高等学校化学学报

高等学校化学学报 ›› 2013, Vol. 34 ›› Issue (1): 142.doi: 10.7503/cjcu20120359

• 物理化学 • 上一篇    下一篇

ABEEMσπ和OPLS-AA力场对蛋白质GA88/GB88的分子动力学模拟

王晶晶, 刘翠, 杨忠志   

  1. 辽宁师范大学化学化工学院, 大连 116029
  • 收稿日期:2012-04-16 发布日期:2012-12-31
  • 通讯作者: 杨忠志,男,博士,教授,博士生导师,主要从事理论与计算化学研究.E-mail:zzyang@lnnu.edu.cn;刘翠,女,博士,讲师,主要从事理论与计算化学研究.E-mail:liuc@lnnu.edu.cn E-mail:zzyang@lnnu.edu.cn;liuc@lnnu.edu.cn
  • 基金资助:

    国家自然科学基金重点项目(批准号: 21133005, 21073080)资助.

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

WANG Jing-Jing, LIU Cui, YANG Zhong-Zhi   

  1. School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian 116029, China
  • Received:2012-04-16 Published:2012-12-31

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摘要：

将原子与键电负性均衡方法融入分子力学方法, 即利用ABEEMσπ浮动电荷力场与ABEEM-7P水模型相结合的方法及OPLS-AA固定电荷力场方法, 对GA88和GB88蛋白进行了水溶液(温度295 K)和真空中的分子动力学模拟. 比较两种方法得到的两个蛋白质的结构与实验结构的均方根偏差, 分析了两种方法得到的两个蛋白质的回旋半径、 氢键分布、 径向分布及电荷分布情况. 结果表明, ABEEMσπ和OPLS-AA力场均能正确模拟蛋白质结构, 得到的各项偏差值接近, 但从各偏差的波动大小可见, ABEEMσπ力场的模拟更稳定; 回旋半径模拟很好地体现了蛋白质的"电致紧缩"现象; 氢键分布、 径向分布及电荷分布表明, 与OPLS-AA固定电荷力场相比, ABEEMσπ浮动电荷力场能更好地体现蛋白质和周围水分子的极化效应.

关键词: 原子与键电负性均衡方法/分子力场, OPLS-AA固定电荷力场, GA88/GB88蛋白, 分子动力学模拟, 动力学性质

Abstract:

The dynamic behavior of proteins GA88 and GB88 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 GA88/GB88, Molecular dynamics simulation, Dynamic property

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