correlation analysis for protein evolutionary family based on amino acid position mutations and application in pdz domain相关分析基于氨基酸的蛋白质进化位置突变pdz域和应用程序.pdfVIP

Correlation Analysis for Protein Evolutionary Family Based on Amino Acid Position Mutations and Application in PDZ Domain Qi-Shi Du1,2,4*, Cheng-Hua Wang1,3, Si-Ming Liao1,2, Ri-Bo Huang1,2,3 1 State Key Laboratory of Bioenergy Enzyme Technology, National Engineering Research Center for Non-food Biorefinery, Guangxi Academy of Sciences, Nanning, Guangxi, China, 2 Life Science and Biotechnology College, Guangxi University, Nanning, Guangxi, China, 3 Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology, Nanjing, Jiangsu, China, 4 Gordon Life Science Institute, San Diego, California, United States of America Abstract Background: It has been widely recognized that the mutations at specific directions are caused by the functional constraints in protein family and the directional mutations at certain positions control the evolutionary direction of the protein family. The mutations at different positions, even distantly separated, are mutually coupled and form an evolutionary network. Finding the controlling mutative positions and the mutative network among residues are firstly important for protein rational design and enzyme engineering. Methodology: A computational approach, namely amino acid position conservation-mutation correlation analysis (CMCA), is developed to predict mutually mutative positions and find the evolutionary network in protein family. The amino acid position mutative function, which is the foundational equation of CMCA measuring the mutation of a residue at a position, is derived from the MSA (multiple structure alignment) database of protein evolutionary family. Then the position conservation correlation matrix and position mutation correlation matrix is constructed