东南大学学报（自然科学版）2011，Vol.41Issue(4)：778-783,6.DOI:10.3969/j.issn.1001-0505.2011.04.023
蛋白质-核酸复合物氢键与范德华力作用位点分析
Comprehensive analysis of hydrogen bonding and van del Waals contacting interfaces in protein-nucleic acid complexes
摘要
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 a-mong 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 ami-no 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.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Key words
protein-nucleic acid complexes/ hydrogen bonding interfaces/ van del Waals contacting interfaces/ propensity/ polarity of amino acids/ cooperative interaction分类
生物科学引用本文复制引用
吴建盛,胡栋,晏善成,马昕,谢建明,孙啸..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):778-783,6.基金项目
国家自然科学基金资助项目(61073141,60771024) （61073141,60771024）
南京邮电大学科研启动基金资助项目(NY209027). （NY209027）
