Prediction of protein-protein interaction sites using patch analysis

Abstract

A method for defining and analysing a series of residue patches on the surface of protein structures is used to predict the location of protein-protein interaction sites. Each residue patch is analysed for six parameters; solvation potential, residue interface propensity, hydrophobicity, planarity, protrusion and accessible surface area. The method involves the calculation of a relative combined score that gives the probability of a surface patch forming protein-protein interactions. Predictions are made for the known structures of protomers from 28 homo-dimers, large protomers from 11 hetero-complexes, small protomers from 14 hetero-complexes, and antigens from six antibody-antigen complexes. The predictions are successful for 66% (39/59) of the structures and the remainder can usually be rationalized in terms of additional interaction sites.