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

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

Research output: Contribution to journalArticle

30 Citations (Scopus)

Abstract

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.

Original languageEnglish
Article number155104
JournalJournal of Chemical Physics
Volume135
Issue number15
DOIs
Publication statusPublished - Oct 21 2011
Externally publishedYes

Fingerprint

multipoles
Electrostatics
electrostatics
Solvation
Atoms
solvation
simulation
atoms
intermolecular forces
Dipeptides
polypeptides
alanine
replicas
Alanine
strands
helices
field theory (physics)
Molecular dynamics
Ion exchange
Gases

ASJC Scopus subject areas

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

Cite this

Gay-Berne and electrostatic multipole based coarse-grain potential in implicit solvent. / Wu, Johnny; Zhen, Xia; Shen, Hujun; Li, Guohui; Ren, Pengyu.

In: Journal of Chemical Physics, Vol. 135, No. 15, 155104, 21.10.2011.

Research output: Contribution to journalArticle

Wu, Johnny ; Zhen, Xia ; Shen, Hujun ; Li, Guohui ; Ren, Pengyu. / Gay-Berne and electrostatic multipole based coarse-grain potential in implicit solvent. In: Journal of Chemical Physics. 2011 ; Vol. 135, No. 15.
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