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Membrane protein orientation and refinement using a knowledge-based statistical potential.

Nugent, T; Jones, DT; (2013) Membrane protein orientation and refinement using a knowledge-based statistical potential. BMC Bioinformatics , 14 (Septem) , Article 276. 10.1186/1471-2105-14-276. Green open access

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Abstract

Background: Recent increases in the number of deposited membrane protein crystal structures necessitate the use of automated computational tools to position them within the lipid bilayer. Identifying the correct orientation allows us to study the complex relationship between sequence, structure and the lipid environment, which is otherwise challenging to investigate using experimental techniques due to the difficulty in crystallising membrane proteins embedded within intact membranes. Results: We have developed a knowledge-based membrane potential, calculated by the statistical analysis of transmembrane protein structures, coupled with a combination of genetic and direct search algorithms, and demonstrate its use in positioning proteins in membranes, refinement of membrane protein models and in decoy discrimination. Conclusions: Our method is able to quickly and accurately orientate both alpha-helical and beta-barrel membrane proteins within the lipid bilayer, showing closer agreement with experimentally determined values than existing approaches. We also demonstrate both consistent and significant refinement of membrane protein models and the effective discrimination between native and decoy structures. Source code is available under an open source license from http://bioinf.cs.ucl.ac.uk/downloads/memembed/ webcite.

Type: Article
Title: Membrane protein orientation and refinement using a knowledge-based statistical potential.
Location: England
Open access status: An open access version is available from UCL Discovery
DOI: 10.1186/1471-2105-14-276
Publisher version: http://dx.doi.org/10.1186/1471-2105-14-276
Language: English
Additional information: © 2013 Nugent and Jones; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Keywords: Membrane protein; Statistical potential; Orientation; Refinement; Genetic algorithm.
UCL classification: UCL
UCL > Provost and Vice Provost Offices > UCL BEAMS
UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Engineering Science
UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Engineering Science > Dept of Computer Science
URI: https://discovery.ucl.ac.uk/id/eprint/1417701
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