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J Mol Biol. 2008 Sep 5;381(3):785-802. doi: 10.1016/j.jmb.2008.04.071. Epub 2008 May 6.

Architectures and functional coverage of protein-protein interfaces.

Author information

1
Center for Computational Biology and Bioinformatics, College of Engineering, Koc University, Rumeli Feneri Yolu, 34450 Sariyer, Istanbul, Turkey.

Abstract

The diverse range of cellular functions is performed by a limited number of protein folds existing in nature. One may similarly expect that cellular functional diversity would be covered by a limited number of protein-protein interface architectures. Here, we present 8205 interface clusters, each representing a unique interface architecture. This data set of protein-protein interfaces is analyzed and compared with older data sets. We observe that the number of both biological and crystal interfaces increases significantly compared to the number of Protein Data Bank entries. Furthermore, we find that the number of distinct interface architectures grows at a much faster rate than the number of folds and is yet to level off. We further analyze the growth trend of the functional coverage by constructing functional interaction networks from interfaces. The functional coverage is also found to steadily increase. Interestingly, we also observe that despite the diversity of interface architectures, some are more favorable and frequently used, and of particular interest, are the ones that are also preferred in single chains.

PMID:
18620705
PMCID:
PMC2605427
DOI:
10.1016/j.jmb.2008.04.071
[Indexed for MEDLINE]
Free PMC Article

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