Mining the Characteristic Interaction Patterns on Protein鈥揚rotein Binding Interfaces

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• 作者：Yan Li ; Zhihai Liu ; Li Han ; Chengke Li ; Renxiao Wang
• 刊名：Journal of Chemical Information and Modeling
• 出版年：2013
• 出版时间：September 23, 2013
• 年：2013
• 卷：53
• 期：9
• 页码：2437-2447
• 全文大小：495K
• 年卷期：v.53,no.9(September 23, 2013)
• ISSN：1549-960X

文摘

Protein鈥損rotein interactions are observed in various biological processes. They are important for understanding the underlying molecular mechanisms and can be potential targets for developing small-molecule regulators of such processes. Previous studies suggest that certain residues on protein鈥損rotein binding interfaces are 鈥砲ot spots鈥? As an extension to this concept, we have developed a residue-based method to identify the characteristic interaction patterns (CIPs) on protein鈥損rotein binding interfaces, in which each pattern is a cluster of four contacting residues. Systematic analysis was conducted on a nonredundant set of 1,222 protein鈥損rotein binding interfaces selected out of the entire Protein Data Bank. Favored interaction patterns across different protein鈥損rotein binding interfaces were retrieved by considering both geometrical and chemical conservations. As demonstrated on two test tests, our method was able to predict hot spot residues on protein鈥損rotein binding interfaces with good recall scores and acceptable precision scores. By analyzing the function annotations and the evolutionary tree of the protein鈥損rotein complexes in our data set, we also observed that protein鈥損rotein interfaces sharing common characteristic interaction patterns are normally associated with identical or similar biological functions.