Align Protein Surface Structures to IdentifyEvolutionally and Structurally Conserved Residues
Protein-protein interface underlies the protein protein interaction. Alanine mutation of protein-protein interface residues has shown that the distribution of binding free energy is not average among the interface residues. Actually, there are hot spots in the protein interfaces that contribute most binding energy. Here we provide a new method based on integer quadratic programming that systematically aligns protein surface structures shared by a set of proteins. This method incorporates protein sequence and structure data, and can correctly identify residues having evolutional and structural conservation between different proteins. It is sequence order independent, so can unravel the evolutional similarity between distant proteins. Furthermore, it can be used to predict hot spots with ROC area AUC=0.6. Compared with most hot spot prediction methods, our method does not need prior knowledge for the structure of protein complex or even the structure of the binding partner.
Hot spots Protein surface Residue conservation Integer quadratic programming
Lin Wang Ji-Guang Wang Luonan Chen
Computer Science and Information Engineering College,Tianjin University of Science and Technology,Ti Academy of Mathematics and Systems Science,Chinese Academy of Sciences,Beijing 100190,China Department of Electronics,Information and Communication Engineering,Osaka Sangyo University,Osaka 57
国际会议
The 3rd International Symposium on Optimization and System Biology(第三届最优化与系统生物学国际会议 OSB09)
张家界
英文
296-303
2009-09-20（万方平台首次上网日期，不代表论文的发表时间）