Uncovering New Pathogen-Host Protein-Protein Interactions by Pairwise Structure Similarity

PloS One
Tao CuiZheng-Guo He

Abstract

Pathogens usually evade and manipulate host-immune pathways through pathogen-host protein-protein interactions (PPIs) to avoid being killed by the host immune system. Therefore, uncovering pathogen-host PPIs is critical for determining the mechanisms underlying pathogen infection and survival. In this study, we developed a computational method, which we named pairwise structure similarity (PSS)-PPI, to predict pathogen-host PPIs. First, a high-quality and non-redundant structure-structure interaction (SSI) template library was constructed by exhaustively exploring heteromeric protein complex structures in the PDB database. New interactions were then predicted by searching for PSS with complex structures in the SSI template library. A quantitative score named the PSS score, which integrated structure similarity and residue-residue contact-coverage information, was used to describe the overall similarity of each predicted interaction with the corresponding SSI template. Notably, PSS-PPI yielded experimentally confirmed pathogen-host PPIs of human immunodeficiency virus type 1 (HIV-1) with performance close to that of in vitro high-throughput screening approaches. Finally, a pathogen-host PPI network of human pathogen Mycobacteriu...Continue Reading

References

Dec 11, 1999·Nucleic Acids Research·H M BermanP E Bourne
Aug 3, 2001·Nature Reviews. Molecular Cell Biology·D G Russell
Oct 22, 2003·Proceedings of the National Academy of Sciences of the United States of America·Christopher M Sassetti, Eric J Rubin
Jan 22, 2004·Nature Reviews. Genetics·Albert-László Barabási, Zoltán N Oltvai
Apr 15, 2004·Nature Reviews. Microbiology·Anil KoulAxel Ullrich
Apr 26, 2005·Nucleic Acids Research·Yang Zhang, Jeffrey Skolnick
Jun 2, 2005·Proceedings of the National Academy of Sciences of the United States of America·Jyothi RengarajanEric J Rubin
Aug 2, 2005·Nature Cell Biology·Zhijian J Chen
Dec 3, 2005·PLoS Pathogens·Graham R StewartDouglas B Young
Oct 19, 2006·Science's STKE : Signal Transduction Knowledge Environment·Hans Häcker, Michael Karin
Jul 25, 2007·Bioinformatics·Matthew D DyerBruno W Sobral
Oct 19, 2007·Nature·Amit P BhavsarB Brett Finlay
Oct 20, 2007·Nature Protocols·Melissa S ClineGary D Bader
Feb 22, 2008·Proceedings of the National Academy of Sciences of the United States of America·Jennifer A PhilipsNorbert Perrimon
Oct 18, 2008·Nucleic Acids Research·William FuRoger G Ptak
Mar 7, 2009·The Journal of Immunology : Official Journal of the American Association of Immunologists·Chul-Su YangEun-Kyeong Jo
Apr 17, 2009·Nature Reviews. Microbiology·Ronald S FlannaganSergio Grinstein
Dec 17, 2009·BMC Bioinformatics·Christiam CamachoThomas L Madden
Jan 16, 2010·Nature Reviews. Microbiology·Lautaro Diacovich, Jean-Pierre Gorvel
Oct 22, 2010·BMC Bioinformatics·Ranjit Kumar, Bindu Nanduri
Nov 19, 2010·PloS One·Nicole A KruhKaren M Dobos
Jan 20, 2011·Infection and Immunity·Collin R Diedrich, Joanne L Flynn
Mar 2, 2011·PLoS Neglected Tropical Diseases·Janet M Doolittle, Shawn M Gomez
Mar 9, 2011·Nature Reviews. Microbiology·Masmudur M Rahman, Grant McFadden
Sep 17, 2011·Journal of Proteomics·Gustavo A de SouzaHarald G Wiker
Nov 22, 2011·Nucleic Acids Research·UNKNOWN UniProt Consortium
Dec 23, 2011·Nature·Stefanie JägerNevan J Krogan
Feb 14, 2012·Nature·Nicholas NoinajSusan K Buchanan
Mar 1, 2012·PLoS Pathogens·Andrzej PawlowskiGunilla Källenius
Mar 12, 2013·Bulletin of the World Health Organization
Apr 5, 2013·Bulletin of the World Health Organization·Haileyesus GetahunMario Raviglione
Jun 27, 2013·Molecular & Cellular Proteomics : MCP·Vesna MemisevićAnders Wallqvist
May 8, 2014·Nature Reviews. Microbiology·Hiroshi AshidaChihiro Sasakawa

❮ Previous
Next ❯

Citations

Jul 26, 2018·Journal of Biomolecular Structure & Dynamics·Jing ChenJia Wang
Mar 27, 2019·Autophagy·Padhmanand SudhakarIoannis P Nezis
Feb 20, 2020·Medical Microbiology and Immunology·Sounak ChowdhuryJohan Malmström
May 29, 2021·Frontiers in Microbiology·Padhmanand SudhakarSéverine Vermeire

❮ Previous
Next ❯

Methods Mentioned

BETA
affinity purification
X-ray
GTPases
GTPase
ubiquitination

Software Mentioned

BLAST
TM
align
PPI
Cytoscape
PSS

Related Concepts

Related Feeds

Bacterial Protein Structures

Bacterial protein structures can expedite the development of novel antibiotics. Here is the latest research on bacterial proteins and the resolution of their structures.

Bacterial Protein Structures (ASM)

Bacterial protein structures can expedite the development of novel antibiotics. Here is the latest research on bacterial proteins and the resolution of their structures.