Tyagi Nidhi, Krishnadev Oruganty, Srinivasan Narayanaswamy
Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India.
Mol Biosyst. 2009 Dec;5(12):1630-5. doi: 10.1039/b906543c. Epub 2009 Sep 28.
A lack of information on protein-protein interactions at the host-pathogen interface is impeding the understanding of the pathogenesis process. A recently developed, homology search-based method to predict protein-protein interactions is applied to the gastric pathogen, Helicobacter pylori to predict the interactions between proteins of H. pylori and human proteins in vitro. Many of the predicted interactions could potentially occur between the pathogen and its human host during pathogenesis as we focused mainly on the H. pylori proteins that have a transmembrane region or are encoded in the pathogenic island and those which are known to be secreted into the human host. By applying the homology search approach to protein-protein interaction databases DIP and iPfam, we could predict in vitro interactions for a total of 623 H. pylori proteins with 6559 human proteins. The predicted interactions include 549 hypothetical proteins of as yet unknown function encoded in the H. pylori genome and 13 experimentally verified secreted proteins. We have recognized 833 interactions involving the extracellular domains of transmembrane proteins of H. pylori. Structural analysis of some of the examples reveals that the interaction predicted by us is consistent with the structural compatibility of binding partners. Examples of interactions with discernible biological relevance are discussed.
宿主-病原体界面处蛋白质-蛋白质相互作用信息的缺乏阻碍了对发病机制过程的理解。一种最近开发的基于同源性搜索来预测蛋白质-蛋白质相互作用的方法被应用于胃部病原体幽门螺旋杆菌，以预测幽门螺旋杆菌蛋白质与人类蛋白质在体外的相互作用。由于我们主要关注具有跨膜区域或在致病岛中编码的幽门螺旋杆菌蛋白质以及那些已知会分泌到人类宿主中的蛋白质，所以许多预测的相互作用可能在发病过程中发生在病原体与其人类宿主之间。通过将同源性搜索方法应用于蛋白质-蛋白质相互作用数据库DIP和iPfam，我们可以预测总共623种幽门螺旋杆菌蛋白质与6559种人类蛋白质的体外相互作用。预测的相互作用包括幽门螺旋杆菌基因组中编码的549种功能未知的假设蛋白质和13种经实验验证的分泌蛋白。我们已经识别出833种涉及幽门螺旋杆菌跨膜蛋白胞外结构域的相互作用。对一些实例的结构分析表明，我们预测的相互作用与结合伴侣的结构相容性一致。讨论了具有明显生物学相关性的相互作用实例。
