Architectures and functional coverage of protein-protein interfaces

JOURNAL OF MOLECULAR BIOLOGY

卷:381

Article

Tuncbag, Nurcan¹  Gursoy, Attila¹  Guney, Emre¹  Nussinov, Ruth^2,3  Keskin, Ozlem¹ 

[1] Koc Univ, Coll Engn, Ctr Computat Biol & Bioinformat, TR-34450 Istanbul, Turkey

[2] NCI, Basic Res Program, SAIC Frederick Inc, Ctr Canc Res Nanobiol Program, Frederick, MD 21702 USA

[3] Tel Aviv Univ, Sackler Sch Med, Dept Human Genet & Mol Med, Sackler Inst Mol Med, IL-69978 Tel Aviv, Israel

关键词: protein interfaces;    protein interaction;    structure and function;    binding;    interface database;   

DOI  :  10.1016/j.jmb.2008.04.071

来源: Elsevier

【 摘 要 】

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.

【 授权许可】

Free