title: An overview of molecular dynamics simulations of oxidized lipid systems, with a comparison of ELBA and MARTINI force fields for coarse grained lipid simulations.
abstract: Biological membranes and model lipid systems containing high amounts of unsaturated lipids and sterols are subject to chemical and/or photo-induced lipid oxidation, which leads to the creation of exotic oxidized lipid products (OxPLs). OxPLs are known to have significant physiological impact in cellular systems and also affect physical properties of both biological and model lipid bilayers. In this paper we (i) provide a perspective on the existing literature on simulations of lipid bilayer systems containing oxidized lipid species as well as the main related experimental results, (ii) describe our new data of all-atom and coarse-grained simulations of hydroperoxidized lipid monolayer and bilayer systems and (iii) provide a comparison of the MARTINI and ELBA coarse grained force fields for lipid bilayer systems. We show that the better electrostatic treatment of interactions in ELBA is able to resolve previous conflicts between experiments and simulations. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.
authors.affiliation: MEMPHYS-Center for Biomembrane Physics, Department of Physics and Chemistry, University of Southern, Denmark; Departamento de Química, FFCLRP, Universidade de São Paulo, Ribeirão Preto, SP, Brazil.
authors.forename: P
authors.initials: P
authors.lastname: Siani
authors.affiliation: Departamento de Química, FFCLRP, Universidade de São Paulo, Ribeirão Preto, SP, Brazil.
authors.forename: R M
authors.initials: RM
authors.lastname: de Souza
authors.affiliation: Departamento de Química, FFCLRP, Universidade de São Paulo, Ribeirão Preto, SP, Brazil.
authors.forename: L G
authors.initials: LG
authors.lastname: Dias
authors.affiliation: Departamento de Física Aplicada, Instituto de Física, Universidade de São Paulo, São Paulo, SP, Brazil.
authors.forename: R
authors.initials: R
authors.lastname: Itri
authors.affiliation: MEMPHYS-Center for Biomembrane Physics, Department of Physics and Chemistry, University of Southern, Denmark. Electronic address: hkhandel@sdu.dk.
authors.forename: H
authors.initials: H
authors.lastname: Khandelia
mesh_terms: D008051:Lipid Bilayers / Q000737:chemistry*; D008055:Lipids / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D010084:Oxidation-Reduction; D055672:Static Electricity
chemical_list: D008051:Lipid Bilayers; D008055:Lipids
keywords: Coarse-grained; Free energy; Lipid mixing; Molecular dynamics; Oxidized phospholipids; Water permeation