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An analysis of oligomerization interfaces in transmembrane proteins
BACKGROUND: The amount of transmembrane protein (TM) structures solved to date is now large enough to attempt large scale analyses. In particular, extensive studies of oligomeric interfaces in the transmembrane region are now possible. RESULTS: We have compiled the first fully comprehensive set of v...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2013
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4015793/ https://www.ncbi.nlm.nih.gov/pubmed/24134166 http://dx.doi.org/10.1186/1472-6807-13-21 |
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author | Duarte, Jose M Biyani, Nikhil Baskaran, Kumaran Capitani, Guido |
author_facet | Duarte, Jose M Biyani, Nikhil Baskaran, Kumaran Capitani, Guido |
author_sort | Duarte, Jose M |
collection | PubMed |
description | BACKGROUND: The amount of transmembrane protein (TM) structures solved to date is now large enough to attempt large scale analyses. In particular, extensive studies of oligomeric interfaces in the transmembrane region are now possible. RESULTS: We have compiled the first fully comprehensive set of validated transmembrane protein interfaces in order to study their features and assess what differentiates them from their soluble counterparts. CONCLUSIONS: The general features of TM interfaces do not differ much from those of soluble proteins: they are large, tightly packed and possess many interface core residues. In our set, membrane lipids were not found to significantly mediate protein-protein interfaces. Although no G protein-coupled receptor (GPCR) was included in the validated set, we analyzed the crystallographic dimerization interfaces proposed in the literature. We found that the putative dimer interfaces proposed for class A GPCRs do not show the usual patterns of stable biological interfaces, neither in terms of evolution nor of packing, thus they likely correspond to crystal interfaces. We cannot however rule out the possibility that they constitute transient or weak interfaces. In contrast we do observe a clear signature of biological interface for the proposed dimer of the class F human Smoothened receptor. |
format | Online Article Text |
id | pubmed-4015793 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2013 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-40157932014-05-10 An analysis of oligomerization interfaces in transmembrane proteins Duarte, Jose M Biyani, Nikhil Baskaran, Kumaran Capitani, Guido BMC Struct Biol Research Article BACKGROUND: The amount of transmembrane protein (TM) structures solved to date is now large enough to attempt large scale analyses. In particular, extensive studies of oligomeric interfaces in the transmembrane region are now possible. RESULTS: We have compiled the first fully comprehensive set of validated transmembrane protein interfaces in order to study their features and assess what differentiates them from their soluble counterparts. CONCLUSIONS: The general features of TM interfaces do not differ much from those of soluble proteins: they are large, tightly packed and possess many interface core residues. In our set, membrane lipids were not found to significantly mediate protein-protein interfaces. Although no G protein-coupled receptor (GPCR) was included in the validated set, we analyzed the crystallographic dimerization interfaces proposed in the literature. We found that the putative dimer interfaces proposed for class A GPCRs do not show the usual patterns of stable biological interfaces, neither in terms of evolution nor of packing, thus they likely correspond to crystal interfaces. We cannot however rule out the possibility that they constitute transient or weak interfaces. In contrast we do observe a clear signature of biological interface for the proposed dimer of the class F human Smoothened receptor. BioMed Central 2013-10-17 /pmc/articles/PMC4015793/ /pubmed/24134166 http://dx.doi.org/10.1186/1472-6807-13-21 Text en Copyright © 2013 Duarte et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Article Duarte, Jose M Biyani, Nikhil Baskaran, Kumaran Capitani, Guido An analysis of oligomerization interfaces in transmembrane proteins |
title | An analysis of oligomerization interfaces in transmembrane proteins |
title_full | An analysis of oligomerization interfaces in transmembrane proteins |
title_fullStr | An analysis of oligomerization interfaces in transmembrane proteins |
title_full_unstemmed | An analysis of oligomerization interfaces in transmembrane proteins |
title_short | An analysis of oligomerization interfaces in transmembrane proteins |
title_sort | analysis of oligomerization interfaces in transmembrane proteins |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4015793/ https://www.ncbi.nlm.nih.gov/pubmed/24134166 http://dx.doi.org/10.1186/1472-6807-13-21 |
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