Predicting protein interaction interfaces from protein sequences: case studies of subtilisin and phycocyanin.
Identification of protein interaction interfaces is very important for understanding the molecular mechanisms underlying biological phenomena. Here, we present a novel method for predicting protein interaction interfaces from sequences by using PAM matrix (PIFPAM). Sequence alignments for interacting proteins were constructed and parsed into segments using sliding windows. By calculating distance matrix for each segment, the correlation coefficients between segments were estimated. The interaction interfaces were predicted by extracting highly correlated segment pairs from the correlation map. The predictions achieved an accuracy 0.41-0.71 for eight intraprotein interaction examples, and 0.07-0.60 for four interprotein interaction examples. Compared with three previously published methods, PIFPAM predicted more contacting site pairs for 11 out of the 12 example proteins, and predicted at least 34% more contacting site pairs for eight proteins of them. The factors affecting the predictions were also analyzed. Since PIFPAM uses only the alignments of the two interacting proteins as input, it is especially useful when no three-dimensional protein structure data are available.
Xie
Bin-Bin
BB
State Key Lab of Microbial Technology, Shandong University, Jinan 250100, People's Republic of China.
Chen
Xiu-Lan
XL
Zhang
Xi-Ying
XY
He
Hai-Lun
HL
Zhang
Yu-Zhong
YZ
Zhou
Bai-Cheng
BC
D000595:Amino Acid Sequence; D008024:Ligands; D010798:Phycocyanin / Q000737:chemistry / Q000378:metabolism*; D011237:Predictive Value of Tests; D011485:Protein Binding; D025941:Protein Interaction Mapping; D016415:Sequence Alignment; D020539:Sequence Analysis, Protein / Q000379:methods; D020860:Subtilisin / Q000737:chemistry / Q000378:metabolism*; D013816:Thermodynamics
D008024:Ligands; D010798:Phycocyanin; D020860:Subtilisin