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/.
journal_name
BMC Bioinformaticsjournal_title
BMC bioinformaticsauthors
Nugent T,Jones DTdoi
10.1186/1471-2105-14-276subject
Has Abstractpub_date
2013-09-18 00:00:00pages
276issn
1471-2105pii
1471-2105-14-276journal_volume
14pub_type
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