White Robert A, Szurmant Hendrik, Hoch James A, Hwa Terence
Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California, USA.
Methods Enzymol. 2007;422:75-101. doi: 10.1016/S0076-6879(06)22004-4.
As more and more sequence data become available, new approaches for extracting information from these data become feasible. This chapter reports on one such method that has been applied to elucidate protein-protein interactions in bacterial two-component signaling pathways. The method identifies residues involved in the interaction through an analysis of over 2500 functionally coupled proteins and a precise determination of the substitutional constraints placed on one protein by its signaling mate. Once identified, a simple log-likelihood scoring procedure is applied to these residues to build a predictive tool for assigning signaling mates. The ability to apply this method is based on a proliferation of related domains within multiple organisms. Paralogous evolution through gene duplication and divergence of two-component systems has commonly resulted in tens of closely related interacting pairs within one organism with a roughly one-to-one correspondence between signal and response. This provides us with roughly an order of magnitude more protein pairs than there are unique, fully sequenced bacterial species. Consequently, this chapter serves as both a detailed exposition of the method that has provided more depth to our knowledge of bacterial signaling and a look ahead to what would be possible on a more widespread scale, that is, to protein-protein interactions that have only one example per genome, as the number of genomes increases by a factor of 10.
随着越来越多的序列数据可用，从这些数据中提取信息的新方法变得可行。本章报道了一种已被应用于阐明细菌双组分信号通路中蛋白质-蛋白质相互作用的方法。该方法通过分析2500多个功能耦合蛋白，并精确确定其信号伴侣对一种蛋白质施加的替代限制，来识别参与相互作用的残基。一旦识别出来，就对这些残基应用一个简单的对数似然评分程序，以构建一个用于分配信号伴侣的预测工具。应用这种方法的能力基于多种生物体内相关结构域的大量存在。通过双组分系统的基因复制和分化进行的旁系同源进化通常导致一个生物体内有数十个密切相关的相互作用对，信号与反应之间大致呈一对一对应。这为我们提供的蛋白质对数量比独特的、已完全测序的细菌物种数量多大约一个数量级。因此，本章既是对该方法的详细阐述，该方法为我们对细菌信号传导的认识提供了更多深度，也是对更广泛范围内可能实现的情况的展望，即随着基因组数量增加10倍，对于每个基因组只有一个实例的蛋白质-蛋白质相互作用。
