Evolutionary conservation in multiple faces of protein interaction

Protein interfaces are believed to be evolutionarily more conserved than the rest of the protein surface, but this has not been properly verified using a large protein structural set. Furthermore, recent systematic protein interaction analyses have proved that proteins interacting with many partners have multiple interfaces to connect protein interaction networks, which have never taken into account for conservation analysis of protein interface. Here, we studied the evolutionary conservation of protein interfaces using a large‐scale dataset of 2646 protein interfaces with the classification of homodimeric/heterodimeric and obligatory/transient interactions, considering all their known multiple interfaces. We found that protein interfaces were indeed more conserved than noninterface surfaces, and the conservation level of protein interfaces increased when multiple interfaces were properly considered. These findings suggest that conservation analysis should be a good descriptor for protein interface identification and protein–protein interaction predictions. We applied this evolutionary feature to filter docking decoys and found that protein interface conservation worked remarkably well in selecting the near‐native structures from the large number of generated docking complexes. Moreover, we discovered that a strong correlation exist between protein interface size and protein interface conservation, which could be a useful filter for the prediction of protein–protein interactions. Proteins 2009. © 2009 Wiley‐Liss, Inc.