title: Prediction of protein-protein interactions between human host and a pathogen and its application to three pathogenic bacteria.
abstract: Molecular understanding of disease processes can be accelerated if all interactions between the host and pathogen are known. The unavailability of experimental methods for large-scale detection of interactions across host and pathogen organisms hinders this process. Here we apply a simple method to predict protein-protein interactions across a host and pathogen organisms. We use homology detection approaches against the protein-protein interaction databases, DIP and iPfam in order to predict interacting proteins in a host-pathogen pair. In the present work, we first applied this approach to the test cases involving the pairs phage T4 -Escherichia coli and phage lambda -E. coli and show that previously known interactions could be recognized using our approach. We further apply this approach to predict interactions between human and three pathogens E. coli, Salmonella enterica typhimurium and Yersinia pestis. We identified several novel interactions involving proteins of host or pathogen that could be thought of as highly relevant to the disease process. Serendipitously, many interactions involve hypothetical proteins of yet unknown function. Hypothetical proteins are predicted from computational analysis of genome sequences with no laboratory analysis on their functions yet available. The predicted interactions involving such proteins could provide hints to their functions.
authors.affiliation: Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, Karnataka, India.
authors.forename: O
authors.initials: O
authors.lastname: Krishnadev
authors.forename: N
authors.initials: N
authors.lastname: Srinivasan
mesh_terms: D001426:Bacterial Proteins / Q000378:metabolism*; D017122:Bacteriophage T4 / Q000378:metabolism; D010582:Bacteriophage lambda / Q000378:metabolism; D030562:Databases, Protein; D004926:Escherichia coli / Q000378:metabolism* / Q000821:virology; D054884:Host-Pathogen Interactions / Q000502:physiology*; D006801:Humans; D016328:NF-kappa B / Q000378:metabolism; D025941:Protein Interaction Mapping / Q000379:methods*; D018124:Receptors, Tumor Necrosis Factor / Q000378:metabolism; D012486:Salmonella typhimurium / Q000378:metabolism*; D050826:Suppressor of Cytokine Signaling Proteins / Q000378:metabolism; D051197:Toll-Like Receptor 4 / Q000378:metabolism; D014764:Viral Proteins / Q000378:metabolism; D015010:Yersinia pestis / Q000378:metabolism*
chemical_list: D001426:Bacterial Proteins; D016328:NF-kappa B; D018124:Receptors, Tumor Necrosis Factor; D050826:Suppressor of Cytokine Signaling Proteins; D051197:Toll-Like Receptor 4; D014764:Viral Proteins