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

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].Peer reviewe

Implementation of a Lipoprotein Isolation Method in a Lipidomic High-throughput Workflow

Lipoproteins play a central role in the disease mechanisms of cardiovascular diseases (CVD) and therefore they have been studied widely. They carry several classes of apolipoproteins where apo-A1 and apo-B are the major classes. The sucrose based sequential lipoprotein isolation method can retrieve the lipoprotein fractions suitable for lipidomics analyses. The main lipoprotein classes are very low-density lipoprotein (VLDL), low-density lipoprotein (LDL) and high density lipoprotein (HDL) that can be isolated easily by their density from human blood plasma or serum. Lipidomics analyses can quantify lipids that lipoproteins carry in the circulation. Mainly they carry cholesterol and its esterified forms, glycerolipids, small amounts of sphingolipids and phospholipids form their monolayer membrane. The isolation method was set-up together with scaled-down sample volumes. The protein and lipid content of the main lipoprotein fractions were evaluated by electrophoresis analysis, various enzymatic assays and lipidomics analyses. The total protein and apolipoprotein content was found to be similar as in the literature. Apo-B was found to be the main apolipoprotein in the VLDL and the LDL fractions whereas apo-A1 was the main apolipoprotein in the HDL fractions. Triglycerides (TG) were measured by enzymatic analysis and TG was mainly found in LDL and VLDL. The lipidomics analyses demonstrated the lipid content of the lipoproteins were similar as in the literature with minor changes. The main lipid class found in all the lipoproteins was cholesteryl esters (CE) followed by phosphatidylcholines (PC) that are commonly found in cell membranes. Sphingolipids such as ceramides were also detected in lipid class level only in small quantities in the lipoprotein fractions. The low initial sample volume did not correlate linearly with higher sample volume and low sample volume is not recommended to use in this specific isolation method. Based on the results of the comprehensive screening of isolated lipoproteins the isolation method was successfully established

Shotgun Lipidomics by Sequential Precursor Ion Fragmentation on a Hybrid Quadrupole Time-of-Flight Mass Spectrometer

metabolite

The Ether Lipid Precursor Hexadecylglycerol Causes Major Changes in the Lipidome of HEp-2 Cells

<div><p>The ether-lipid precursor <i>sn-1</i>-O-hexadecylglycerol (HG) can be used to compensate for early metabolic defects in ether-lipid biosynthesis. To investigate a possible metabolic link between ether-linked phospholipids and the rest of the cellular lipidome, we incubated HEp-2 cells with HG. Mass spectrometry analysis revealed major changes in the lipidome of HG-treated cells compared to that of untreated cells or cells treated with palmitin, a control substance for HG containing an acyl group instead of the ether group. We present quantitative data for a total of 154 species from 17 lipid classes. These species are those constituting more than 2% of their lipid class for most lipid classes, but more than 1% for the ether lipids and glycosphingolipids. In addition to the expected ability of HG to increase the levels of ether-linked glycerophospholipids with 16 carbon atoms in the <i>sn-1</i> position, this precursor also decreased the amounts of glycosphingolipids and increased the amounts of ceramide, phosphatidylinositol and lysophosphatidylinositol. However, incubation with palmitin, the fatty acyl analogue of HG, also increased the amounts of ceramide and phosphatidylinositols. Thus, changes in these lipid classes were not ether lipid-dependent. No major effects were observed for the other lipid classes, and cellular functions such as growth and endocytosis were unaffected. The data presented clearly demonstrate the importance of performing detailed quantitative lipidomic studies to reveal how the metabolism of ether-linked glycerophospholipids is coupled to that of glycosphingolipids and ester-linked glycerophospholipids, especially phosphatidylinositols.</p></div

Biosynthesis of ether and ester glycerophospholipids and the chemical structures of the precursors used.

<p>(<b>A</b>) Schematic overview of the biosynthesis of ether and ester glycerophospholipids. Note that 1-alkylglycerols such as HG (red box) may enter the pathway through phosphorylation to 1-alkylglycerol 3-phosphate by an alkylglycerol kinase. For abbreviations of the compounds and enzymes, see below. (<b>B</b>) The chemical structure of the compounds used in this study, HG and palmitin. DHAP; dihydroxyacetone phosphate, G3P; glycerol 3-phoshpate, DHAPAT; dihydroxyacetone phosphate acyltransferase, GPAT; glycerol phosphate acyltransferase, ADHAPS; alkyldihydroxyacetone phosphate synthase, LPA; lysophosphatidic acid, LPAAT; lysophosphatidic acid acyltransferase, PAP; phosphatidic acid phosphatase, EPT; ethanolamine phosphotransferase, CEPT; choline/ethanolamine phosphotransferase.</p

Quantitative analysis of ceramide and glycosphingolipids after HG or palmitin treatment.

<p>The major species of (<b>A</b>) Cer, (<b>B</b>) GlcCer, (<b>C</b>) LacCer, and (<b>D</b>) Gb3 in HEp-2 cells treated with HG (20 µM), palmitin (20 µM) or ethanol (0.1%, as control) for 24 hours. The species shown here are species comprising more than 1% of the total mass of any of the classes.</p

Quantitative analysis of glycerophospholipids after HG or palmitin treatment.

<p>The major species of (<b>A</b>) PC O, (<b>B</b>) PC P, (<b>C</b>) PE O, (<b>D</b>) PE P, (<b>E</b>) PC and (<b>F</b>) PE, in HEp-2 cells treated with HG (20 µM), palmitin (20 µM) or ethanol (0.1%, as control) for 24 hours. The species shown here are species comprising more than 1% of the total mass of the ether lipids and more than 2% of PC and PE for at least one of the samples.</p

Overall changes in the lipidome of HEp-2 cells after treatment with HG or palmitin.

<p>HEp-2 cells were treated for 24 hours with HG (20 µM), palmitin (20 µM) or ethanol (0.1%, as control) before analyzing the lipidome by MS. (<b>A</b>) The total amount of the different lipid classes are shown as absolute values (note the logarithmic scale) and (<b>B</b>) the difference between treated cells and control cells are expressed as relative values.</p