Identification of protein interaction partners and protein-protein interaction sites

Journal of Molecular Biology
Sophie Sacquin-MoraRichard Lavery

Abstract

Rigid-body docking has become quite successful in predicting the correct conformations of binary protein complexes, at least when the constituent proteins do not undergo large conformational changes upon binding. However, determining whether two given proteins interact is a more difficult problem. Successful docking procedures often give equally good scores for proteins that do not interact experimentally. This is the case for the multiple minimization approach we use here. An analysis of the results where all proteins within a set are docked with all other proteins (complete cross-docking) shows that the predictions can be greatly improved if the location of the correct binding interface on each protein is known, since the experimental complexes are much more likely to bring these two interfaces into contact, at the same time as yielding good interaction energy scores. While various methods exist for identifying binding interfaces, it is shown that simply studying the interaction of all potential protein pairs within a data set can itself help to identify the correct interfaces.

References

Sep 15, 1978·Journal of Molecular Biology·S J Wodak, J Janin
Apr 1, 1975·Proceedings of the National Academy of Sciences of the United States of America·C LevinthalA K Dadivanian
Aug 28, 1975·Nature·C Chothia, J Janin
Jan 9, 1996·Proceedings of the National Academy of Sciences of the United States of America·S Jones, J M Thornton
Mar 29, 1996·Journal of Molecular Biology·O LichtargeF E Cohen
Feb 1, 1996·Journal of Molecular Graphics·W HumphreyK Schulten
Feb 2, 1999·Journal of Molecular Biology·L Lo ConteJ Janin
Feb 19, 2000·Current Opinion in Structural Biology·A P Minton
Jan 11, 2000·Nucleic Acids Research·G D BaderC W Hogue
Jan 3, 2001·Nature Structural Biology·M WürteleA Wittinghofer
Apr 3, 2001·Proceedings of the National Academy of Sciences of the United States of America·T ItoY Sakaki
May 1, 2001·Journal of Molecular Biology·H ClaussenT Lengauer
Sep 12, 2001·Current Opinion in Biotechnology·I Xenarios, D Eisenberg
Feb 13, 2002·Current Opinion in Structural Biology·Olivier Lichtarge, Mathew E Sowa
Apr 19, 2002·The Journal of Biological Chemistry·Aline DesmyterChristian Cambillau
May 31, 2002·Acta Crystallographica. Section D, Biological Crystallography·Helen M BermanChristine Zardecki
Jun 6, 2002·Proceedings of the National Academy of Sciences of the United States of America·Ludovic R OtterbeinRoberto Dominguez
Jul 16, 2002·Molecular & Cellular Proteomics : MCP·Charlotte M DeaneDavid Eisenberg
Sep 5, 2002·Proteins·Natasja BrooijmansIrwin D Kuntz
May 23, 2003·Protein Science : a Publication of the Protein Society·Martin Zacharias
Jun 5, 2003·Proteins·Rong ChenZhiping Weng
Sep 5, 2003·Nature·R John Ellis, Allen P Minton
Dec 23, 2003·Journal of Molecular Biology·Juan Fernández-RecioRuben Abagyan
Mar 30, 2004·Proteins·Jinn-Moon Yang, Chun-Chen Chen
Mar 31, 2004·Journal of Molecular Biology·Hani NeuvirthGideon Schreiber
Apr 21, 2004·Journal of Molecular Biology·Ranjit Prasad BahadurJoël Janin
Aug 3, 2004·Nature Biotechnology·Antonio MacchiaruloJanet M Thornton
Apr 29, 2005·Journal of Medicinal Chemistry·Christoph A Sotriffer, Ingo Dramburg
Jun 28, 2005·Proteins·Julian MintserisZhiping Weng
Dec 24, 2005·Proteins·Karine BastardMartin Zacharias
Jan 24, 2006·Biophysical Journal·Sophie Sacquin-Mora, Richard Lavery
Feb 22, 2007·Proteins·Sophie Sacquin-MoraRichard Lavery
Apr 3, 2007·PLoS Computational Biology·Benjamin A Shoemaker, Anna R Panchenko
May 25, 2007·Proteins·Yong Zhao, Michel F Sanner
Jun 26, 2007·Bioinformatics·Huan-Xiang Zhou, Sanbo Qin

❮ Previous
Next ❯

Citations

Dec 14, 2012·Journal of the Royal Society, Interface·Panagiotis L Kastritis, Alexandre M J J Bonvin
May 9, 2012·BMC Biophysics·Juliette Martin, Richard Lavery
Oct 24, 2014·Faraday Discussions·Guillaume LevieuxMatthieu Montes
Apr 19, 2011·Current Opinion in Structural Biology·Mark N WassMichael J E Sternberg
Nov 26, 2015·Journal of Chemical Theory and Computation·Agustí EmperadorModesto Orozco
Jul 7, 2015·Structure·Christina E M SchindlerMartin Zacharias
Jul 21, 2015·ELife·Anna Vangone, Alexandre Mjj Bonvin
Apr 29, 2014·Journal of Molecular Biology·Panagiotis L KastritisAlexandre M J J Bonvin
Jan 14, 2017·Scientific Reports·Guillaume LaunayJuliette Martin
Oct 14, 2017·Bioinformatics·Francesca Nadalin, Alessandra Carbone
Mar 16, 2018·PLoS Computational Biology·Nika AbdollahiAnne Lopes
Jan 8, 2019·PLoS Computational Biology·Raji ViswanathanAndras Fiser
Mar 7, 2019·Current Topics in Medicinal Chemistry·Vittoria CicaloniOttavia Spiga
Jun 15, 2019·Proteins·Chloé DequekerAlessandra Carbone
Jun 16, 2018·Nucleic Acids Research·Sébastien ReilleGuillaume Launay
Jun 10, 2020·Computational and Structural Biotechnology Journal·Jorge Roel-Touris, Alexandre M J J Bonvin
May 13, 2009·Journal of Chemical Information and Modeling·Tatsuya YoshikawaKazuhiko Fukui
Oct 11, 2017·Journal of Chemical Information and Modeling·Chloé DequekerAlessandra Carbone
Jan 14, 2020·Journal of Molecular Biology·Hugo SchwekeAnne Lopes

❮ Previous
Next ❯

Related Concepts

Related Feeds

Bacterial Cell Wall Structure (ASM)

Bacterial cell walls are made of peptidoglycan (also called murein), which is made from polysaccharide chains cross-linked by unusual peptides containing D-amino acids. Here is the latest research on bacterial cell wall structures.

Bacterial Cell Wall Structure

Bacterial cell walls are made of peptidoglycan (also called murein), which is made from polysaccharide chains cross-linked by unusual peptides containing D-amino acids. Here is the latest research on bacterial cell wall structures.

Related Papers

Protein Science : a Publication of the Protein Society
Panagiotis L KastritisJoël Janin
Current Opinion in Structural Biology
Alexandre M J J Bonvin
© 2022 Meta ULC. All rights reserved