Ranking models of transmembrane β-barrel proteins using Z-coordinate predictions.
BACKGROUND
Transmembrane β-barrels exist in the outer membrane of gram-negative bacteria as well as in chloroplast and mitochondria. They are often involved in transport processes and are promising antimicrobial drug targets. Structures of only a few β-barrel protein families are known. Therefore, a method that could automatically generate such models would be valuable. The symmetrical arrangement of the barrels suggests that an approach based on idealized geometries may be successful.


RESULTS
Here, we present tobmodel; a method for generating 3D models of β-barrel transmembrane proteins. First, alternative topologies are obtained from the BOCTOPUS topology predictor. Thereafter, several 3D models are constructed by using different angles of the β-sheets. Finally, the best model is selected based on agreement with a novel predictor, ZPRED3, which predicts the distance from the center of the membrane for each residue, i.e. the Z-coordinate. The Z-coordinate prediction has an average error of 1.61 Å. Tobmodel predicts the correct topology for 75% of the proteins in the dataset which is a slight improvement over BOCTOPUS alone. More importantly, however, tobmodel provides a Cα template with an average RMSD of 7.24 Å from the native structure.


BACKGROUND
Tobmodel is freely available as a web server at: http://tobmodel.cbr.su.se/. The datasets used for training and evaluations are also available from this site.
Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm Bioinformatics Center, Science for Life Laboratory, Swedish E-science Research Center, Stockholm University, SE-10691 Stockholm, Sweden.
Sikander
S
Hayat
Arne
A
Elofsson
D019295:Computational Biology / Q000379:methods*; D008565:Membrane Proteins / Q000737:chemistry*; D008958:Models, Molecular; D017434:Protein Structure, Tertiary; D012984:Software
D008565:Membrane Proteins