物理化学学报 >> 2008, Vol. 24 >> Issue (06): 1035-1040.doi: 10.3866/PKU.WHXB20080621

研究论文 上一篇    下一篇

微过氧化物酶水溶液的ABEEM/MM动力学模拟

崔宝秋; 宫利东; 赵东霞   

  1. 辽宁师范大学化学化工学院, 辽宁 大连 116029; 锦州师范高等专科学校化学系, 辽宁 锦州 121000
  • 收稿日期:2007-12-04 修回日期:2008-03-14 发布日期:2008-06-03
  • 通讯作者: 宫利东 E-mail:gongjw@lnnu.edu.cn

Molecular Dynamics Simulation of Microperoxidase in Aqueous Solution in Terms of the ABEEM/MM Method

CUI Bao-Qiu; GONG Li-Dong; ZHAO Dong-Xia   

  1. College of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian 116029, Liaoning Province, P. R. China; Department of Chemistry, Jinzhou Teacher College, Jinzhou 121000, Liaoning Province, P. R. China
  • Received:2007-12-04 Revised:2008-03-14 Published:2008-06-03
  • Contact: GONG Li-Dong E-mail:gongjw@lnnu.edu.cn

摘要: 应用原子-键电负性均衡浮动电荷分子力场(ABEEM/MM), 对微过氧化物酶水溶液进行了分子动力学模拟. 研究了水溶液对微过氧化物酶的结构, 血红素的皱裂构象以及轴配体咪唑基的取向的影响. 结果表明, 在水溶液中微过氧化物酶的骨架氨基酸是稳定的, 而血红素的皱裂构象在水分子的作用下趋于平面. 与血红素轴配体咪唑基键连的组氨酸决定着咪唑基的空间取向, 而咪唑基与血红素侧链的丙酸基的静电作用对其取向仅起次要作用.

关键词: ABEEM/MM浮动电荷分子力场, 微过氧化物酶, 血红素, 构象, 分子动力学模拟

Abstract: In terms of the atom-bond electronegativity equilization fluctuating charge molecularmechanics(ABEEM/MM), molecular dynamics simulation on aqueous microperoxidases (MP) was performed. The impact of water molecules on the structure of MP, the ruffling conformation of the heme, and the orientation of the axially ligated imidazole were investigated. Results show that, in the aqueous solution, the backbone amino acids of the MP are stable, while the ruffling conformation of heme turns to be planar, which comes from the interaction between water and MP. The orientation of the axially coordinated imidazole is mainly determined by the histidine bonded with the imidazole, while the electrostatic force between the imidazole and the side-chained propionic acid group of the heme is only a subsidiary factor.

Key words: ABEEM/MMfluctuating charge molecular force field, Microperoxidase, Heme, Conformation, Molecular dynamics simulation

MSC2000: 

  • O642