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 (Universitat Autònoma de Barcelona. Laboratori de Medicina Computacional)
Lugtenburg, Ivar (Universitat Autònoma de Barcelona. Laboratori de Medicina Computacional)
Mayol, Eduardo (Universitat Autònoma de Barcelona. Laboratori de Medicina Computacional)
Cordomí Montoya, Arnau (Universitat Autònoma de Barcelona. Laboratori de Medicina Computacional)
Deupi, Xavier (Condensed Matter Theory Group and Laboratory of Biomolecular Research, Paul Scherrer Institut, Villigen PSI, Switzeland)
Pardo Carrasco, Leonardo (Universitat Autònoma de Barcelona. Laboratori de Medicina Computacional)
Olivella, Mireia (Universitat de Vic. Departament de Biologia de Sistemes)

Date:	2015
Abstract:	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. 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 side chain torsion angle, unit bend and unit twist. 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.
Grants:	Ministerio de Economía y Competitividad SAF2013-48271-C2-2-R Ministerio de Ciencia e Innovación CD09/00150
Rights:	Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original.
Language:	Anglès
Document:	Article ; recerca ; Versió publicada
Subject:	Membrane proteins ; Transmembrane segments ; Sequence motifs ; Structural distortion
Published in:	BMC bioinformatics, Vol. 16, Num. 1 (august 2015) , ISSN 1471-2105

DOI: 10.1186/s12859-015-0699-5
PMID: 26289158

6 p, 1.4 MB

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