Tuncbag Nurcan, Gursoy Attila, Guney Emre, Nussinov Ruth, Keskin Ozlem
Center for Computational Biology and Bioinformatics, College of Engineering, Koc University, Rumeli Feneri Yolu, 34450 Sariyer, Istanbul, Turkey.
J Mol Biol. 2008 Sep 5;381(3):785-802. doi: 10.1016/j.jmb.2008.04.071. Epub 2008 May 6.
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.
自然界中存在的有限数量的蛋白质折叠执行着各种各样的细胞功能。同样可以预期，细胞功能多样性将由有限数量的蛋白质 - 蛋白质界面结构所涵盖。在此，我们展示了8205个界面簇，每个簇代表一种独特的界面结构。对这个蛋白质 - 蛋白质界面数据集进行了分析，并与旧的数据集进行了比较。我们观察到，与蛋白质数据库条目的数量相比，生物界面和晶体界面的数量都显著增加。此外，我们发现不同界面结构的数量增长速度比折叠的数量快得多，并且尚未趋于平稳。我们通过从界面构建功能相互作用网络进一步分析功能覆盖的增长趋势。还发现功能覆盖稳步增加。有趣的是，我们还观察到，尽管界面结构具有多样性，但有些结构更有利且经常被使用，特别值得关注的是那些在单链中也被优先选择的结构。
