University of Hertfordshire

Lipid models for united-atom molecular dynamics simulations of proteins

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Original languageEnglish
Pages (from-to)615-626
JournalJournal of Chemical Theory and Computation
Journal publication date2009
Volume5
Issue3
DOIs
Publication statusPublished - 2009

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.

Notes

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]

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