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

Content Provider	PubMed Central
Author	Wu, Johnny Zhen, Xia Shen, Hujun Li, Guohui Ren, Pengyu
Copyright Year	2011
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.
Related Links	http://dx.doi.org/10.1063/1.3651626
Starting Page	155104
File Format	PDF
ISSN	00219606
e-ISSN	10897690
Journal	The Journal of Chemical Physics
Issue Number	15
Volume Number	135
Language	English
Publisher	American Institute of Physics
Publisher Date	2011-01-01
Access Restriction	Open
Rights Holder	American Institute of Physics
Subject Keyword	Physical and Theoretical Chemistry Physics and Astronomy(all) Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Physics and Astronomy Medicine Physical and Theoretical Chemistry

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