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The ELBA force field for coarse-grain modeling of lipid membranes

The ELBA force field for coarse-grain modeling of lipid membranes
The ELBA force field for coarse-grain modeling of lipid membranes
A new coarse-grain model for molecular dynamics simulation of lipid membranes is presented. Following a simple and conventional approach, lipid molecules are modeled by spherical sites, each representing a group of several atoms. In contrast to common coarse-grain methods, two original (interdependent) features are here adopted. First, the main electrostatics are modeled explicitly by charges and dipoles, which interact realistically through a relative dielectric constant of unity (?r=1). Second, water molecules are represented individually through a new parametrization of the simple Stockmayer potential for polar fluids; each water molecule is therefore described by a single spherical site embedded with a point dipole. The force field is shown to accurately reproduce the main physical properties of single-species phospholipid bilayers comprising dioleoylphosphatidylcholine (DOPC) and dioleoylphosphatidylethanolamine (DOPE) in the liquid crystal phase, as well as distearoylphosphatidylcholine (DSPC) in the liquid crystal and gel phases. Insights are presented into fundamental properties and phenomena that can be difficult or impossible to study with alternative computational or experimental methods. For example, we investigate the internal pressure distribution, dipole potential, lipid diffusion, and spontaneous self-assembly. Simulations lasting up to 1.5 microseconds were conducted for systems of different sizes (128, 512 and 1058 lipids); this also allowed us to identify size-dependent artifacts that are expected to affect membrane simulations in general. Future extensions and applications are discussed, particularly in relation to the methodology's inherent multiscale capabilities.
1932-6203
e28637
Orsi, Mario
62904259-9a93-4d02-8ce6-d8ef53dfcbf1
Essex, Jonathan W.
1f409cfe-6ba4-42e2-a0ab-a931826314b5
Fraternali, Franca
28f6ff16-64de-406c-ac25-728eaf65c8c9
Fraternali, Franca
28f6ff16-64de-406c-ac25-728eaf65c8c9
Orsi, Mario
62904259-9a93-4d02-8ce6-d8ef53dfcbf1
Essex, Jonathan W.
1f409cfe-6ba4-42e2-a0ab-a931826314b5

Orsi, Mario and Essex, Jonathan W. , Fraternali, Franca (ed.) (2011) The ELBA force field for coarse-grain modeling of lipid membranes. PLoS ONE, 6 (12), e28637. (doi:10.1371/journal.pone.0028637).

Record type: Article

Abstract

A new coarse-grain model for molecular dynamics simulation of lipid membranes is presented. Following a simple and conventional approach, lipid molecules are modeled by spherical sites, each representing a group of several atoms. In contrast to common coarse-grain methods, two original (interdependent) features are here adopted. First, the main electrostatics are modeled explicitly by charges and dipoles, which interact realistically through a relative dielectric constant of unity (?r=1). Second, water molecules are represented individually through a new parametrization of the simple Stockmayer potential for polar fluids; each water molecule is therefore described by a single spherical site embedded with a point dipole. The force field is shown to accurately reproduce the main physical properties of single-species phospholipid bilayers comprising dioleoylphosphatidylcholine (DOPC) and dioleoylphosphatidylethanolamine (DOPE) in the liquid crystal phase, as well as distearoylphosphatidylcholine (DSPC) in the liquid crystal and gel phases. Insights are presented into fundamental properties and phenomena that can be difficult or impossible to study with alternative computational or experimental methods. For example, we investigate the internal pressure distribution, dipole potential, lipid diffusion, and spontaneous self-assembly. Simulations lasting up to 1.5 microseconds were conducted for systems of different sizes (128, 512 and 1058 lipids); this also allowed us to identify size-dependent artifacts that are expected to affect membrane simulations in general. Future extensions and applications are discussed, particularly in relation to the methodology's inherent multiscale capabilities.

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Published date: 16 December 2011
Organisations: Chemistry, Faculty of Natural and Environmental Sciences, Computational Systems Chemistry

Identifiers

Local EPrints ID: 352702
URI: http://eprints.soton.ac.uk/id/eprint/352702
ISSN: 1932-6203
PURE UUID: 6d3eeb98-6b9b-4ed7-9e01-94c69d849c4e
ORCID for Jonathan W. Essex: ORCID iD orcid.org/0000-0003-2639-2746

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Date deposited: 20 May 2013 12:07
Last modified: 17 Dec 2019 02:00

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