Ranking models of transmembrane beta-barrel proteins using Z-coordinate predictions
2012 (English)In: Bioinformatics, ISSN 1367-4803, E-ISSN 1460-2059, Vol. 28, no 12, i90-I96 p.Article in journal (Refereed) Published
Motivation: Transmembrane beta-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 beta-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 beta-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 beta-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 A. 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 C alpha template with an average RMSD of 7.24 A from the native structure.
Place, publisher, year, edition, pages
2012. Vol. 28, no 12, i90-I96 p.
Biochemistry and Molecular Biology
IdentifiersURN: urn:nbn:se:su:diva-80010DOI: 10.1093/bioinformatics/bts233ISI: 000305419800012OAI: oai:DiVA.org:su-80010DiVA: diva2:552468
FunderSwedish Research Council, 000305419800012; VR-M 2010-3555Swedish Foundation for Strategic Research EU, FP7, Seventh Framework Programme, 201924