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Open Access Research article

Reuse of structural domain–domain interactions in protein networks

Benjamin Schuster-Böckler* and Alex Bateman

Author Affiliations

Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK

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BMC Bioinformatics 2007, 8:259  doi:10.1186/1471-2105-8-259

Published: 18 July 2007

Abstract

Background

Protein interactions are thought to be largely mediated by interactions between structural domains. Databases such as iPfam relate interactions in protein structures to known domain families. Here, we investigate how the domain interactions from the iPfam database are distributed in protein interactions taken from the HPRD, MPact, BioGRID, DIP and IntAct databases.

Results

We find that known structural domain interactions can only explain a subset of 4–19% of the available protein interactions, nevertheless this fraction is still significantly bigger than expected by chance. There is a correlation between the frequency of a domain interaction and the connectivity of the proteins it occurs in. Furthermore, a large proportion of protein interactions can be attributed to a small number of domain interactions. We conclude that many, but not all, domain interactions constitute reusable modules of molecular recognition. A substantial proportion of domain interactions are conserved between E. coli, S. cerevisiae and H. sapiens. These domains are related to essential cellular functions, suggesting that many domain interactions were already present in the last universal common ancestor.

Conclusion

Our results support the concept of domain interactions as reusable, conserved building blocks of protein interactions, but also highlight the limitations currently imposed by the small number of available protein structures.