物理化学学报 >> 2013, Vol. 29 >> Issue (12): 2551-2557.doi: 10.3866/PKU.WHXB201310293

理论与计算化学 上一篇    下一篇

碱基腺嘌呤与多肽酰胺间氢键作用的最佳位点

刘帅, 李书实, 刘冬佳, 王长生   

  1. 辽宁师范大学化学化工学院, 辽宁大连 116029
  • 收稿日期:2013-08-11 修回日期:2013-10-28 发布日期:2013-11-28
  • 通讯作者: 王长生 E-mail:chwangcs@lnnu.edu.cn
  • 基金资助:

    国家自然科学基金(21173109), 教育部高等学校博士点基金(20102136110001), 辽宁省优秀人才基金(LR2012037)和大连市领军人才资助项目

Site Preferences of Adenine Hydrogen Bonding to Peptide Amides

LIU Shuai, LI Shu-Shi, LIU Dong-Jia, WANG Chang-Sheng   

  1. School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian 116029, Liaoning Province, P. R. China
  • Received:2013-08-11 Revised:2013-10-28 Published:2013-11-28
  • Contact: WANG Chang-Sheng E-mail:chwangcs@lnnu.edu.cn
  • Supported by:

    The project was supported by the National Natural Science Foundation of China (21173109), Specialized Research Fund for the Doctoral Program of Higher Education of China (20102136110001), Program for Liaoning Excellent Talents in University, China (LR2012037), and Program for Leading Figures in Dalian, China.

摘要:

正确理解核酸碱基和蛋白质多肽间的作用机制有助于人们利用这些生物分子有效地进行分子设计, 进而制备具有特殊纳米结构和功能的生物分子材料. 本文优化得到了碱基腺嘌呤与N-甲基乙酰胺、甘氨酸二肽、丙氨酸二肽形成的20 个氢键复合物的结构并计算了结合能, 探讨了腺嘌呤与多肽酰胺间氢键作用的最佳位点. 研究发现: 腺嘌呤可以使用两个不同位点(A1 位点和A2 位点)与N-甲基乙酰胺形成N―H…N型或者N―H…O=C型氢键复合物, 腺嘌呤使用A1 位点与N-甲基乙酰胺形成的N―H…N型氢键复合物更稳定; 二肽分子可以使用主链上两个不同位点(丙氨酸的Ala7位点和Ala5位点或者甘氨酸的Gly7位点和Gly5位点)与腺嘌呤形成含有N―H…N和N―H…O=C两条氢键的复合物, 二肽分子使用Ala7 或Gly7 位点与腺嘌呤形成的氢键复合物更稳定; 腺嘌呤与多肽间的氢键作用强于其与N-甲基乙酰胺的作用. 基于分子中的原子理论与自然键轨道计算结果分析了氢键作用的本质.

关键词: 碱基腺嘌呤, N-甲基乙酰胺, 甘氨酸二肽, 丙氨酸二肽, 氢键, 结合能

Abstract:

A detailed understanding of how nucleobases interact with protein peptides will allow us to gain valuable insights into how these interesting biological molecules could be used to construct complex nanostructures and materials. In this work, the optimal structures and binding energies of 20 hydrogenbonded complexes, which contained the nucleic acid base adenine, N-methylacetamide, a glycine dipeptide, and an alanine dipeptide, were obtained. The site preferences of adenine hydrogen bonding to peptide amides were explored. The calculation results show that adenine can use two binding sites (site A1 and site A2) to form N―H…N or N―H…O=C hydrogen-bonded complexes with N-methylacetamide; the N―H…N hydrogen-bonded complexes formed at site A1 of adenine are more stable. The calculation results also show that the glycine dipeptide can use either site Gly7 or site Gly5, and the alanine dipeptide can use either site Ala7 or site Ala5 to form hydrogen-bonded complexes with adenine; the hydrogenbonded complexes formed at site Gly7 of the glycine dipeptide and at site Ala7 of the alanine dipeptide are more stable. The hydrogen-bonded complexes formed by adenine and a dipeptide have larger negative binding energies than the complexes formed by adenine and N-methylacetamide, indicating that the interaction between adenine and the peptide is preferred to that between adenine and N-methylacetamide. The nature of the hydrogen bonding in these complexes was further explored based on the atoms in molecules calculations and the natural bond orbital analysis.

Key words: Adenine, N-methylacetamide, Glycine dipeptide, Alanine dipeptide, Hydrogen bond, Binding energy

MSC2000: 

  • O641