Róg Tomasz, Orłowski Adam, Llorente Alicia, Skotland Tore, Sylvänne Tuulia, Kauhanen Dimple, Ekroos Kim, Sandvig Kirsten, Vattulainen Ilpo
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.
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.
Data Brief. 2016 Mar 26;7:1171-1174. doi: 10.1016/j.dib.2016.03.067. eCollection 2016 Jun.
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].
在这篇《数据简报》文章中，我们提供了一组GROMACS输入文件数据包，用于使用OPLS - AA力场对多组分不对称脂质双层进行原子分子动力学模拟。这些数据包括由8种不同脂质分子组成的14种模型双层。这些模型中存在的脂质有：胆固醇（CHOL）、1 - 棕榈酰 - 2 - 油酰 - sn - 甘油 - 3 - 磷脂酰胆碱（POPC）、1 - 棕榈酰 - 2 - 油酰 - sn - 甘油 - 3 - 磷脂酰乙醇胺（POPE）、1 - 硬脂酰 - 2 - 油酰 - sn - 甘油 - 3 - 磷脂酰乙醇胺（SOPE）、1 - 棕榈酰 - 2 - 油酰 - sn - 甘油 - 3 - 磷脂酰丝氨酸（POPS）、1 - 硬脂酰 - 2 - 油酰 - sn - 甘油 - 3 - 磷脂酰丝氨酸（SOPS）、N - 棕榈酰 - D - 赤藓糖基 - 鞘氨醇 - 磷脂酰胆碱（SM16）和N - 木蜡酰 - D - 赤藓糖基 - 鞘氨醇 - 磷脂酰胆碱（SM24）。双层的组成基于Llorente等人（2013年）[1]中讨论的PC - 3前列腺癌细胞和外泌体的脂质组学研究，显示出外泌体长链脂质种类（SOPS、SOPE和SM24）部分增加。模型中考虑了关于细胞膜脂质不对称性的先前知识，这意味着内膜层模型由PC、PS、PE和胆固醇的混合物组成，而细胞外膜层由Van Meer等人（2008年）[2]中讨论的SM、PC和胆固醇组成。提供的数据包括脂质的拓扑结构、不对称双层的平衡结构、所有力场参数以及描述模拟条件的参数输入文件（md.mdp）。这些数据与研究文章《长链鞘磷脂的相互交错以胆固醇依赖的方式诱导膜叶耦合》（Róg等人，2016年）[3]相关。
