Prediction of protein–protein interactions between Helicobacter pylori and a human host

Abstract

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 proteinsin 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. pyloriproteins 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. pyloriproteins with 6559 human proteins. The predicted interactions include 549 hypothetical proteins of as yet unknown function encoded in the H. pylorigenome and 13 experimentally verified secreted proteins. We have recognized 833 interactions involving the extracellular domains of transmembraneproteins 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.