SCPC: A method to structurally compare protein complexes

Abstract

Motivation: Protein-protein interactions play vital functional roles in various biological phenomena. Physical contacts between proteins have been revealed using experimental approaches that have solved the structures of protein complexes at atomic resolution. To examine the huge number of protein complexes available in the Protein Data Bank, an efficient automated method that compares protein complexes is required. Results: We have developed Structural Comparison of Protein Complexes (SCPC), a novel method to structurally compare protein complexes. SCPC compares the spatial arrangements of subunits in a complex with those in another complex using secondary structure elements. Similar substructures are detected in two protein complexes and the similarity is scored. SCPC was applied to dimers, homo-oligomers and haemoglobins. SCPC properly estimated structural similarities between the dimers examined as well as an existing method, MM-align. Conserved substructures were detected in a homo-tetramer and a homo-hexamer composed of homologous proteins. Classification of quaternary structures of haemoglobins using SCPC was consistent with the conventional classification. The results demonstrate that SCPC is a valuable tool to investigate the structures of protein complexes. © The Author 2011. Published by Oxford University Press. All rights reserved.