Structure and Dynamics of Glycosphingolipids in Lipid Bilayers: Insights from Molecular Dynamics Simulations

Table 1

Summary of literature reporting simulations of glycolipid containing lipid bilayer.

System studied	Summary of simulations	Reference
MD simulations of glycolipids focusing on behavior of glycolipids at lipid bilayers
Single GD1a in DMPC bilayer	One simulation of single GD1a in a bilayer composed of 15 DMPC molecules was performed for 0.6 ns	[16]
Single GM1 in DPC micelle	Single GM1 and GM1-Os was simulated for 1 ns in 84 DPC micelle and water. The effect of chain length of GM1 on the conformation and dynamics of head-group was also evaluated	[17]
Single GM1 in DMPC bilayer	One simulation of single GM1 in a bilayer composed of 15 DMPC molecules was performed for 1 ns	[18]
Single GM1* in DOPC bilayer	3.8 ns simulations of GM1* in a system composed of 278 DOPC lipid bilayer	[19]
Single GM1 in DPPC bilayer	11 simulations of a GM1 in a bilayer composed of 97 DPPC were performed. The dynamics of GM1 in lipid bilayer was compared with that of GM1-Os in water	[20]
Single GM3 in DMPC bilayer	30 ns long simulations of GM3 in DMPC bilayer and GM3-Os in water were performed	[14]
One GM1* in each monolayer of DOPC molecules	40 ns long simulations of a system composed of two GM1* molecules, one in each leaflet, in 278 DOPC lipid bilayer	[21]
MD simulations of glycolipids focusing on study of glycolipid enriched microdomains
Pure GM3 bilayer	50 ns simulation of a bilayer composed of 128 GM3 was performed as a model system to study gangliosides aggregates	[22, 23]
Glucosyl-glycerol bilayer	Five different sets of parameters were used to simulate bilayer composed of 128 palmitoyl-glucosyl glycerols. Simulations were performed for 10–25 ns. The goal of study was to find correct parameters set that reproduce experimental data	[24]
GalCer and DPPG bilayer	Lipid bilayers composed of 1024 molecules of DPPG and consisting of 10% and 25% GalCer were simulated for 10 ns	[25]
Glucosyl and galactosyl glycerolipid	Bilayers composed of 128 glucosyl and galactosyl glycerolipids were simulated. Structural and dynamical properties of these bilayers were compared with that of PC and PE bilayers	[26]
4 GM1 in a bilayer composed of POPC and cholesterol	40 ns simulation of ternary bilayer composed of GM1, cholesterol and POPC was performed. The structure and dynamics of this lipid bilayer was compared with that of pure and binary lipid bilayers	[27]
Varying concentrations of GM1 in DPPC bilayer	Lipid bilayers composed of varying concentrations of GM1 in DPPC bilayer (~5–25%) were studied using 20 ns MD simulations. Simulations were performed for systems containing GM1 in single as well as both leaflets of bilayer	[28]
Simulations of GalCer in a raft like membrane	200 ns simulations of GalCer in raft like membrane composed of POPC, PSM, and cholesterol	[29]