Department of Biochemistry and Molecular and Cellular Biology, Georgetown University, Washington, DC, USA.
J Mol Biol. 2010 Jan 29;395(4):860-70. doi: 10.1016/j.jmb.2009.10.052. Epub 2009 Oct 30.
The evolution of protein interactions cannot be deciphered without a detailed analysis of interaction interfaces and binding modes. We performed a large-scale study of protein homooligomers in terms of their symmetry, interface sizes, and conservation of binding modes. We also focused specifically on the evolution of protein binding modes from nine families of homooligomers and mapped 60 different binding modes and oligomerization states onto the phylogenetic trees of these families. We observed a significant tendency for the same binding modes to be clustered together and conserved within clades on phylogenetic trees; this trend is especially pronounced for close homologs with 70% sequence identity or higher. Some binding modes are conserved among very distant homologs, pointing to their ancient evolutionary origin, while others are very specific for a certain phylogenetic group. Moreover, we found that the most ancient binding modes have a tendency to involve symmetrical (isologous) homodimer binding arrangements with larger interfaces, while recently evolved binding modes more often exhibit asymmetrical arrangements and smaller interfaces.
如果不详细分析相互作用界面和结合模式，就无法破译蛋白质相互作用的演变。我们从对称性、界面大小和结合模式的保守性方面，对蛋白质同源寡聚体进行了大规模的研究。我们还特别关注了 9 个同源寡聚体家族中蛋白质结合模式的进化，并将 60 种不同的结合模式和寡聚状态映射到这些家族的系统发育树上。我们观察到，相同的结合模式在系统发育树上的分支中具有显著的聚类和保守性趋势；对于具有 70%或更高序列同一性的密切同源物，这种趋势尤为明显。一些结合模式在非常远缘的同源物中是保守的，这表明它们具有古老的进化起源，而另一些结合模式则非常特定于特定的系统发育群。此外，我们发现最古老的结合模式倾向于涉及具有较大界面的对称（同系同源）同源二聚体结合排列，而最近进化的结合模式则更经常表现出不对称排列和较小的界面。
