Classification of α-helical membrane proteins using predicted helix architectures.

Despite significant methodological advances in protein structure determination high-resolution structures of membrane proteins are still rare, leaving sequence-based predictions as the only option for exploring the structural variability of membrane proteins at large scale. Here, a new structural cl...

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Autores principales:	Sindy Neumann, Angelika Fuchs, Barbara Hummel, Dmitrij Frishman
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/d8b4d3257ec1474bbe5ee9a36a61ca08
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spelling	oai:doaj.org-article:d8b4d3257ec1474bbe5ee9a36a61ca082021-11-18T08:49:27ZClassification of α-helical membrane proteins using predicted helix architectures.1932-620310.1371/journal.pone.0077491https://doaj.org/article/d8b4d3257ec1474bbe5ee9a36a61ca082013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24204844/?tool=EBIhttps://doaj.org/toc/1932-6203Despite significant methodological advances in protein structure determination high-resolution structures of membrane proteins are still rare, leaving sequence-based predictions as the only option for exploring the structural variability of membrane proteins at large scale. Here, a new structural classification approach for α-helical membrane proteins is introduced based on the similarity of predicted helix interaction patterns. Its application to proteins with known 3D structure showed that it is able to reliably detect structurally similar proteins even in the absence of any sequence similarity, reproducing the SCOP and CATH classifications with a sensitivity of 65% at a specificity of 90%. We applied the new approach to enhance our comprehensive structural classification of α-helical membrane proteins (CAMPS), which is primarily based on sequence and topology similarity, in order to find protein clusters that describe the same fold in the absence of sequence similarity. The total of 151 helix architectures were delineated for proteins with more than four transmembrane segments. Interestingly, we observed that proteins with 8 and more transmembrane helices correspond to fewer different architectures than proteins with up to 7 helices, suggesting that in large membrane proteins the evolutionary tendency to re-use already available folds is more pronounced.Sindy NeumannAngelika FuchsBarbara HummelDmitrij FrishmanPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 10, p e77491 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Sindy Neumann Angelika Fuchs Barbara Hummel Dmitrij Frishman Classification of α-helical membrane proteins using predicted helix architectures.
description	Despite significant methodological advances in protein structure determination high-resolution structures of membrane proteins are still rare, leaving sequence-based predictions as the only option for exploring the structural variability of membrane proteins at large scale. Here, a new structural classification approach for α-helical membrane proteins is introduced based on the similarity of predicted helix interaction patterns. Its application to proteins with known 3D structure showed that it is able to reliably detect structurally similar proteins even in the absence of any sequence similarity, reproducing the SCOP and CATH classifications with a sensitivity of 65% at a specificity of 90%. We applied the new approach to enhance our comprehensive structural classification of α-helical membrane proteins (CAMPS), which is primarily based on sequence and topology similarity, in order to find protein clusters that describe the same fold in the absence of sequence similarity. The total of 151 helix architectures were delineated for proteins with more than four transmembrane segments. Interestingly, we observed that proteins with 8 and more transmembrane helices correspond to fewer different architectures than proteins with up to 7 helices, suggesting that in large membrane proteins the evolutionary tendency to re-use already available folds is more pronounced.
format	article
author	Sindy Neumann Angelika Fuchs Barbara Hummel Dmitrij Frishman
author_facet	Sindy Neumann Angelika Fuchs Barbara Hummel Dmitrij Frishman
author_sort	Sindy Neumann
title	Classification of α-helical membrane proteins using predicted helix architectures.
title_short	Classification of α-helical membrane proteins using predicted helix architectures.
title_full	Classification of α-helical membrane proteins using predicted helix architectures.
title_fullStr	Classification of α-helical membrane proteins using predicted helix architectures.
title_full_unstemmed	Classification of α-helical membrane proteins using predicted helix architectures.
title_sort	classification of α-helical membrane proteins using predicted helix architectures.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/d8b4d3257ec1474bbe5ee9a36a61ca08
work_keys_str_mv	AT sindyneumann classificationofahelicalmembraneproteinsusingpredictedhelixarchitectures AT angelikafuchs classificationofahelicalmembraneproteinsusingpredictedhelixarchitectures AT barbarahummel classificationofahelicalmembraneproteinsusingpredictedhelixarchitectures AT dmitrijfrishman classificationofahelicalmembraneproteinsusingpredictedhelixarchitectures
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Classification of α-helical membrane proteins using predicted helix architectures.

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