A polarizable force field of dipalmitoylphosphatidylcholine based on the classical Drude model for molecular dynamics simulations of lipids.

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TitleA polarizable force field of dipalmitoylphosphatidylcholine based on the classical Drude model for molecular dynamics simulations of lipids.
Publication TypeJournal Article
Year of Publication2013
AuthorsChowdhary, J, Harder, E, Lopes, PEM, Huang, L, Mackerell, AD, Roux, B
JournalJ Phys Chem B
Volume117
Issue31
Pagination9142-60
Date Published2013 Aug 08
ISSN1520-5207
Keywords1,2-Dipalmitoylphosphatidylcholine, Acetates, Alkanes, Deuterium, Lipid Bilayers, Lipids, Molecular Dynamics Simulation, Quantum Theory, Static Electricity, Thermodynamics, Water
Abstract

A polarizable force field of saturated phosphatidylcholine-containing lipids based on the classical Drude oscillator model is optimized and used in molecular dynamics simulations of bilayer and monolayer membranes. The hierarchical parametrization strategy involves the optimization of parameters for small molecules representative of lipid functional groups, followed by their application in larger model compounds and full lipids. The polar headgroup is based on molecular ions tetramethyl ammonium and dimethyl phosphate, the esterified glycerol backbone is based on methyl acetate, and the aliphatic lipid hydrocarbon tails are based on linear alkanes. Parameters, optimized to best represent a collection of gas and liquid properties for these compounds, are assembled into a complete model of dipalmitoylphosphatidylcholine (DPPC) lipids that is tested against the experimental properties of bilayer and monolayer membranes. The polarizable model yields average structural properties that are in broad accord with experimental data. The area per lipid of the model is 60 Å(2), slightly smaller than the experimental value of 63 Å(2). The order parameters from nuclear magnetic resonance deuterium quadrupolar splitting measures, the electron density profile, and the monolayer dipole potential are in reasonable agreement with experimental data, and with the nonpolarizable CHARMM C36 lipid force field.

DOI10.1021/jp402860e
Alternate JournalJ Phys Chem B
PubMed ID23841725
PubMed Central IDPMC3799809
Grant ListR01 GM072558 / GM / NIGMS NIH HHS / United States
GM-072558 / GM / NIGMS NIH HHS / United States