TMalphaDB and TMbetaDB: web servers to study the structural role of sequence motifs in α-helix and β-barrel domains of membrane proteins

Background Membrane proteins represent over 25 % of human protein genes and account for more than 60 % of drug targets due to their accessibility from the extracellular environment. The increasing number of available crystal structures of these proteins in the Protein Data Bank permits an initial es...

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Autores: Perea, Marc, Lugtenburg, Ivan, Mayol, Eduardo, Cordomí Montoya, Arnau, Deupi, Xavier, Pardo Carrasco, Leonardo, Olivella, Mireia
Tipo de recurso: artículo
Fecha de publicación:2015
País:España
Institución:UVic-UCC
Repositorio:RiUVic. Repositori institucional de la UVic-UCC
OAI Identifier:oai:dspace.uvic.cat:10854/4264
Acceso en línea:http://hdl.handle.net/10854/4264
https://doi.org/10.1186/s12859-015-0699-5
Access Level:acceso abierto
Palabra clave:Proteïnes de membrana
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spelling TMalphaDB and TMbetaDB: web servers to study the structural role of sequence motifs in α-helix and β-barrel domains of membrane proteinsPerea, MarcLugtenburg, IvanMayol, EduardoCordomí Montoya, ArnauDeupi, XavierPardo Carrasco, LeonardoOlivella, MireiaProteïnes de membranaBackground Membrane proteins represent over 25 % of human protein genes and account for more than 60 % of drug targets due to their accessibility from the extracellular environment. The increasing number of available crystal structures of these proteins in the Protein Data Bank permits an initial estimation of their structural properties. Description We have developed two web servers—TMalphaDB for α-helix bundles and TMbetaDB for β-barrels—to analyse the growing repertoire of available crystal structures of membrane proteins. TMalphaDB and TMbetaDB permit to search for these specific sequence motifs in a non-redundant structure database of transmembrane segments and quantify structural parameters such as ϕ and ψ backbone dihedral angles, χ 1 side chain torsion angle, unit bend and unit twist. Conclusions The structural information offered by TMalphaDB and TMbetaDB permits to quantify structural distortions induced by specific sequence motifs, and to elucidate their role in the 3D structure. This specific structural information has direct implications in homology modeling of the growing sequences of membrane proteins lacking experimental structure. TMalphaDB and TMbetaDB are freely available at http://lmc.uab.cat/TMalphaDB and http://lmc.uab.cat/TMbetaDB.BioMed CentralUniversitat de Vic - Universitat Central de Catalunya. Facultat de Ciències i Tecnologia2015201520152015info:eu-repo/semantics/articleinfo:eu-repo/publishedVersionapplication/pdf6 p.application/pdfhttp://hdl.handle.net/10854/4264https://doi.org/10.1186/s12859-015-0699-5reponame:RiUVic. Repositori institucional de la UVic-UCCinstname:UVic-UCCInglésAquest document està subjecte a aquesta llicència Creative Commonshttp://creativecommons.org/licenses/by-nc/3.0/es/info:eu-repo/semantics/openAccessoai:dspace.uvic.cat:10854/42642026-06-07T19:15:21Z
dc.title.none.fl_str_mv TMalphaDB and TMbetaDB: web servers to study the structural role of sequence motifs in α-helix and β-barrel domains of membrane proteins
title TMalphaDB and TMbetaDB: web servers to study the structural role of sequence motifs in α-helix and β-barrel domains of membrane proteins
spellingShingle TMalphaDB and TMbetaDB: web servers to study the structural role of sequence motifs in α-helix and β-barrel domains of membrane proteins
Perea, Marc
Proteïnes de membrana
title_short TMalphaDB and TMbetaDB: web servers to study the structural role of sequence motifs in α-helix and β-barrel domains of membrane proteins
title_full TMalphaDB and TMbetaDB: web servers to study the structural role of sequence motifs in α-helix and β-barrel domains of membrane proteins
title_fullStr TMalphaDB and TMbetaDB: web servers to study the structural role of sequence motifs in α-helix and β-barrel domains of membrane proteins
title_full_unstemmed TMalphaDB and TMbetaDB: web servers to study the structural role of sequence motifs in α-helix and β-barrel domains of membrane proteins
title_sort TMalphaDB and TMbetaDB: web servers to study the structural role of sequence motifs in α-helix and β-barrel domains of membrane proteins
dc.creator.none.fl_str_mv Perea, Marc
Lugtenburg, Ivan
Mayol, Eduardo
Cordomí Montoya, Arnau
Deupi, Xavier
Pardo Carrasco, Leonardo
Olivella, Mireia
author Perea, Marc
author_facet Perea, Marc
Lugtenburg, Ivan
Mayol, Eduardo
Cordomí Montoya, Arnau
Deupi, Xavier
Pardo Carrasco, Leonardo
Olivella, Mireia
author_role author
author2 Lugtenburg, Ivan
Mayol, Eduardo
Cordomí Montoya, Arnau
Deupi, Xavier
Pardo Carrasco, Leonardo
Olivella, Mireia
author2_role author
author
author
author
author
author
dc.contributor.none.fl_str_mv Universitat de Vic - Universitat Central de Catalunya. Facultat de Ciències i Tecnologia
dc.subject.none.fl_str_mv Proteïnes de membrana
topic Proteïnes de membrana
description Background Membrane proteins represent over 25 % of human protein genes and account for more than 60 % of drug targets due to their accessibility from the extracellular environment. The increasing number of available crystal structures of these proteins in the Protein Data Bank permits an initial estimation of their structural properties. Description We have developed two web servers—TMalphaDB for α-helix bundles and TMbetaDB for β-barrels—to analyse the growing repertoire of available crystal structures of membrane proteins. TMalphaDB and TMbetaDB permit to search for these specific sequence motifs in a non-redundant structure database of transmembrane segments and quantify structural parameters such as ϕ and ψ backbone dihedral angles, χ 1 side chain torsion angle, unit bend and unit twist. Conclusions The structural information offered by TMalphaDB and TMbetaDB permits to quantify structural distortions induced by specific sequence motifs, and to elucidate their role in the 3D structure. This specific structural information has direct implications in homology modeling of the growing sequences of membrane proteins lacking experimental structure. TMalphaDB and TMbetaDB are freely available at http://lmc.uab.cat/TMalphaDB and http://lmc.uab.cat/TMbetaDB.
publishDate 2015
dc.date.none.fl_str_mv 2015
2015
2015
2015
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/publishedVersion
format article
dc.identifier.none.fl_str_mv http://hdl.handle.net/10854/4264
https://doi.org/10.1186/s12859-015-0699-5
url http://hdl.handle.net/10854/4264
https://doi.org/10.1186/s12859-015-0699-5
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.rights.none.fl_str_mv Aquest document està subjecte a aquesta llicència Creative Commons
http://creativecommons.org/licenses/by-nc/3.0/es/
info:eu-repo/semantics/openAccess
rights_invalid_str_mv Aquest document està subjecte a aquesta llicència Creative Commons
http://creativecommons.org/licenses/by-nc/3.0/es/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
6 p.
application/pdf
dc.publisher.none.fl_str_mv BioMed Central
publisher.none.fl_str_mv BioMed Central
dc.source.none.fl_str_mv reponame:RiUVic. Repositori institucional de la UVic-UCC
instname:UVic-UCC
instname_str UVic-UCC
reponame_str RiUVic. Repositori institucional de la UVic-UCC
collection RiUVic. Repositori institucional de la UVic-UCC
repository.name.fl_str_mv
repository.mail.fl_str_mv
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