremely efficient (i.e., only about 50% slower than in vacuo simulations). The limitations and range of applicability of the SASA model are assessed by simulations of proteins and structured peptides. For the latter, the present study and results reported elsewhere show that with the SASA model it is possible to sample a significant amount of folding/unfolding transitions, which permit the study of the thermodynamics and kinetics of folding at an atomic level of detail.

DOI10.1002/prot.10001
pubindex

0040

Alternate JournalProteins
PubMed ID11746700
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