The quantification of protein-protein interaction interfaces using solvent-excluded surface-defined properties

Protein-protein interaction (PPI) is the cornerstone of nearly every biological process. During last forty years PPI interfaces have been investigated extensively both in vitro and in silico in order to understand both the strength and specificity of PPI. At least three different models, the buried surface model, the O-ring model and the rim- and-core model, have been proposed for PPI interface. However none of them provide much detail about PPI and a single model that reconciles them remains elusive. To identify common physical and geometrical features shared by various PPI interfaces we have analyzed several solvent-excluded surface (SES)-defined properties for a set of well-studied protein-protein complexes with crystal structures. Our analysis shows that the SES-defined properties for the interface atoms of a PPI partner are in general different from those for the surface atoms of a water-soluble protein. Most significantly we find that the partially-buried atoms of a PPI partner have unique SES-defined properties that set them well apart from either the buried atoms or the accessible atoms. Based on distinct SES-defined properties for the accessible, buried and partially-buried atoms shared by various PPI interfaces we propose a new model specified by a list of SES-defined properties shared by various PPI interfaces. Our model is quantitative in nature and should be useful for PPI site identification, protein-protein docking and structure-based design of chemicals targeting PPI.