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Accurate Prediction of Peptide Binding Sites on Protein Surfaces

Figure 3

Examples of applying the method.

Predicted peptides are depicted as spheres on the protein surface colored by amino acid type (prolines – pink, alanines and glycines - white, serines - orange, asparagines and glutamines - teal and aspartic/glutamic acid – red). (A) Binding of a collagen peptide (GPAGPPGA) on a human matrix metalloproteinase 2 (1eak). The peptide bound in the solved X-ray structure is colored in red. Note the predicted binding site differs however it is likely correct (see text). (B) Binding of the Ago hook peptide (PDNGTSAWGEPNESSPGWGEMD) on the PIWI domain of the Argonaute protein (PDB IDs: 1ytu [38]; 1w9h [39]): i) the best, though incorrect binding site; ii) the location of the other top scoring predictions (correct). (C) Prediction for the binding of an RGRGRGRG peptide to the human SMN tudor domain (PDB ID: 1mhn [40]), which agrees with NMR data. (D) Prediction of the leucine zipper (helical region 243–264) of the DBC1 sequence binding site on the catalytic domain of SIRT1 (PDB ID: 1m2g [42]) (E) Prediction for the binding of the LMP1 protein of the Epstein-Barr virus peptide DDPHGPVQLS on the TRADD protein (PDB ID: 1f2h [45]).

Figure 3