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 estimation of their structural properties.


METHODS
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, χ1 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.
Laboratori de Medicina Computacional, Unitat de Bioestadística, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra, Spain.
Marc
M
Perea
Laboratori de Medicina Computacional, Unitat de Bioestadística, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra, Spain.
Ivar
I
Lugtenburg
Laboratori de Medicina Computacional, Unitat de Bioestadística, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra, Spain.
Eduardo
E
Mayol
Laboratori de Medicina Computacional, Unitat de Bioestadística, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra, Spain.
Arnau
A
Cordomí
Laboratori de Medicina Computacional, Unitat de Bioestadística, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra, Spain.|Present address: Condensed Matter Theory Group and Laboratory of Biomolecular Research, Paul Scherrer Institut, Villigen PSI, Switzeland.
Xavier
X
Deupí
Laboratori de Medicina Computacional, Unitat de Bioestadística, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra, Spain. Leonardo.pardo@uab.es.
Leonardo
L
Pardo
Department de Biologia de Sistemes, Universitat de Vic, Vic, Barcelona, Spain. mireia.olivella@uvic.cat.
Mireia
M
Olivella
D020816:Amino Acid Motifs; D030562:Databases, Protein; D006801:Humans; D020407:Internet; D008565:Membrane Proteins / Q000737:chemistry*; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D020539:Sequence Analysis, Protein / Q000379:methods*
D008565:Membrane Proteins