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A Structure-Based Classification and Analysis of Protein Domain Family Binding Sites and Their Interactions

While the number of solved 3D protein structures continues to grow rapidly, the structural rules that distinguish protein-protein interactions between different structural families are still not clear. Here, we classify and analyse the secondary structural features and promiscuity of a comprehensive...

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Autores principales: Ghoorah, Anisah W., Devignes, Marie-Dominique, Alborzi, Seyed Ziaeddin, Smaïl-Tabbone, Malika, Ritchie, David W.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4498303/
https://www.ncbi.nlm.nih.gov/pubmed/25860777
http://dx.doi.org/10.3390/biology4020327
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author Ghoorah, Anisah W.
Devignes, Marie-Dominique
Alborzi, Seyed Ziaeddin
Smaïl-Tabbone, Malika
Ritchie, David W.
author_facet Ghoorah, Anisah W.
Devignes, Marie-Dominique
Alborzi, Seyed Ziaeddin
Smaïl-Tabbone, Malika
Ritchie, David W.
author_sort Ghoorah, Anisah W.
collection PubMed
description While the number of solved 3D protein structures continues to grow rapidly, the structural rules that distinguish protein-protein interactions between different structural families are still not clear. Here, we classify and analyse the secondary structural features and promiscuity of a comprehensive non-redundant set of domain family binding sites (DFBSs) and hetero domain-domain interactions (DDIs) extracted from our updated KBDOCK resource. We have partitioned 4001 DFBSs into five classes using their propensities for three types of secondary structural elements (“α” for helices, “β” for strands, and “γ” for irregular structure) and we have analysed how frequently these classes occur in DDIs. Our results show that β elements are not highly represented in DFBSs compared to α and γ elements. At the DDI level, all classes of binding sites tend to preferentially bind to the same class of binding sites and α/β contacts are significantly disfavored. Very few DFBSs are promiscuous: 80% of them interact with just one Pfam domain. About 50% of our Pfam domains bear only one single-partner DFBS and are therefore monogamous in their interactions with other domains. Conversely, promiscuous Pfam domains bear several DFBSs among which one or two are promiscuous, thereby multiplying the promiscuity of the concerned protein.
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spelling pubmed-44983032015-07-10 A Structure-Based Classification and Analysis of Protein Domain Family Binding Sites and Their Interactions Ghoorah, Anisah W. Devignes, Marie-Dominique Alborzi, Seyed Ziaeddin Smaïl-Tabbone, Malika Ritchie, David W. Biology (Basel) Article While the number of solved 3D protein structures continues to grow rapidly, the structural rules that distinguish protein-protein interactions between different structural families are still not clear. Here, we classify and analyse the secondary structural features and promiscuity of a comprehensive non-redundant set of domain family binding sites (DFBSs) and hetero domain-domain interactions (DDIs) extracted from our updated KBDOCK resource. We have partitioned 4001 DFBSs into five classes using their propensities for three types of secondary structural elements (“α” for helices, “β” for strands, and “γ” for irregular structure) and we have analysed how frequently these classes occur in DDIs. Our results show that β elements are not highly represented in DFBSs compared to α and γ elements. At the DDI level, all classes of binding sites tend to preferentially bind to the same class of binding sites and α/β contacts are significantly disfavored. Very few DFBSs are promiscuous: 80% of them interact with just one Pfam domain. About 50% of our Pfam domains bear only one single-partner DFBS and are therefore monogamous in their interactions with other domains. Conversely, promiscuous Pfam domains bear several DFBSs among which one or two are promiscuous, thereby multiplying the promiscuity of the concerned protein. MDPI 2015-04-09 /pmc/articles/PMC4498303/ /pubmed/25860777 http://dx.doi.org/10.3390/biology4020327 Text en © 2015 by the authors; licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Ghoorah, Anisah W.
Devignes, Marie-Dominique
Alborzi, Seyed Ziaeddin
Smaïl-Tabbone, Malika
Ritchie, David W.
A Structure-Based Classification and Analysis of Protein Domain Family Binding Sites and Their Interactions
title A Structure-Based Classification and Analysis of Protein Domain Family Binding Sites and Their Interactions
title_full A Structure-Based Classification and Analysis of Protein Domain Family Binding Sites and Their Interactions
title_fullStr A Structure-Based Classification and Analysis of Protein Domain Family Binding Sites and Their Interactions
title_full_unstemmed A Structure-Based Classification and Analysis of Protein Domain Family Binding Sites and Their Interactions
title_short A Structure-Based Classification and Analysis of Protein Domain Family Binding Sites and Their Interactions
title_sort structure-based classification and analysis of protein domain family binding sites and their interactions
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4498303/
https://www.ncbi.nlm.nih.gov/pubmed/25860777
http://dx.doi.org/10.3390/biology4020327
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