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蛋白质-核酸复合物中氢键和范德华力作用位点偏好性分析

Analysis of Propensities at Hydrogen Bonding/Van der Waals Contacting Interfaces in Protein-nucleic Acid Complexes
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摘要 对蛋白质-核酸复合物结构中氢键/范德华力作用位点氨基酸与核苷酸的偏好性(即相对使用频率)进行了统计分析。发现:(1)在蛋白质-DNA复合物结构中,范德华力作用对与氢键数量相当;而在蛋白质-RNA复合物结构中,范德华力作用对数量要远多于氢键;(2)复合物结构中氢键和范德华力作用位点上对氨基酸的偏好性差异显著;(3)氨基酸的极性大小及方向在决定它是否与DNA/RNA分子形成氢键/范德华力相互作用时起到重要的作用。 Statistical analysis is made of propensities of amino acids and nucleotides usage at protein-nucleic acid interfaces by hydrogen bonds or van der Waals contacts.The results have shown that：（1） For the number of van der Waals contacts,it is roughly the same as that of hydrogen bonds in the protein-DNA complex structures,but is far more than the latter in the protein-RNA complex structures.（2） In protein-nucleic acid complex structures,there are significant differences between the interaction propensities of amino acids recognizing nucleotides by hydrogen bonds and by van der Waals contacts.（3） The size and orientation of the polarity of amino acids play important roles in determining whether they bind DNA /RNA molecules by hydrogen bonds or van der Waals contacts.
作者 吴建盛 晏善成 武灵芝 汤丽华
机构地区 南京邮电大学地理与生物信息学院 东南大学生物电子学国家重点实验室生物科学与医学工程学院
出处 《南京邮电大学学报（自然科学版）》 2011年第4期138-144,共7页 Journal of Nanjing University of Posts and Telecommunications：Natural Science Edition
基金 南京邮电大学科研启动基金项目(NY209027)资助项目
关键词 蛋白质-核酸复合物 氢键 范德华力 偏好性 氨基酸极性 protein-nucleic acid complex hydrogen bonds van der Waals contacts binding propensity polarity of amino acids
分类号 Q527.2 [生物学—生物化学]
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参考文献17

  • 1LUSCOMBE N M, LASKOWSKI R A, THORNTON J M. Amino acid-base interactions:a three-dimensional analysis of protein-DNA interactions at an atomic level [J]. Nucleic Acids Res,2001,29 ( 13 ) :2860 - 2874.
  • 2SEEMAN N C, ROSENBERG J M, RICH A. Sequence-specific recognition of double helical nucleic acids by proteins [ J ]. Proc Natl Acad Sci USA, 1976,73 (3) :804 - 808.
  • 3MANDEL-GUTFREUND Y, SCHUELER O, MARGALIT H. Comprehensive analysis of hydrogen bonds in regulatory protein DNA- complexes:in search of common principles[ J]. J Mol Biol, 1995, 253 (2) :370 - 382.
  • 4JONES S, DALEY D T, LUSCOMBE N M,et al. Protein-RNA interactions : A structural analysis [ J ]. Nucleic Acids Res,2001,29 ( 4 ) :943 -954.
  • 5TREGER M,WESTHOF E. Statistical analysis of atomic contacts at RNA-protein interfaces [ J ]. J Mol Recognit, 2001,14 ( 4 ) : 199 -214.
  • 6JEONG E, KIM H,LEE S W,et al. Discovering the interaction propensities of amino acids and nucleotides from protein-RNA complexes[ J]. Mol Cells,2003,16(2) : 161 - 167.
  • 7LEJEUNE D, DELSAUX N, CHARLOTEAUX B, et al. Protein-nucleic acid recognition:statistical analysis of atomic interactions and influence of DNA structure[ J]. Proteins,2005,61 (2) :258 -271.
  • 8ELLIS J J, BROOM M, JONES S. Protein-RNA interactions : structural analysis and functional classes [ J ]. Proteins, 2007,66 ( 4 ) : 903 - 911.
  • 9BERMAN H M, WESTBROOK J, FENG Z, et al. The Protein Data Bank [ J ]. Nucleic Acids Res ,2000,28 ( 1 ) :235 - 242.
  • 10SHEN Juwen, ZHANG Jian, LUO Xiaomin, et al. Predicting protein-protein interactions based only on sequences information [ J]. Proc Natl Acad Sci USA,2007,104( 11 ) :4337 -4341.

二级参考文献21

  • 1Pabo CO, Sauer RT. Transcription factors: structural families and principles of DNA recognition. Annu Rev Biochem, 1992, 61:1053-1095.
  • 2Lesser BH, Comings DE. Specific interaction between mouse liver non-histone chromosomal proteins and mouse DNA demonstrated by a sequential DNA-protein binding procedure. Biochim Biophys Acta, 1978, 521(1): 117-125.
  • 3Cate JH. Construction of low-resolution x-ray crystallographic electron density maps of the ribosome. Methods, 2001, 25(3): 303-308.
  • 4Bentum P J, Janssen JW, Kentgens AP. Towards nuclear magnetic resonance micro-spectroscopy and micro-imaging. Analyst, 2004, 129(9): 793-803.
  • 5Nadassy K, Wodak S J, Janin J. Structural features of protein-nucleic acid recognition sites. Biochemistry, 1999, 38(7); 1999-2017.
  • 6Ahmad S, Gromiha MM, Sarai A. Analysis and prediction of DNA-binding proteins and their binding residues based on composition, sequence and structural information. Bioinformatics, 2004, 20(4): 477-486.
  • 7Ahmad S, Sarai A. PSSM-based prediction of DNA binding sites in proteins. BMC Bioinformatics, 2005, 6:33.
  • 8Yan C, Terribilini M, Wu F, Jemigan RL, Dobbs D, Honavar V. Predicting DNA-binding sites of proteins from amino acid sequence. BMC Bioinformatics, 2006, 7:262.
  • 9Wang L, Brown SJ. BindN: a web-based tool for efficient prediction of DNA and RNA binding sites in amino acid sequences. Nucleic Acids Res, 2006, 34:W243-248.
  • 10Bhardwaj N, Lu H. Residue-level prediction of DNA-binding sites and its application on DNA-binding protein predictions. FEBS Lett, 2007, 581(5): 1058-1066.

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南京邮电大学学报（自然科学版）
2011年 第4期

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