[1]吴建盛,胡栋,晏善成,等.蛋白质-核酸复合物氢键与范德华力作用位点分析[J].东南大学学报(自然科学版),2011,41(4):778-783.[doi:10.3969/j.issn.1001-0505.2011.04.023]
 Wu Jiansheng,Hu Dong,Yan Shancheng,et al.Comprehensive analysis of hydrogen bonding and van del Waals contacting interfaces in protein-nucleic acid complexes[J].Journal of Southeast University (Natural Science Edition),2011,41(4):778-783.[doi:10.3969/j.issn.1001-0505.2011.04.023]
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蛋白质-核酸复合物氢键与范德华力作用位点分析()
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《东南大学学报(自然科学版)》[ISSN:1001-0505/CN:32-1178/N]

卷:
41
期数:
2011年第4期
页码:
778-783
栏目:
生物医学工程
出版日期:
2011-07-20

文章信息/Info

Title:
Comprehensive analysis of hydrogen bonding and van del Waals contacting interfaces in protein-nucleic acid complexes
作者:
吴建盛1胡栋1晏善成1马昕2谢建明2孙啸2
(1南京邮电大学地理与生物信息学院,南京 210046)
(2东南大学生物电子学国家重点实验室,南京 210096)
Author(s):
Wu Jiansheng 1Hu Dong 1Yan Shancheng 1Ma Xin2Xie Jianming2Sun Xiao 2
(1School of Geography and Biological Information, Nanjing University of Posts and Telecommunications, Nanjing 210046, China)
(2 State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China)
关键词:
蛋白质-核酸复合物氢键作用位点范德华力作用位点偏好性氨基酸极性协同作用
Keywords:
protein-nucleic acid complexes hydrogen bonding interfaces van del Waals contacting interfaces propensity polarity of amino acids cooperative interaction
分类号:
Q527+.2
DOI:
10.3969/j.issn.1001-0505.2011.04.023
摘要:
为了深入了解蛋白质-核酸相互作用模式,对复合物结构中氢键/范德华力作用力位点上的氨基酸和核苷酸的偏好性(即相对使用频率)进行了统计分析.结果表明:氢键/范德华力作用位点上对氨基酸的偏好性差异均极其显著,与蛋白质-核酸特异作用密切相关的残基侧链与核苷酸碱基间相互作用力位点对氨基酸类型的选择特异性更高; 单链RNA分子与蛋白质发生相互作用时对氨基酸残基的偏好性和双链RNA分子差异不显著; 氨基酸的极性大小及方向在决定其是否与核酸分子形成范德华力作用具有重要贡献,氨基酸侧链形成的空间位阻会阻碍其与核酸分子形成氢键作用; 蛋白质-DNA复合物结构氢键/范德华力作用位点上残基间空间协同作用时对氨基酸类型的选择与蛋白质-RNA复合物结构间存在显著差异.
Abstract:
To further explore the motifs of protein-nucleic acid interaction, the propensities (i. e. relative frequency)of amino acids and nucleotides usage at protein-nucleic acid interfaces by hydrogen bonds and van del Waals contacts are analyzed. The results show that it presents significant differences among propensities of amino acids recognizing nucleotides by hydrogen bonds or van der Waals contacts in protein-nucleic acid complex structures, in addition, specific interacting sites between atoms of the side chain of amino acids and base atoms present higher propensity for choosing amino acids; propensities of amino acids at hydrogen bonding/van del Waals contacting interfaces among the interaction of protein with single-stranded RNA molecules present no significant differences with those among the interaction of protein with double-stranded RNA molecules; the size and orientation of the polarity of amino acids play important roles in determining whether they act with nucleic acid molecules by van der Waals contacts, and the steric hindrances formed by the side chain of amino acids appear to influence the course of formation of hydrogen bonds between amino acids and nucleotides; the choice of the type of amino acids for space-adjacent residues with cooperative interactions at hydrogen bonding/van del Waals contacting interfaces of protein-DNA complexes are significantly different from those of protein-RNA complexes.

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备注/Memo

备注/Memo:
作者简介:吴建盛(1979—),男,博士,讲师;孙啸(联系人):男,博士,教授,博士生导师,xsun@seu.edu.cn.
基金项目:国家自然科学基金资助项目(61073141,60771024)、南京邮电大学科研启动基金资助项目(NY209027).
引文格式: 吴建盛,胡栋,晏善成,等.蛋白质-核酸复合物氢键与范德华力作用位点分析[J].东南大学学报:自然科学版,2011,41(4):778-783.[doi:10.3969/j.issn.1001-0505.2011.04.023]
更新日期/Last Update: 2011-07-20