物理化学学报 >> 2006, Vol. 22 >> Issue (10): 1243-1247.doi: 10.3866/PKU.WHXB20061014

研究论文 上一篇    下一篇

环多肽晶体的浮动电荷极化力场模拟

张强;张霞;杨忠志   

  1. 渤海大学化学化工学院, 辽宁 锦州 121000; 辽宁师范大学化学化工学院, 辽宁 大连 116029
  • 收稿日期:2006-03-09 修回日期:2006-05-29 发布日期:2006-10-11
  • 通讯作者: 杨忠志 E-mail:zq_science@sina.com.cn

Modeling of Cyclic Peptides by the ABEEM/MM Fluctuating Charge Force Field

ZHANG Qiang;ZHANG Xia;YANG Zhong-Zhi   

  1. Bohai University, Jinzhou 121000, P. R. China; Liaoning Normal University, Dalian 116029, P. R. China
  • Received:2006-03-09 Revised:2006-05-29 Published:2006-10-11
  • Contact: YANG Zhong-Zhi E-mail:zq_science@sina.com.cn

摘要: 利用原子键电负性均衡结合分子力场方法(ABEEM/MM)对五种环多肽晶体进行了研究. 与传统力场相比, 该方法中的静电势包含了分子内和分子间的静电极化作用, 以及分子内电荷转移影响, 同时加入了化学键等非原子中心电荷位点, 合理地体现了分子中的电荷分布. 相对其他极化力场模型, 具有计算量较小的特点. 该模型下计算得到的环多肽分子单元相对实验测得的结构的原子位置、氢键长度和二面角的均方根偏差分别为0.009 nm、0.013 nm和5.16°, 能够很好地重复实验结果. 总体上, 其结果优于或相当于其他力场模型, 适用于对实际蛋白质体系的模拟和研究.

关键词: 原子键电负性均衡结合分子力场方法(ABEEM/MM), 环多肽, 极化力场, 浮动电荷模型, 氢键

Abstract: The ABEEM/MM (atom-bond electronegativity equalization fused into molecular mechanic) fluctuating charge model was applied to simulate five realistic cyclic peptides. In the ABEEM/MM model, comparing to the classical force field with fixed charge electrostatic potential, the partial charges were allowed to fluctuate in the same molecule in response to the environment. The important non-atomic-center charge sites (chemical bond and lone pair) were added into this model to describe the charge population reasonably. The CPU time was not longer than that in other polarized force fields. The relevant structural information was analyzed, such as the root-mean-square deviation of the atomic coordinate shift, the deviation of hydrogen bond lengths and the deviation of dihedral angle of five cyclic peptides from the corresponding experimental data, whose values are 0.009 nm, 0.013 nm, and 5.16° respectively. The ABEEM/MM model could well reproduce the experimental structures of realistic peptides. All in all, the results from the ABEEM/MM model present higher accuracy than those from other force fields. It is proved to be suitable to explore and simulate the realistic protein systems.

Key words: Atom-bond electronegativity equalization fused into molecular mechanic(ABEEM/MM), Cyclic peptides, Polarized force field, Fluctuating charge model, Hydrogen bond