The identification of short linear motif-mediated interfaces within the human interactome.

Bioinformatics
Robert J WeatherittToby J Gibson

Abstract

Eukaryotic proteins are highly modular, containing multiple interaction interfaces that mediate binding to a network of regulators and effectors. Recent advances in high-throughput proteomics have rapidly expanded the number of known protein-protein interactions (PPIs); however, the molecular basis for the majority of these interactions remains to be elucidated. There has been a growing appreciation of the importance of a subset of these PPIs, namely those mediated by short linear motifs (SLiMs), particularly the canonical and ubiquitous SH2, SH3 and PDZ domain-binding motifs. However, these motif classes represent only a small fraction of known SLiMs and outside these examples little effort has been made, either bioinformatically or experimentally, to discover the full complement of motif instances. In this article, interaction data are analysed to identify and characterize an important subset of PPIs, those involving SLiMs binding to globular domains. To do this, we introduce iELM, a method to identify interactions mediated by SLiMs and add molecular details of the interaction interfaces to both interacting proteins. The method identifies SLiM-mediated interfaces from PPI data by searching for known SLiM-domain pairs. This ap...Continue Reading

References

Jan 10, 1991·Nature·M GlotzerM W Kirschner
Oct 5, 1990·Journal of Molecular Biology·S F AltschulD J Lipman
Jan 27, 1999·Bioinformatics·S R Eddy
Dec 26, 2001·Nucleic Acids Research·Alex BatemanErik L L Sonnhammer
Apr 16, 2003·The Journal of Biological Chemistry·Marcos R M FontesBostjan Kobe
Jun 26, 2003·Nucleic Acids Research·John C ObenauerMichael B Yaffe
Jun 28, 2005·Nucleic Acids Research·Joost SchymkowitzLuis Serrano
Aug 20, 2005·PLoS Computational Biology·Pedro Beltrao, Luis Serrano
Nov 29, 2005·BMC Genomics·Richard R Copley
Jan 24, 2006·Nature·Anne-Claude GavinGiulio Superti-Furga
Aug 10, 2006·Nature Reviews. Molecular Cell Biology·Jan-Michael Peters
Aug 29, 2006·Journal of Molecular Biology·Amrita MohanVladimir N Uversky
Sep 16, 2006·Molecular Cell·Xiang-Jiao Yang, Serge Grégoire
Dec 1, 2006·Nucleic Acids Research·Arnaud CeolGianni Cesareni
Feb 24, 2007·Current Opinion in Cell Biology·Tony Pawson
Jun 16, 2007·Cell·Rune LindingTony Pawson
Jun 20, 2007·Nucleic Acids Research·Norman E DaveyDenis C Shields
Sep 26, 2007·PLoS Computational Biology·Doron BetelChristopher W V Hogue
Oct 20, 2007·Nature Protocols·Melissa S ClineGary D Bader
Oct 25, 2007·Molecular & Cellular Proteomics : MCP·Haiming HuangShawn S-C Li
Feb 14, 2008·Briefings in Functional Genomics & Proteomics·Claus Jørgensen, Rune Linding
Apr 23, 2008·Current Protocols in Bioinformatics·Narayanan EswarAndrej Sali
Apr 29, 2008·BMC Bioinformatics·Emmanuel PerrodouJulie D Thompson
May 30, 2008·Frontiers in Bioscience : a Journal and Virtual Library·Tomonori KanekoShawn S-C Li
May 30, 2008·Frontiers in Bioscience : a Journal and Virtual Library·Francesca DiellaToby J Gibson
Jun 6, 2008·Nucleic Acids Research·Sylvain BrohéeJacques van Helden
Mar 28, 2009·PLoS Computational Biology·Evangelia PetsalakiRobert B Russell
May 5, 2009·PLoS Computational Biology·Bálint MészárosZsuzsanna Dosztányi
May 29, 2009·The Journal of Biological Chemistry·Cristina Pop, Guy S Salvesen
Oct 22, 2009·Nucleic Acids Research·UNKNOWN UniProt Consortium
Nov 19, 2009·Nucleic Acids Research·Robert D FinnAlex Bateman
May 11, 2010·Trends in Biochemical Sciences·Christian U StirnimannChristoph W Müller
May 27, 2010·PLoS Computational Biology·Amelie Stein, Patrick Aloy
Jun 1, 2010·Cell Communication and Signaling : CCS·Ho-Jin Lee, Jie J Zheng
Oct 14, 2010·BMC Bioinformatics·Shirley Hui, Gary D Bader
Oct 19, 2010·Proteins·Christopher A King, Philip Bradley
Nov 4, 2010·Nucleic Acids Research·Damian SzklarczykChristian von Mering
Nov 13, 2010·Nucleic Acids Research·Chris StarkMike Tyers
Apr 5, 2011·Acta Crystallographica. Section D, Biological Crystallography·Sameer Velankar, Gerard J Kleywegt

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Citations

May 29, 2012·Nucleic Acids Research·Robert J WeatherittToby J Gibson
May 29, 2012·Nucleic Acids Research·Robert J WeatherittToby J Gibson
Jun 14, 2013·BMC Genomics·Alessio ColantoniFabrizio Ferrè
Aug 26, 2014·Nature Structural & Molecular Biology·Robert J WeatherittM Madan Babu
Mar 10, 2015·Progress in Biophysics and Molecular Biology·Célia Caillet-SaguyNicolas Wolff
Jun 19, 2012·Trends in Biochemical Sciences·Robert J Weatheritt, Toby J Gibson
Apr 30, 2014·Chemical Reviews·Robin van der LeeM Madan Babu
Feb 7, 2013·Proteins·Ronit HodYael Mandel-Gutfreund
Aug 31, 2013·The Biochemical Journal·Alexander CumberworthJörg Gsponer
Jul 4, 2012·Molecular Cell·Jonathan D EllisBenjamin J Blencowe
Apr 16, 2013·Biochimie·Jaroslav KubrychtJiří Hudeček
May 6, 2015·PLoS Computational Biology·T Scott ChenBarry Honig
Oct 21, 2015·Trends in Biochemical Sciences·Sara Calabretta, Stéphane Richard
Dec 15, 2017·PLoS Computational Biology·Gábor ErdősZsuzsanna Dosztányi
Jan 8, 2015·Journal of Physics. Condensed Matter : an Institute of Physics Journal·Guillaume BrysbaertRalf Blossey
Apr 18, 2021·The FEBS Journal·Célia Caillet-SaguyNicolas Wolff
Jun 25, 2020·Journal of Proteome Research·Raghavender Surya Upadhyayula

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Methods Mentioned

BETA
phage display
ubiquitination

Software Mentioned

Neat
Gopher
HMMBuild
IUPred
Muscle
SVM
MODELLER
SLiMDom
STRING
NetworKIN

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