Data including GROMACS input files for atomistic molecular dynamics simulations of mixed, asymmetric bilayers including molecular topologies, equilibrated structures, and force field for lipids compatible with OPLS-AA parameters

Show full item record



Permalink

http://hdl.handle.net/10138/190721

Citation

Rog , T J , Orlowski , A , llorente , A , Skotland , T , Sylvänne , T , Kauhanen , D , Ekroos , K , Sandvig , K & Vattulainen , I T 2016 , ' Data including GROMACS input files for atomistic molecular dynamics simulations of mixed, asymmetric bilayers including molecular topologies, equilibrated structures, and force field for lipids compatible with OPLS-AA parameters ' , Data in Brief , vol. 7 , pp. 1171-1174 . https://doi.org/10.1016/j.dib.2016.03.067

Title: Data including GROMACS input files for atomistic molecular dynamics simulations of mixed, asymmetric bilayers including molecular topologies, equilibrated structures, and force field for lipids compatible with OPLS-AA parameters
Author: Rog, Tomasz Jakub; Orlowski, Adam; llorente, Alicia; Skotland, Tore; Sylvänne, Tuulia; Kauhanen, Dimple; Ekroos, Kim; Sandvig, Kirsten; Vattulainen, Ilpo Tapio
Contributor: University of Helsinki, Department of Physics
University of Helsinki, Department of Physics
Date: 2016
Language: eng
Number of pages: 4
Belongs to series: Data in Brief
ISSN: 2352-3409
URI: http://hdl.handle.net/10138/190721
Abstract: In this Data in Brief article we provide a data package of GROMACS input files for atomistic molecular dynamics simulations of multi- component, asymmetric lipid bilayers using the OPLS-AA force field. These data include 14 model bilayers composed of 8 different lipid molecules. The lipids present in these models are: cholesterol (CHOL), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylcholine (POPC), 1-pal- mitoyl-2-oleoyl-sn-glycero-3-phosphatidylethanolamine (POPE), 1-stearoyl-2-oleoyl-sn-glycero-3-phosphatidyl-ethanolamine (SOPE), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylserine (POPS), 1-stear- oyl-2-oleoyl-sn-glycero-3-phosphatidylserine (SOPS), N-palmitoyl-D- erythro-sphingosyl-phosphatidylcholine (SM16), and N-lignoceroy l-D-erythro-sphingosyl-phosphatidylcholine (SM24). The bilayers' compositions are based on lipidomic studies of PC-3 prostate cancer cells and exosomes discussed in Llorente et al. (2013) [1], showing an increase in the section of long-tail lipid species (SOPS, SOPE, and SM24) in the exosomes. Former knowledge about lipid asymmetry in cell membranes was accounted for in the models, meaning that the model of the inner leaflet is composed of a mixture of PC, PS, PE, and cholesterol, while the extracellular leaflet is composed of SM, PC and cholesterol discussed in Van Meer et al. (2008) [2]. The provided data include lipids' topologies, equilibrated structures of asymmetric bilayers, all force field parameters, and input files with parameters describing simulation conditions (md.mdp). The data is associated with the research article “Interdigitation of Long-Chain Sphingomyelin Induces Coupling of Membrane Leaflets in a Cholesterol Dependent Manner” (Róg et al., 2016) [3].
Subject: 114 Physical sciences
Biological Physics
Biophysics
Rights:


Files in this item

Total number of downloads: Loading...

Files Size Format View
1_s2.0_S2352340916301755_main.pdf 560.6Kb PDF View/Open

This item appears in the following Collection(s)

Show full item record