Contributors

I. Gould, L. Rosso
Department of Chemistry, Imperial College London, UK

Reference

Lula Rosso, Ian R. Gould
Journal of Computational Chemistry 2008,19,24
Structure and dynamics of phospholipid bilayers using recently developed general all-atom force fields
Two fully hydrated pure-species phospholipids bilayers, 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and 1,2-dioleoyl-sn-glycero-3-phosphorylcholine (DOPC), in the fluid phase and explicit solvent have been studied using molecular dynamics simulation. Atom interactions were modeled using recently developed force fields based on AMBER with full atomistic details. Several representative liquid phase properties for the structure and dynamics of lipids with different length of hydrocarbon chains and different level of saturation have been reproduced without artificially biasing the system in order to match experimental data. In particular, as the new GAFF (General Amber Force Field) has not been explicitly developed to reproduce lipid characteristics and is naturally compatible with standard AMBER nucleic acids and proteins parameters, it is here proven a promising tool to study mixed lipid-protein processes as protein activity dependence on membrane composition, permeation of solute across membranes, and other cellular processes. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2008

Comments

The PREP and FRCMOD files refer to GAFF parameters. Please also find the coordinates restart and topology file of the DOPC bilayer (72 DOPC molecules + 2935 rigid TIP3P water) and the DMPC bilayer (72 DMPC + 2449 rigid TIP3P water) after 10 ns of NPT equilibration with GAFF as described in the paper.

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Last modified 7 MAR 2008