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Bioinformatics Advance Access published online on November 15, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti782
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© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received July 12, 2005
Revised November 10, 2005
Accepted November 12, 2005

Article

Equivalent binding sites reveal convergently evolved interaction motifs

Andreas Henschel 1 *, Wan Kyu Kim 1, and Michael Schroeder 1

1 Bioinformatics Group, Biotechnological Centre, TU Dresden, Germany

* To whom correspondence should be addressed.
Andreas Henschel, E-mail: ah{at}biotec.tu-dresden.de


  Abstract

Motivation: Much research has been devoted to the characterization of interaction interfaces found in complexes with known structure. In this context, the interactions of non-homologous domains at equivalent binding sites are of particular interest, as they can reveal convergently evolved interface motifs. Such motifs are an important source of information to formulate rules for interaction specificity and to design ligands based on the common features shared among diverse partners.

Results: We develop a novel method to identify non-homologous structural domains which bind at equivalent sites when interacting with a common partner. We systematically apply this method to all pairs of interactions with known structure and derive a comprehensive database for these interactions. Of all non-homologous domains, which bind with a common interaction partner, 4.2% use the same interface of the common interaction partner (excluding immunoglobulins and proteases). This rises to 16% if immunoglobulin and proteases are included. We demonstrate two applications of our database: First, the systematic screening for viral protein interfaces, which can mimic native interfaces and thus interfere and second, structural motifs in enzymes and its inhibitors. We highlight several cases of virus protein mimicry: Viral M3 protein interferes with a chemokine dimer interface. The virus has evolved the motif SVSPLP, which mimics the native SSDTTP motif. A second example is the regulatory factor Nef in HIV which can mimic a kinase when interacting with SH3. Among others the virus has evolved the kinase's PxxP motif. Further, we elucidate motif resemblences in Baculovirus p35 and HIV capsid proteins. Finally, chymotrypsin is subject to scrutiny wrt. its structural similarity to subtilisin and wrt. its inhibitor's similar recognition sites.

Supplementary material: A database is online at scoppi.biotec.tu-dresden.de/abac/.


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