Structural space of protein-protein interfaces is degenerate, close to complete, and highly connected.

ABSTRACT: At the heart of protein-protein interactions are protein-protein interfaces where the direct physical interactions occur. By developing and applying an efficient structural alignment method, we study the structural similarity of representative protein-protein interfaces involving interactions between dimers. Even without structural similarity between individual monomers that form dimeric complexes, ∼90% of native interfaces have a close structural neighbor with similar backbone C(α) geometry and interfacial contact pattern. About 80% of the interfaces form a dense network, where any two interfaces are structurally related using a transitive set of at most seven intermediate interfaces. The degeneracy of interface space is largely due to the packing of compact, hydrogen-bonded secondary str

SUBMITTER: Gao M 

PROVIDER: S-EPMC3012513 | biostudies-literature | 2010 Dec

REPOSITORIES: biostudies-literature