物理化学学报 >> 2004, Vol. 20 >> Issue (07): 676-679.doi: 10.3866/PKU.WHXB20040702

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蛋白质-蛋白质相互作用界面统计分析

高莹;来鲁华   

  1. 分子动态与稳态结构国家重点实验室,北京大学化学与分子工程学院 北京 100871
  • 收稿日期:2004-03-30 修回日期:2004-05-10 发布日期:2004-07-15
  • 通讯作者: 来鲁华 E-mail:lhlai@pku.edu.cn

Analysis of Protein-Protein Interface

Gao Ying;Lai Lu-Hua   

  1. State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871
  • Received:2004-03-30 Revised:2004-05-10 Published:2004-07-15
  • Contact: Lai Lu-Hua E-mail:lhlai@pku.edu.cn

摘要: 以作者开发的从蛋白质结合部位推导出其界面所具有的疏水性质和氢键性质的计算程序PP_SITE为基础,利用蛋白质结构数据库(PDB),对蛋白质-蛋白质相互作用界面进行了统计分析.从PDB中挑出非冗余的链间相互作用对,计算出这个数据集中所有链间界面的疏水和氢键相互作用特征.对得到的界面特征进行统计分析,寻找能够明显聚类的界面特征.结果表明,界面大小、氢键和疏水相互作用在界面所占比例以及疏水相互作用的集中程度可以作为分类的依据.

关键词: 蛋白质-蛋白质相互作用, PP_SITE程序, 界面分类

Abstract: Analysis of protein-protein interface is crucial to understand protein interactions and to develop drugs targeting protein complexes. PP_SITE is a method developed by the author's group to deduce hydrogen bond and hydrophobic properties for protein-protein interface. We have used PP_SITE to perform statistical analysis on protein-protein interfaces. A two-chain non-redundant interface dataset from PDB was constructed and used in the study. According to the hydrophobicity and hydrogen bond characteristics, criteria were selected to differentiate protein interfaces into distinct groups. The size of interface, the proportion of hydrophobic and hydrophilic property and the extent of concentration in hydrophobicity were found to be important for interface classification.

Key words: Protein-protein interaction, PP_SITE procedure, Interface classification