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Ranking models of transmembrane beta-barrel proteins using Z-coordinate predictions
Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).ORCID iD: 0000-0002-7115-9751
2012 (English)In: Bioinformatics, ISSN 1367-4803, E-ISSN 1460-2059, Vol. 28, no 12, i90-I96 p.Article in journal (Refereed) Published
Abstract [en]

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.
National Category
Biochemistry and Molecular Biology
URN: urn:nbn:se:su:diva-80010DOI: 10.1093/bioinformatics/bts233ISI: 000305419800012OAI: diva2:552468
Swedish Research Council, 000305419800012; VR-M 2010-3555Swedish Foundation for Strategic Research EU, FP7, Seventh Framework Programme, 201924


Available from: 2012-09-14 Created: 2012-09-12 Last updated: 2014-11-10Bibliographically approved

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Hayat, SikanderElofsson, Arne
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