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Protein-Protein Interfaces

Herbert Edelsbrunner,

Arts and Sciences
Departments of Computer Science and Mathematics,
Duke University, Durham, North Carolina, and
Geomagic, Research Triangle Park, North Carolina

ABSTRACT: Protein-protein interactions form the basis for most cellular processes and result in the formation of protein interfaces. Believing that the local shape of proteins is crucial in most interactions, we take a geometric approach and present a definition of an interface surface formed by two or more proteins as a subset of their Voronoi diagram.The definition deals with the difficult and important problem of specifying interface boundaries. We present an algorithm to construct the surface and define a hierarchy that distinguishes core and peripheral regions. This hierarchy is shown to have correlation with hot-spots in protein-protein interactions.

We visualize interface surfaces by flattening them to a disk and using color to convey information about contributing residues as well as local geometric and physical properties.