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化学进展 2012, Vol. 24 Issue (06): 1214-1226 前一篇   

所属专题： 计算化学

• 量子化学专辑 •

准确快速计算含多肽酰胺和核酸碱基的氢键复合物的氢键强度和氢键作用势能曲线

黄翠英, 李阳, 王长生*   

  1. 辽宁师范大学化学化工学院 大连 116029
  • 收稿日期:2011-11-01 修回日期:2012-03-01 出版日期:2012-06-24 发布日期:2012-05-11
  • 通讯作者: 王长生 E-mail:chwangcs@lnnu.edu.cn
  • 基金资助:

    国家自然科学基金项目(No.20973088, No.21173109)和教育部高等学校博士点基金项目(No.20102136110001)资助

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Accurate and Rapid Calculation of the Hydrogen Bond Strengths and Hydrogen Bonding Potential Energy Curves for the Hydrogen-Bonded Complexes Containing Peptide Amides and/or Nucleic Acid Bases

Huang Cuiying, Li Yang, Wang Changsheng   

  1. School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian 116029
  • Received:2011-11-01 Revised:2012-03-01 Online:2012-06-24 Published:2012-05-11
N-H···O=C、C-H···O=C、N-H···N和C-H···N等氢键作用是蛋白质a-螺旋结构、b-折叠结构和DNA双螺旋结构形成的主要因素,在生物分子识别、蛋白质复制以及遗传信息传递等过程中起重要作用。准确快速计算生物体系中存在的N-H···O=C、C-H···O=C、N-H···N和C-H···N等氢键作用强度以及氢键强度随分子几何结构(距离和角度)变化的势能曲线对正确模拟(从而正确认识和理解)蛋白质折叠机制和DNA双螺旋结构形成机制等生物过程意义重大,对设计合成具有特殊功能的生物分子材料有重要指导价值。本文主要介绍了近年来建立的偶极-偶极氢键作用模型及其在快速预测多肽-多肽分子间和核酸碱基-多肽分子间氢键作用强度和氢键作用势能曲线方面的应用。
关键词： 蛋白质多肽, 核酸碱基, 偶极-偶极作用, 氢键强度, 氢键作用势能曲线, 结合能
N-H···OC、C-H···OC、N-H···N and C-H···N hydrogen bonds are the main factors for the formation of protein a-helices and b-sheets and for the formation of the double helices of the deoxyribonucleic acid. These hydrogen bonds also play important roles in the processes of the protein-nucleic acid recognition, in the processes of the protein replication, and in the processes of transcription and expression of genetic information from DNA to protein. Accurate and rapid determination of the strengths of the hydrogen bonds and their dynamic properties in DNA and protein systems is very important for correctly simulating and therefore deeply understanding the mechanism of protein folding processes and the formation mechanism of the double helices of the deoxyribonucleic acid and for designing new biomolecular materials possessing special function. In this review, a dipole-dipole hydrogen bonding model and its applications to the hydrogen-bonded complexes containing peptide amides and/or nucleic acid bases are introduced. Contents
1 Introduction
2 Hydrogen bond model and parameterization
2.1 The dipole-dipole hydrogen bonding model
2.2 Parameterization
3 Applications
3.1 Calculation of the hydrogen bond strengths and hydrogen bonding potential energy curves for amide-amide and amide-water hydrogen-bonded dimers
3.2 Calculation of the total binding energies and potential energy curves for hydrogen-bonded complexes made of peptide amides and nucleic acid bases
3.3 Calculation of the total binding energies and potential energy curves for protein β-sheets
4 Conclusion and outlook
Key words: protein peptide, nucleic acid bases, dipole-dipole interaction, hydrogen bond strength, hydrogen bonding potential energy curve, Binding energy

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