Lipid model membranes intended for all-atom molecular dynamics (2021)
Data creator : Timothée Rivel  
 : Laboratoire Chrono-environnement (UMR 6249) (Université de Franche-Comté)
 : Observatoire des Sciences de l'Univers - Terre, Homme, Environnement, Temps, Astronomie (UAR 3245) (Université de Franche-Comté)
 : National Academy of Sciences of Ukraine
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.
Access details :
To access the data, please contact the scientific data manager.
Data acquisition date : from 1 Oct 2015 to 30 Sep 2019
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.
Language : English (eng)
Formats : chemical/x-pdb
Audience : University: master, Research
- Curvature increases permeability of the plasma membrane for ions, water and the anti-cancer drugs cisplatin and gemcitabine (doi:10.1038/s41598-019-53952-2)
- The asymmetry of plasma membranes and their cholesterol content influence the uptake of cisplatin (https://www.nature.com/articles/s41598-019-41903-w)
- The influence of curvature on the properties of the plasma membrane. Insights from atomistic molecular dynamics simulations (https://www.nature.com/articles/s41598-017-16450-x)
- Numerical simulations of the interaction of platinum salts with lipid asymmetric membranes (hal:tel-03128929)
Publisher : Laboratoire Chrono-environnement (UMR 6249)
Label : Mésocentre(s) UBFC
Projects and funders :
- The influence of the cell membrane asymmetry and curvature on the functioning of membrane proteins and the transport of therapeutic compounds
- H2020-MSCA-RISE-2015 Project №690853 assymcurv (European project)
- Thèse de doctorat en biophysique - Timothée Rivel
- Contrat doctoral Ministère de l'Enseignement Supérieur, de la Recherche et de l'Innovation (MESRI) (Ministry)
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).
Record created 28 Apr 2021 by Timothée Rivel.
Local identifier: FR-18008901306731-2021-04-28.