Gay-Berne and electrostatic multipole based coarse-grain potential in implicit solvent

Johnny Wu, Xia Zhen, Hujun Shen, Guohui Li, Pengyu Ren

研究成果: 雜誌貢獻文章

31 引文 斯高帕斯(Scopus)

摘要

A general, transferable coarse-grain (CG) framework based on the Gay-Berne potential and electrostatic point multipole expansion is presented for polypeptide simulations. The solvent effect is described by the Generalized Kirkwood theory. The CG model is calibrated using the results of all-atom simulations of model compounds in solution. Instead of matching the overall effective forces produced by atomic models, the fundamental intermolecular forces such as electrostatic, repulsion-dispersion, and solvation are represented explicitly at a CG level. We demonstrate that the CG alanine dipeptide model is able to reproduce quantitatively the conformational energy of all-atom force fields in both gas and solution phases, including the electrostatic and solvation components. Replica exchange molecular dynamics and microsecond dynamic simulations of polyalanine of 5 and 12 residues reveal that the CG polyalanines fold into alpha helix and beta sheet structures. The 5-residue polyalanine displays a substantial increase in the beta strand fraction relative to the 12-residue polyalanine. The detailed conformational distribution is compared with those reported from recent all-atom simulations and experiments. The results suggest that the new coarse-graining approach presented in this study has the potential to offer both accuracy and efficiency for biomolecular modeling.
原文英語
文章編號155104
期刊Journal of Chemical Physics
135
發行號15
DOIs
出版狀態已發佈 - 十月 21 2011
對外發佈Yes

ASJC Scopus subject areas

  • Physics and Astronomy(all)
  • Physical and Theoretical Chemistry

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