物理化学学报 >> 2012, Vol. 28 >> Issue (08): 1837-1842.doi: 10.3866/PKU.WHXB201205021

理论与计算化学 上一篇    下一篇

丙氨酸二肽分子二级结构与振动光谱特性

蔡开聪, 留珊红, 刘的文, 林深   

  1. 福建师范大学化学与化工学院, 福州 350007
  • 收稿日期:2012-03-12 修回日期:2012-05-02 发布日期:2012-07-10
  • 通讯作者: 蔡开聪, 林深 E-mail:ckc1117@iccas.ac.cn; shenlin@fjnu.edu.cn
  • 基金资助:

    国家自然科学基金(21103021), 福建省自然科学基金(2011J05022)和福建师范大学优秀青年骨干教师培养基金(fjsdjk2012066)资助项目

Secondary Structure and Vibrational Spectral Feature of Alanine Dipeptide

CAI Kai-Cong, LIU Shan-Hong, LIU Di-Wen, LIN Shen   

  1. College of Chemistry and Chemical Engineering, Fujian Normal University, Fuzhou 350007, P. R. China
  • Received:2012-03-12 Revised:2012-05-02 Published:2012-07-10
  • Contact: CAI Kai-Cong, LIN Shen E-mail:ckc1117@iccas.ac.cn; shenlin@fjnu.edu.cn
  • Supported by:

    The project was supported by the National Natural Science Foundation of China (21103021), Natural Science Foundation of Fujian Province, China (2011J05022), and Outstanding Young Teachers Research Foundation of Fujian Normal University, China (fjsdjk2012066).

摘要:

利用从头算方法探索蛋白质模型分子——丙氨酸二肽的二级结构布居特性以及体系势能变化. 引入对分子结构敏感的振动探针(酰胺振动吸收带), 借助其光谱表象, 寻求振动光谱参数与分子结构之间的联系. 研究结果表明: 丙氨酸二肽分子处于C7eq构型(Φ/Ψ=-80°/80°)时具有最低能量值, 且分子易形成β折叠、PPII、C5及C7等能量较低的稳定构型. 通过简正模式分析, 得到分子3N-6 个振动模式的吸收光谱, 并通过势能分布分析方法对分子骨架上酰胺振动吸收带的特征振动模式进行了指认. 重点考察分子骨架上酰胺-I带振动光谱参数与分子构型变化之间的相关性, 建立振动光谱参数与蛋白质二级结构之间的联系, 为在化学键水平上研究蛋白质的结构及其发挥作用的机制提供科学依据.

关键词: 从头算, 丙氨酸二肽, 振动光谱, 酰胺-I带, 简正模式分析, 势能分布

Abstract:

Ab initio calculation was performed on the model peptide compound alanine dipeptide. The population of the secondary structures and the corresponding potential energies of alanine dipeptide were investigated. Normal mode analysis was performed on the amide vibrational modes, which are known to be quite sensitive to the molecular structure, and the correlation between the vibrational feature and the molecular structure was then revealed. The results show that alanine dipeptide has a minimum potential energy when the backbone dihedral is positioned at Φ/Ψ =-80°/80° , which can be denoted as a C7eq conformation. It is also possible to form the secondary structures with β sheet, PPII, C5, and C7 conformations for their low potential energies. The vibrational parameters of the 3N-6 vibrational motions were obtained through normal mode analysis. The amide vibrational modes were then assigned by the potential energy distribution analysis. The amide-I mode, mostly consisting of backbone C=O stretching, was introduced for the prediction of the secondary structure of alanine dipeptide. The correlation between the amide-I vibrational parameters and the molecular structures is then demonstrated. Thus is a new way for the prediction of structural features of peptide and protein systems at the chemical bond level.

Key words: Ab initio calculation, Alanine dipeptide, Vibrational spectroscopy, Amide-I mode, Normal mode analysis, Potential energy distribution

MSC2000: 

  • O641