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

Tomasz Róg; Adam Orłowski; Alicia Llorente; Tore Skotland; Tuulia Sylvänne; Dimple Kauhanen; Kim Ekroos; Kirsten Sandvig; Ilpo Vattulainen

doi:10.1016/j.dib.2016.03.067

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 Brief. 2016 Mar 26:7:1171-1174. doi: 10.1016/j.dib.2016.03.067. eCollection 2016 Jun.

Authors

Tomasz Róg¹, Adam Orłowski², Alicia Llorente³, Tore Skotland³, Tuulia Sylvänne⁴, Dimple Kauhanen⁴, Kim Ekroos⁴, Kirsten Sandvig⁵, Ilpo Vattulainen⁶

Affiliations

¹ Department of Physics, Tampere University of Technology, P. O. Box 692, FI-33101 Tampere, Finland; Department of Physics, University of Helsinki, P. O. Box 64, FI-00014, Finland.
² Department of Physics, Tampere University of Technology, P. O. Box 692, FI-33101 Tampere, Finland; Department of Physics and Energy, University of Limerick, Limerick, Ireland.
³ Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital - The Norwegian Radium Hospital, 0379 Oslo, Norway; Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, 0379 Oslo, Norway.
⁴ Zora Biosciences Oy, 02150 Espoo, Finland.
⁵ Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital - The Norwegian Radium Hospital, 0379 Oslo, Norway; Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, 0379 Oslo, Norway; Department of Biosciences, University of Oslo, 0316 Oslo, Norway.
⁶ Department of Physics, Tampere University of Technology, P. O. Box 692, FI-33101 Tampere, Finland; Department of Physics, University of Helsinki, P. O. Box 64, FI-00014, Finland; MEMPHYS - Center for Biomembrane Physics, University of Southern Denmark, Odense, Denmark.

Abstract

In this Data in Brief article we provide a data package of GROMACS input files for atomistic molecular dynamics simulations of multicomponent, 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-palmitoyl-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-stearoyl-2-oleoyl-sn-glycero-3-phosphatidylserine (SOPS), N-palmitoyl-D-erythro-sphingosyl-phosphatidylcholine (SM16), and N-lignoceroyl-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].

Keywords: Force field; GROMACS; Lipid; Lipidomics; Molecular dynamics simulations; Topology.