物理化学学报 >> 2007, Vol. 23 >> Issue (09): 1332-1336.doi: 10.1016/S1872-1508(07)60068-0

研究论文 上一篇    下一篇

血红素近轴侧基氢键的ABEEM/MM分子动力学模拟

杨忠志; 崔宝秋   

  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:2007-04-24 修回日期:2007-05-22 发布日期:2007-09-06
  • 通讯作者: 杨忠志 E-mail:zzyang@lnnu.edu.cn

Dynamic Simulations of the Hydrogen-bondings on the Proximal Side of the Heme in Terms of ABEEM/MM Method

YANG Zhong-Zhi; CUI Bao-Qiu   

  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:2007-04-24 Revised:2007-05-22 Published:2007-09-06
  • Contact: YANG Zhong-Zhi E-mail:zzyang@lnnu.edu.cn

摘要: 应用ABEEM/MM浮动电荷力场对鲸鱼肌红蛋白及突变体进行了分子动力学模拟. 结果表明, 血红素近轴侧基不存在稳定的双氢键, 该氢键对轴配体咪唑的取向不起决定性作用, 而咪唑的取向与键联的组氨酸有密切联系. 同时表明, 血红素轴配体的柔性与其邻近的氨基酸和咪唑体积有关.

关键词: ABEEM/MM力场, 动力学模拟, 血红素, 咪唑基, 氢键

Abstract: The structures of spermwhale myoglobin (Mb) and mutants were investigated in terms of the ABEEM/MM method. The molecular dynamic simulations showed that the bifurcated hydrogen-bondings in the proximal side of the heme in Mb were not stable. These simulations indicated that hydrogen-bondings could not determine the overall orientation of imidazole, which could be related to the histidine residue. The amide acids and the bulk of the imidazole can have effects on the flexibility of proximal ligands.

Key words: ABEEM/MMmethod, Dynamic simulation, Heme, Ligated imidazole, Hydrogen-bonding

MSC2000: 

  • O642