Molecular Dynamics Simulations of Proteins GA88 and GB88 by ABEEMσπ and OPLS-AA Force Fields

doi:10.7503/cjcu20120359

Abstract

Abstract:

The dynamic behavior of proteins G_A88 and G_B88 was investigated at 295 K, using aqueous solution and vacuum molecular dynamics simulations by means of atom-bond electronegativity equalization method fused into molecular mechanics i.e., ABEEMσπ fluctuating charge force field and the explicit ABEEM-7P water solvent model as well as OPLS-AA fixed-point charge force field. The root-mean-square deviations(RMSDs) of these two proteins’ structures obtained from ABEEMσπ and OPLS-AA force fields were compared. The radius of gyration, the distribution of hydrogen bond, the radial distribution function, and the distribution of charge were also analyzed by these two force fields. The results demonstrate that both force fields simulate crystal structures correctly, and the RMSDs simulated are close to each other, but the systems simulated from ABEEMσπ force field are more stable than those from OPLS-AA force field according to the fluctuating; simulating results of radius of gyration in aqueous solution and in vacuum show the "electrostatic compactness" phenomenon; the distributions of hydrogen bond and radial distribution function, and the distribution of charge indicate that ABEEMσπ fluctuating charge force field account for the polarization effect better than OPLS-AA fixed-point charge force field.

Key words: Atom-bond electronegativity equalization method/molecular mechanics, OPLS-AA fixed-point charge force field, Protein G_A88/G_B88, Molecular dynamics simulation, Dynamic property

CLC Number:

O641

TrendMD:

WANG Jing-Jing, LIU Cui, YANG Zhong-Zhi. Molecular Dynamics Simulations of Proteins G_A88 and G_B88 by ABEEMσπ and OPLS-AA Force Fields[J]. Chem. J. Chinese Universities, 2013, 34(1): 142.

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Molecular Dynamics Simulations of Proteins G_A88 and G_B88 by ABEEMσπ and OPLS-AA Force Fields

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