Structural Modeling of Protein Interactions by Analogy: Application to PSD-95
Figure 2
Examples of Predicted Protein Interface between Two Subunits for a Pyruvate Formate–Lyase Protein Complex from Our Benchmark Set
Shown are the structures of the native complex (grey) together with the best-scoring models that were predicted by comparative patch analysis using binding site information for (A) both, or (B) just one of the interacting subunits, and (C) by conventional protein docking, where no binding site information is provided. The predicted and native structures are superposed using one of the two subunits, which is represented by its accessible surface. The remaining subunits of the predicted structures are shown in the ribbon representation colored red, blue, and orange, correspondingly. In both scenarios, comparative patch analysis was significantly more accurate than protein docking. Using both binding sites, comparative patch analysis accurately predicted the protein interaction interface, including the relative orientation of subunits. The accuracy of interface prediction by our approach using only one binding site was significantly reduced, while it was still able to predict the binding sites near their native locations. The conventional protein docking failed to accurately predict either the relative orientation of subunits or the locations of their binding sites.