物理化学学报 >> 2014, Vol. 30 >> Issue (7): 1239-1246.doi: 10.3866/PKU.WHXB201405151

理论与计算化学 上一篇    下一篇

海藻糖和氨基酸之间相互作用的分子动力学模拟

白姝1,2, 常颖1, 刘小娟1, 刘夫锋1,2   

  1. 1. 天津大学化工学院生物工程系, 系统生物工程教育部重点实验室, 天津 300072;
    2. 天津化学化工协同创新中心, 天津 300072
  • 收稿日期:2014-03-04 修回日期:2014-05-14 发布日期:2014-06-30
  • 通讯作者: 刘夫锋 E-mail:fufengliu@tju.edu.cn
  • 基金资助:

    国家自然科学基金（20906068）和中国博士后科学基金（2013M530115，2012T50241）资助项目

Interactions between Trehalose and Amino Acids by Molecular Dynamics Simulations

BAI Shu1,2, CHANG Ying1, LIU Xiao-Juan1, LIU Fu-Feng1,2   

  1. 1. Key Laboratory of Systems Bioengineering of the Ministry of Education, Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China;
    2. Collaborative Innovation Center of Chemical Science and Engineering Tianjin, Tianjin 300072, P. R. China
  • Received:2014-03-04 Revised:2014-05-14 Published:2014-06-30
  • Contact: LIU Fu-Feng E-mail:fufengliu@tju.edu.cn
  • Supported by:

    The project was supported by the National Natural Science Foundation of China (20906068) and China Postdoctoral Science Foundation (2013M530115, 2012T50241).

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摘要：

虽然海藻糖已经广泛用于蛋白质稳定性研究，但海藻糖稳定蛋白质的作用机理尚不清晰. 本文利用全原子分子动力学模拟研究了20种常见氨基酸和海藻糖之间的分子机理. 结果表明，所有氨基酸，尤其是极性和带电氨基酸，均优先与水分子结合. 相反，仅有疏水性氨基酸与海藻糖发生相互作用，尤其是芳香族和疏水性氨基酸的侧链更易于和海藻糖接触. 所有氨基酸的主链与水分子接触的趋势一致. 虽然氨基酸和海藻糖与水之间均形成氢键，但氨基酸和海藻糖之间的氢键相互作用要弱于氨基酸和水之间的氢键相互作用. 上述分子模拟的结果对于海藻糖稳定蛋白质作用机理的解析及高效蛋白质稳定剂的理性设计具有非常重要的理论指导意义.

关键词: 海藻糖, 渗透剂, 分子动力学模拟, 蛋白质稳定性, 氢键

Abstract:

Although trehalose is used as a protein stabilizer, the mechanism by which this stability is induced is not fully understood at present. In this study, we investigated the interactions between trehalose and all 20 common amino acids using all-atom molecular dynamics simulations. It is found that all the amino acids exhibit a preference for contact with water, especially the polar and charged amino acids. Conversely, only the hydrophobic amino acids were found to have a slight preference for contact with trehalose molecules. This tendency is most pronounced in the case of contact between trehalose and aromatic or hydrophobic side chains, whereas the backbones of each amino acids all show similar propensities for contact with water. Furthermore, hydrogen bonds between amino acids and trehalose were found to be significantly weaker than those between amino acids and water, although both trehalose and water can interact with the amino acids via hydrogen bonds. These findings are important with regard to the exploration of the molecular mechanism of protein stability induced by trehalose and the rational design of highly efficient protein stabilizers.

Key words: Trehalose, Osmolyte, Molecular dynamics simulation, Protein stability, Hydrogen bond

MSC2000: 

  • O641