dc.contributor.author | Kukol, A. | |
dc.date.accessioned | 2013-01-11T13:29:06Z | |
dc.date.available | 2013-01-11T13:29:06Z | |
dc.date.issued | 2009 | |
dc.identifier.citation | Kukol , A 2009 , ' Lipid models for united-atom molecular dynamics simulations of proteins ' , Journal of Chemical Theory and Computation , vol. 5 , no. 3 , pp. 615-626 . https://doi.org/10.1021/ct8003468 | |
dc.identifier.issn | 1549-9626 | |
dc.identifier.other | dspace: 2299/3053 | |
dc.identifier.uri | http://hdl.handle.net/2299/9575 | |
dc.description | Original article can be found at: http://pubs.acs.org/loi/jctcce Copyright American Chemical Society DOI: 10.1021/ct8003468 [Full text of this article is not available in the UHRA] | |
dc.description.abstract | United-atom force fields for molecular dynamics (MD) simulations provide a higher computational efficiency, especially in lipid membrane simulations, with little sacrifice in accuracy, when compared to all-atom force fields. Excellent united-atom lipid models are available, but in combination with depreciated protein force fields. In this work, a united-atom model of the lipid 1,2-dipalmitoyl-sn-glycero-3-phosphocholine has been built with standard parameters of the force field GROMOS96 53a6 that reproduces the experimental area per lipid of a lipid bilayer within 3% accuracy to a value of 0.623 ± 0.011 nm2 without the assumption of a constant surface area or the inclusion of surface pressure. In addition, the lateral self-diffusion constant and deuterium order parameters of the acyl chains are in agreement with experimental data. Furthermore, models for 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol (POPG) result in areas per lipid of 0.625 nm2 (DMPC), 0.693 nm2 (POPC), and 0.700 nm2 (POPG) from 40 ns MD simulations. Experimental lateral self-diffusion coefficients are reproduced satisfactorily by the simulation. The lipid models can form the basis for molecular dynamics simulations of membrane proteins with current and future versions of united-atom protein force fields. | en |
dc.format.extent | 1390311 | |
dc.language.iso | eng | |
dc.relation.ispartof | Journal of Chemical Theory and Computation | |
dc.subject | lipid bilayer | |
dc.subject | modelling | |
dc.subject | molecular dynamics simulation | |
dc.subject | membrane protein | |
dc.title | Lipid models for united-atom molecular dynamics simulations of proteins | en |
dc.contributor.institution | School of Life and Medical Sciences | |
dc.contributor.institution | Biosciences Research Group | |
dc.contributor.institution | Centre for Research in Mechanisms of Disease and Drug Discovery | |
dc.contributor.institution | Department of Clinical, Pharmaceutical and Biological Science | |
dc.contributor.institution | Centre for Future Societies Research | |
dc.description.status | Peer reviewed | |
rioxxterms.versionofrecord | 10.1021/ct8003468 | |
rioxxterms.type | Journal Article/Review | |
herts.preservation.rarelyaccessed | true | |