Structural similarity-based predictions of protein interactions between HIV-1 and Homo sapiens | Doolittle and Gomez Virology Journal 2010 7 82 http content 7 1 82 VIROLOGY JOURNAL RESEARCH Open Access Structural similarity-based predictions of protein interactions between HIV-1 and Homo sapiens Janet M Doolittle1 and Shawn M Gomez 2 3 4 Abstract Background In the course of infection viruses such as HIV-1 must enter a cell travel to sites where they can hijack host machinery to transcribe their genes and translate their proteins assemble and then leave the cell again all while evading the host immune system. Thus successful infection depends on the pathogen s ability to manipulate the biological pathways and processes of the organism it infects. Interactions between HIV-encoded and human proteins provide one means by which HIV-1 can connect into cellular pathways to carry out these survival processes. Results We developed and applied a computational approach to predict interactions between HIV and human proteins based on structural similarity of 9 HIV-1 proteins to human proteins having known interactions. Using functional data from RNAi studies as a filter we generated over 2000 interaction predictions between HIV proteins and 406 unique human proteins. Additional filtering based on Gene Ontology cellular component annotation reduced the number of predictions to 502 interactions involving 137 human proteins. We find numerous known interactions as well as novel interactions showing significant functional relevance based on supporting Gene Ontology and literature evidence. Conclusions Understanding the interplay between HIV-1 and its human host will help in understanding the viral lifecycle and the ways in which this virus is able to manipulate its host. The results shown here provide a potential set of interactions that are amenable to further experimental manipulation as well as potential targets for therapeutic intervention. Background Pathogen invasion and survival requires that the pathogen interact with and manipulate its host. Human .
