Architectures and functional coverage of protein-protein interfaces


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Tuncbag N. , Gursoy A., Guney E., NUSSINOV R., Keskin O.

JOURNAL OF MOLECULAR BIOLOGY, vol.381, no.3, pp.785-802, 2008 (Journal Indexed in SCI) identifier identifier identifier

  • Publication Type: Article / Article
  • Volume: 381 Issue: 3
  • Publication Date: 2008
  • Doi Number: 10.1016/j.jmb.2008.04.071
  • Title of Journal : JOURNAL OF MOLECULAR BIOLOGY
  • Page Numbers: pp.785-802
  • Keywords: protein interfaces, protein interaction, structure and function, binding, interface database, STRUCTURAL GENOMICS, INTERACTION NETWORKS, MOLECULAR BIOLOGIST, REFERENCE DATABASE, SYSTEMS BIOLOGY, HOT-SPOTS, SEQUENCE, DOMAIN, RECOGNITION, PREDICTION

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. (C) 2008 Elsevier Ltd. All rights reserved.