Architectures and Functional Coverage of Protein–Protein Interfaces

• Published in: Journal of molecular biology 2008-09, Vol.381 (3), p.785-802
• Main Authors: Tuncbag, Nurcan, Gursoy, Attila, Guney, Emre, Nussinov, Ruth, Keskin, Ozlem
• Format: Article
• Language: English
• Subjects: binding; Binding Sites; Databases, Protein; interface database; Models, Molecular; Protein Binding; Protein Conformation; protein interaction; protein interfaces; Proteins - metabolism; structure and function
• ISSN: 0022-2836; 1089-8638
• DOI: 10.1016/j.jmb.2008.04.071

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.