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dc.contributor.authorCAFFREY, MARTINen
dc.date.accessioned2015-12-09T12:36:21Z
dc.date.available2015-12-09T12:36:21Z
dc.date.created2015en
dc.date.issued2015en
dc.date.submitted2015en
dc.identifier.citationStansfeld P.J, Goose J.E, Caffrey M, Carpenter E.P, Parker J.L, Newstead S, Sansom M.S.P, MemProtMD: Automated Insertion of Membrane Protein Structures into Explicit Lipid Membranes, Structure, 23, 7, 2015, 1350 - 1361en
dc.identifier.otherYen
dc.identifier.urihttp://hdl.handle.net/2262/75228
dc.description.abstractThere has been exponential growth in the number of membrane protein structures determined. Nevertheless, these structures are usually resolved in the absence of their lipid environment. Coarse-grained molecular dynamics (CGMD) simulations enable insertion of membrane proteins into explicit models of lipid bilayers. We have automated the CGMD methodology, enabling membrane protein structures to be identified upon their release into the PDB and embedded into a membrane. The simulations are analyzed for protein-lipid interactions, identifying lipid binding sites, and revealing local bilayer deformations plus molecular access pathways within the membrane. The coarse-grained models of membrane protein/bilayer complexes are transformed to atomistic resolution for further analysis and simulation. Using this automated simulation pipeline, we have analyzed a number of recently determined membrane protein structures to predict their locations within a membrane, their lipid/protein interactions, and the functional implications of an enhanced understanding of the local membrane environment of each protein.en
dc.description.sponsorshipWe thank members of the M.S.P.S. laboratory for helpful discussions. This work was supported by Biotechnology and Biological Sciences Research Council grants BB/L002531/1 and BB/I019855/1, the Wellcome Trust, the Science Foundation Ireland (12/IA/1255), and the Irish Centre for High End Computing.en
dc.format.extent1350en
dc.format.extent1361en
dc.relation.ispartofseriesStructureen
dc.relation.ispartofseries23en
dc.relation.ispartofseries7en
dc.rightsYen
dc.subjectmembrane protein structuresen
dc.subject.lcshmembrane protein structuresen
dc.titleMemProtMD: Automated Insertion of Membrane Protein Structures into Explicit Lipid Membranesen
dc.typeJournal Articleen
dc.type.supercollectionscholarly_publicationsen
dc.type.supercollectionrefereed_publicationsen
dc.identifier.peoplefinderurlhttp://people.tcd.ie/mcaffreen
dc.identifier.rssinternalid105477en
dc.identifier.doihttp://dx.doi.org/10.1016/j.str.2015.05.006en
dc.rights.ecaccessrightsopenAccess
dc.identifier.rssurihttp://www.scopus.com/inward/record.url?eid=2-s2.0-84936845938&partnerID=40&md5=039e13661ade7f0fb62be1f2696a9261en


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