Dataset : Lipid model membranes intended for all-atom molecular dynamics

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Quotation

Timothée Rivel (2021): Lipid model membranes intended for all-atom molecular dynamics. Laboratoire Chrono-environnement (UMR 6249). FR-18008901306731-2021-04-28

General metadata

Identifier : local : FR-18008901306731-2021-04-28
Description :
The data are a series of lipid model membranes designed for the use in all-atoms Molecular dynamics simulations. They are lipid membranes modelling the composition of the lipid matrix of the plasma membrane of eukaryotes with a 5-component model involving phosphatidylcholine (PC), phosphatidylserine (PS), phosphatidylethanolamine (PE), sphingomyelin (SM), and cholesterol (CHOL). For keeping the system small enough, only one type of fatty acid was considered: the oleyl. The models either preserve the asymmetric composition of the membrane of normal eukaryotes or they induce a scrambling mimicking the lipid composition of plasma membrane of both cancer or apoptotic cells by inducing an overexposure of PS and PE in the extracellular leaflet. Each of these two models was equilibrated for 9 curvature ranging from -0.2 to +0.2 nm^(-1) resulting in 18 models equilibrated for 500 ns each. The use of the so-called Slipids force fields - which is known to reproduce accurately the membrane properties - was made. The simulations were carried out with a 1 fs time step, in the NpT ensemble, using the Berendsen pressure coupling and the velocity rescale thermostat, and running on the Gromacs package v 2016.1.
Disciplines :
chemistry, physical (chemistry), biophysics (fundamental biology)
Keywords :

Dates :
Data acquisition : from 1 Oct 2015 to 30 Sep 2019
Metadata record :
Creation : 28 Apr 2021

Language : English (eng)
Additional information :
The data were generated in the frame of the PhD studies of T. Rivel, supervised by C. Ramseyer (Prof., Chrono-environnement) and S. Yesylevskyy (Leading researcher, Académie des sciences de Kiev, Ukraine; Chrono-environnement).
Audience : University: master, Research

Administrative metadata

Data creatorAffiliation
Timothée RivelChrono-environnement (FRA)
ContributorsAffiliationRole
Christophe RamseyerChrono-environnement (FRA)related person
Semen YesylevskyyNASU (UKR)related person
Publisher : Laboratoire Chrono-environnement (UMR 6249)
Label : Mésocentre(s) UBFC
Science contact : Christophe Ramseyer website e-mail
Projects and funders :
Access : restricted
Access details :
To access the data, please contact the scientific data manager.

Technical metadata

Formats : chemical/x-pdb
Data acquisition methods :
  • Simulation or computational data :
    The data were obtained by means of all-atom Molecular Dynamics simulations using Gromacs package v. 2016.1. Their design is based on the existing experimental and numerical literature. For further details, please, contact the authors.
Datatype : Dataset

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