Martini Force Field Parameters for Glycolipids

Abstract

We present an extension of the Martini coarse-grained force field to glycolipids. The glycolipids considered here are the glycoglycerolipids monogalactosyldiacylglycerol (MGDG), sulfoquinovosyldiacylglycerol (SQDG), digalactosyldiacylglycerol (DGDG), and phosphatidylinositol (PI) and its phosphorylated forms (PIP, PIP2), as well as the glycosphingolipids galactosylceramide (GCER) and monosialotetrahexosylganglioside (GM1). The parametrization follows the same philosophy as was used previously for lipids, proteins, and carbohydrates focusing on the reproduction of partitioning free energies of small compounds between polar and nonpolar solvents. Bonded parameters are optimized by comparison to lipid conformations sampled with an atomistic force field, in particular with respect to the representation of the most populated states around the glycosidic linkage. Simulations of coarse-grained glycolipid model membranes show good agreement with atomistic simulations as well as experimental data available, especially concerning structural properties such as electron densities, area per lipid, and membrane thickness. Our coarse-grained model opens the way to large scale simulations of biological processes in which glycolipids are important, including recognition, sorting, and clustering of both external and membrane bound proteins.

Nanodomain Formation of Ganglioside GM1 in Lipid Membrane: Effects of Cholera Toxin-Mediated Cross-Linking

“…18 The atomic representation of DPPC, GM1, protein amino acids, and their corresponding CG models are given in Figures S1 and S2 in the Supporting Information. Similar to the Martini model, [17][18][19]39 the DPD beads are sorted into charged (Q), polar (P), nonpolar (N), and apolar (C) types. Each type is further divided into sublevels based on their hydrogen donor capacities (d), hydrogen acceptor capacities (a), and non-hydrogen-bond-forming capacities (0).…”

“…14,15 For example, in a recent work with AAMD simulation, 15 only one CTB, which was binding to a monolayer membrane composed of five GM1 molecules and a hundred phospholipids, was investigated. To handle the entire perspective of phenomena in complex materials, various coarse-grained (CG) methods, including coarse-grained Molecular Dynamics (CGMD) [16][17][18][19][20] and dissipative particle dynamics (DPD) simulations, [21][22][23][24][25][26][27][28][29][30][31][32][33][34][35][36][37][38] have been developed. The CG model groups a few atoms into one mesoscopic pseudoatom and thus can reach the biologically relevant time and length scales efficiently.…”

Hydrocarbons Are Essential for Optimal Cell Size, Division, and Growth of Cyanobacteria

“…In order to understand how hydrocarbons could affect membrane properties, a novel symmetrical membrane model system was simulated based on the pseudoatomistic Martini force field, with an approximately 4:1 mapping of heavy atoms to coarse-grained particles (Supplemental Fig. S9; López et al, 2013). The present model used 16 different lipid types corresponding to the four major groups present in cyanobacteria: phosphatidylglycerol (PG), monogalactosyl-diacylglycerol (MGDG), digalactosyl-diacylglycerol (DGDG), and sulfoquinovosyldiacylglycerol (SQDG), in a ratio as experimentally determined in Synechocystis (Supplemental Table S6; Sheng et al, 2011).…”

“…The composition of the lipid tails in the in silico membranes was adapted to coarse-grained resolution, i.e. an approximately 4:1 mapping of heavy atoms to coarse-grained particles, using the Martini force field (López et al, 2013). The structure of the lipid head groups and representative tails included in the model are compared to their coarse-grained topologies in Supplemental Figure S9, where the mapping of the Martini bead types are shown and labeled.…”

Membrane-Mediated Regulation of the Intrinsically Disordered CD3ϵ Cytoplasmic Tail of the TCR

“…The pressure of the systems also was controlled by weak coupling with a relaxation time of 1.0 ps. Parameters for the CG lipids, glycolipids, and CD3e chain were taken from the MARTINI model (17,18). The polarizable water model (19) was used in combination with the rest of the parameters.…”