Cargando…
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...
Autores principales: | , , , , |
---|---|
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 |
_version_ | 1782380602120470528 |
---|---|
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. |
format | Online Article Text |
id | pubmed-4498303 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
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 |
work_keys_str_mv | AT ghoorahanisahw astructurebasedclassificationandanalysisofproteindomainfamilybindingsitesandtheirinteractions AT devignesmariedominique astructurebasedclassificationandanalysisofproteindomainfamilybindingsitesandtheirinteractions AT alborziseyedziaeddin astructurebasedclassificationandanalysisofproteindomainfamilybindingsitesandtheirinteractions AT smailtabbonemalika astructurebasedclassificationandanalysisofproteindomainfamilybindingsitesandtheirinteractions AT ritchiedavidw astructurebasedclassificationandanalysisofproteindomainfamilybindingsitesandtheirinteractions AT ghoorahanisahw structurebasedclassificationandanalysisofproteindomainfamilybindingsitesandtheirinteractions AT devignesmariedominique structurebasedclassificationandanalysisofproteindomainfamilybindingsitesandtheirinteractions AT alborziseyedziaeddin structurebasedclassificationandanalysisofproteindomainfamilybindingsitesandtheirinteractions AT smailtabbonemalika structurebasedclassificationandanalysisofproteindomainfamilybindingsitesandtheirinteractions AT ritchiedavidw structurebasedclassificationandanalysisofproteindomainfamilybindingsitesandtheirinteractions |