Network analysis of protein-protein interaction  

作　　者：Shan Chang XinQi Gong Xiong Jiao ChunHua Li WeiZu Chen CunXin Wang 

机构地区：[1]Beijing Univ Technol, Coll Life Sci & Bioengn, Beijing 100124, Peoples R China

出　　处：《Chinese Science Bulletin》2010年第9期814-822,共9页

基　　金：supported by the National Natural Science Foundation of China (Grant Nos. 20773006, 30670497, 10974008);Beijing Natural Science Foundation (Grant No. 4102006) ;Specialized Research Fund for the Doctoral Program of Higher Education (Grant No. 200800050003)

摘　　要：Residue networks are constructed by defining the residues as the vertices and atom contacts between them as the edges. The residue network of a protein complex is divided into two types of networks, i.e. the hydrophobic and the hydrophilic residue networks. By analyzing the network parameters, it is found that the correct binding complex conformations are of both higher sum of the interface degree values and lower characteristic path length than those incorrect ones. These features reflect that the correct bind-ing complex conformations have better geometric and/or residue type complementarity, and the correct binding modes are very important for preserving the characteristic path lengths of native protein complexes. In addition, two scoring terms are proposed based on the network parameters, in which the characteristics of the entire complex shape and residue type complementarity are taken into account. These network-based scoring terms have also been used in conjunction with other scoring terms, and the new multi-term scoring HPNCscore is devised in this work. It can improve the discrimination of the combined scoring function of RosettaDock more than 12%. This work might enhance our knowledge of the mechanisms of protein-protein interactions and recognition.Residue networks are constructed by defining the residues as the vertices and atom contacts between them as the edges. The residue network of a protein complex is divided into two types of networks, i.e. the hydrophobic and the hydrophilic residue networks. By analyzing the network parameters, it is found that the correct binding complex conformations are of both higher sum of the interface degree values and lower characteristic path length than those incorrect ones. These features reflect that the correct bind-ing complex conformations have better geometric and/or residue type complementarity, and the correct binding modes are very important for preserving the characteristic path lengths of native protein complexes. In addition, two scoring terms are proposed based on the network parameters, in which the characteristics of the entire complex shape and residue type complementarity are taken into account. These network-based scoring terms have also been used in conjunction with other scoring terms, and the new multi-term scoring HPNCscore is devised in this work. It can improve the discrimination of the combined scoring function of RosettaDock more than 12%. This work might enhance our knowledge of the mechanisms of protein-protein interactions and recognition.

关 键 词：interface CHARACTERISTIC PATH LENGTH RESIDUE network SCORING FUNCTION 

分 类 号：N[自然科学总论]