Architectures and functional coverage of protein-protein interfaces.

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 ofdistinctinterface architectures growsat amuch faster rate thanthenumberoffoldsandisyettoleveloff.Wefurtheranalyzethegrowth 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. © 2008 Elsevier Ltd. All rights reserved.