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Protein social behavior makes a stronger signal for partner identification than surface geometry

Cells are interactive living systems where proteins movements, interactions and regulation are substantially free from centralized management. How protein physico‐chemical and geometrical properties determine who interact with whom remains far from fully understood. We show that characterizing how a...

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Detalles Bibliográficos
Autores principales: Laine, Elodie, Carbone, Alessandra
Formato: Online Artículo Texto
Lenguaje:English
Publicado: John Wiley and Sons Inc. 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5242317/
https://www.ncbi.nlm.nih.gov/pubmed/27802579
http://dx.doi.org/10.1002/prot.25206
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author Laine, Elodie
Carbone, Alessandra
author_facet Laine, Elodie
Carbone, Alessandra
author_sort Laine, Elodie
collection PubMed
description Cells are interactive living systems where proteins movements, interactions and regulation are substantially free from centralized management. How protein physico‐chemical and geometrical properties determine who interact with whom remains far from fully understood. We show that characterizing how a protein behaves with many potential interactors in a complete cross‐docking study leads to a sharp identification of its cellular/true/native partner(s). We define a sociability index, or S‐index, reflecting whether a protein likes or not to pair with other proteins. Formally, we propose a suitable normalization function that accounts for protein sociability and we combine it with a simple interface‐based (ranking) score to discriminate partners from non‐interactors. We show that sociability is an important factor and that the normalization permits to reach a much higher discriminative power than shape complementarity docking scores. The social effect is also observed with more sophisticated docking algorithms. Docking conformations are evaluated using experimental binding sites. These latter approximate in the best possible way binding sites predictions, which have reached high accuracy in recent years. This makes our analysis helpful for a global understanding of partner identification and for suggesting discriminating strategies. These results contradict previous findings claiming the partner identification problem being solvable solely with geometrical docking. Proteins 2016; 85:137–154. © 2016 Wiley Periodicals, Inc.
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spelling pubmed-52423172017-01-25 Protein social behavior makes a stronger signal for partner identification than surface geometry Laine, Elodie Carbone, Alessandra Proteins Articles Cells are interactive living systems where proteins movements, interactions and regulation are substantially free from centralized management. How protein physico‐chemical and geometrical properties determine who interact with whom remains far from fully understood. We show that characterizing how a protein behaves with many potential interactors in a complete cross‐docking study leads to a sharp identification of its cellular/true/native partner(s). We define a sociability index, or S‐index, reflecting whether a protein likes or not to pair with other proteins. Formally, we propose a suitable normalization function that accounts for protein sociability and we combine it with a simple interface‐based (ranking) score to discriminate partners from non‐interactors. We show that sociability is an important factor and that the normalization permits to reach a much higher discriminative power than shape complementarity docking scores. The social effect is also observed with more sophisticated docking algorithms. Docking conformations are evaluated using experimental binding sites. These latter approximate in the best possible way binding sites predictions, which have reached high accuracy in recent years. This makes our analysis helpful for a global understanding of partner identification and for suggesting discriminating strategies. These results contradict previous findings claiming the partner identification problem being solvable solely with geometrical docking. Proteins 2016; 85:137–154. © 2016 Wiley Periodicals, Inc. John Wiley and Sons Inc. 2016-11-20 2017-01 /pmc/articles/PMC5242317/ /pubmed/27802579 http://dx.doi.org/10.1002/prot.25206 Text en © 2016 The Authors Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc. This is an open access article under the terms of the Creative Commons Attribution‐NonCommercial (http://creativecommons.org/licenses/by-nc/4.0/) License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes.
spellingShingle Articles
Laine, Elodie
Carbone, Alessandra
Protein social behavior makes a stronger signal for partner identification than surface geometry
title Protein social behavior makes a stronger signal for partner identification than surface geometry
title_full Protein social behavior makes a stronger signal for partner identification than surface geometry
title_fullStr Protein social behavior makes a stronger signal for partner identification than surface geometry
title_full_unstemmed Protein social behavior makes a stronger signal for partner identification than surface geometry
title_short Protein social behavior makes a stronger signal for partner identification than surface geometry
title_sort protein social behavior makes a stronger signal for partner identification than surface geometry
topic Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5242317/
https://www.ncbi.nlm.nih.gov/pubmed/27802579
http://dx.doi.org/10.1002/prot.25206
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