Gay-Berne and electrostatic multipole based coarse-grain potential in implicit solvent.
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.
Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712-1062, USA.
Johnny
J
Wu
Xia
X
Zhen
Hujun
H
Shen
Guohui
G
Li
Pengyu
P
Ren
D003198:Computer Simulation; D004151:Dipeptides / Q000737:chemistry*; D008958:Models, Molecular; D008968:Molecular Conformation; D055672:Static Electricity; D013816:Thermodynamics
D004151:Dipeptides; C002956:alanylalanine