Protein-protein interactions in a crowded environment: an analysis via cross-docking simulations and evolutionary information.

Large-scale analyses of protein-protein interactions based on coarse-grain molecular docking simulations and binding site predictions resulting from evolutionary sequence analysis, are possible and realizable on hundreds of proteins with variate structures and interfaces. We demonstrated this on the...

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Autores principales:	Anne Lopes, Sophie Sacquin-Mora, Viktoriya Dimitrova, Elodie Laine, Yann Ponty, Alessandra Carbone
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/8115608023b94588a1a038ca817cc4c0
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spelling	oai:doaj.org-article:8115608023b94588a1a038ca817cc4c02021-11-18T05:53:19ZProtein-protein interactions in a crowded environment: an analysis via cross-docking simulations and evolutionary information.1553-734X1553-735810.1371/journal.pcbi.1003369https://doaj.org/article/8115608023b94588a1a038ca817cc4c02013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24339765/?tool=EBIhttps://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358Large-scale analyses of protein-protein interactions based on coarse-grain molecular docking simulations and binding site predictions resulting from evolutionary sequence analysis, are possible and realizable on hundreds of proteins with variate structures and interfaces. We demonstrated this on the 168 proteins of the Mintseris Benchmark 2.0. On the one hand, we evaluated the quality of the interaction signal and the contribution of docking information compared to evolutionary information showing that the combination of the two improves partner identification. On the other hand, since protein interactions usually occur in crowded environments with several competing partners, we realized a thorough analysis of the interactions of proteins with true partners but also with non-partners to evaluate whether proteins in the environment, competing with the true partner, affect its identification. We found three populations of proteins: strongly competing, never competing, and interacting with different levels of strength. Populations and levels of strength are numerically characterized and provide a signature for the behavior of a protein in the crowded environment. We showed that partner identification, to some extent, does not depend on the competing partners present in the environment, that certain biochemical classes of proteins are intrinsically easier to analyze than others, and that small proteins are not more promiscuous than large ones. Our approach brings to light that the knowledge of the binding site can be used to reduce the high computational cost of docking simulations with no consequence in the quality of the results, demonstrating the possibility to apply coarse-grain docking to datasets made of thousands of proteins. Comparison with all available large-scale analyses aimed to partner predictions is realized. We release the complete decoys set issued by coarse-grain docking simulations of both true and false interacting partners, and their evolutionary sequence analysis leading to binding site predictions. Download site: http://www.lgm.upmc.fr/CCDMintseris/Anne LopesSophie Sacquin-MoraViktoriya DimitrovaElodie LaineYann PontyAlessandra CarbonePublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 9, Iss 12, p e1003369 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Anne Lopes Sophie Sacquin-Mora Viktoriya Dimitrova Elodie Laine Yann Ponty Alessandra Carbone Protein-protein interactions in a crowded environment: an analysis via cross-docking simulations and evolutionary information.
description	Large-scale analyses of protein-protein interactions based on coarse-grain molecular docking simulations and binding site predictions resulting from evolutionary sequence analysis, are possible and realizable on hundreds of proteins with variate structures and interfaces. We demonstrated this on the 168 proteins of the Mintseris Benchmark 2.0. On the one hand, we evaluated the quality of the interaction signal and the contribution of docking information compared to evolutionary information showing that the combination of the two improves partner identification. On the other hand, since protein interactions usually occur in crowded environments with several competing partners, we realized a thorough analysis of the interactions of proteins with true partners but also with non-partners to evaluate whether proteins in the environment, competing with the true partner, affect its identification. We found three populations of proteins: strongly competing, never competing, and interacting with different levels of strength. Populations and levels of strength are numerically characterized and provide a signature for the behavior of a protein in the crowded environment. We showed that partner identification, to some extent, does not depend on the competing partners present in the environment, that certain biochemical classes of proteins are intrinsically easier to analyze than others, and that small proteins are not more promiscuous than large ones. Our approach brings to light that the knowledge of the binding site can be used to reduce the high computational cost of docking simulations with no consequence in the quality of the results, demonstrating the possibility to apply coarse-grain docking to datasets made of thousands of proteins. Comparison with all available large-scale analyses aimed to partner predictions is realized. We release the complete decoys set issued by coarse-grain docking simulations of both true and false interacting partners, and their evolutionary sequence analysis leading to binding site predictions. Download site: http://www.lgm.upmc.fr/CCDMintseris/
format	article
author	Anne Lopes Sophie Sacquin-Mora Viktoriya Dimitrova Elodie Laine Yann Ponty Alessandra Carbone
author_facet	Anne Lopes Sophie Sacquin-Mora Viktoriya Dimitrova Elodie Laine Yann Ponty Alessandra Carbone
author_sort	Anne Lopes
title	Protein-protein interactions in a crowded environment: an analysis via cross-docking simulations and evolutionary information.
title_short	Protein-protein interactions in a crowded environment: an analysis via cross-docking simulations and evolutionary information.
title_full	Protein-protein interactions in a crowded environment: an analysis via cross-docking simulations and evolutionary information.
title_fullStr	Protein-protein interactions in a crowded environment: an analysis via cross-docking simulations and evolutionary information.
title_full_unstemmed	Protein-protein interactions in a crowded environment: an analysis via cross-docking simulations and evolutionary information.
title_sort	protein-protein interactions in a crowded environment: an analysis via cross-docking simulations and evolutionary information.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/8115608023b94588a1a038ca817cc4c0
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Protein-protein interactions in a crowded environment: an analysis via cross-docking simulations and evolutionary information.

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