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J Phys Chem B. 2008 Jun 5;112(22):6878-86. doi: 10.1021/jp800282x. Epub 2008 May 10.

A test on peptide stability of AMBER force fields with implicit solvation.

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  • 1Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California 93106-5080, USA. shell@engineering.ucsb.edu

Abstract

We used replica exchange molecular dynamics (REMD) simulations to evaluate four different AMBER force fields and three different implicit solvent models. Our aim was to determine if these physics-based models captured the correct secondary structures of two alpha-helical and two beta-peptides: the 14-mer EK helix of Baldwin and co-workers, the C-terminal helix of ribonuclease, the 16-mer C-terminal hairpin of protein G, and the trpzip2 miniprotein. The different models gave different results, but generally we found that AMBER ff96 plus the implicit solvent model of Onufriev, Bashford, and Case gave reasonable structures, and is fairly well-balanced between helix and sheet. We also observed differences in the strength of ion pairing in the solvent models, we but found that the native secondary structures were retained even when salt bridges were prevented in the conformational sampling. Overall, this work indicates that some of these all-atom physics-based force fields may be good starting points for protein folding and protein structure prediction.

PMID:
18471007
[PubMed - indexed for MEDLINE]
PMCID:
PMC2699260
Free PMC Article

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