Coarse-Grained Molecular Model for the Glycosylphosphatidylinositol Anchor with and without Protein
datasetposted on 26.05.2020, 20:13 by Pallavi Banerjee, Reinhard Lipowsky, Mark Santer
Glycosylphosphatidylinositol (GPI) anchors are a unique class of complex glycolipids that anchor a great variety of proteins to the extracellular leaflet of plasma membranes of eukaryotic cells. These anchors can exist either with or without an attached protein called GPI-anchored protein (GPI-AP) both in vitro and in vivo. Although GPIs are known to participate in a broad range of cellular functions, it is to a large extent unknown how these are related to GPI structure and composition. Their conformational flexibility and microheterogeneity make it difficult to study them experimentally. Simplified atomistic models are amenable to all-atom computer simulations in small lipid bilayer patches but not suitable for studying their partitioning and trafficking in complex and heterogeneous membranes. Here, we present a coarse-grained model of the GPI anchor constructed with a modified version of the MARTINI force field that is suited for modeling carbohydrates, proteins, and lipids in an aqueous environment using MARTINI’s polarizable water. The nonbonded interactions for sugars were reparametrized by calculating their partitioning free energies between polar and apolar phases. In addition, sugar–sugar interactions were optimized by adjusting the second virial coefficients of osmotic pressures for solutions of glucose, sucrose, and trehalose to match with experimental data. With respect to the conformational dynamics of GPI-anchored green fluorescent protein, the accessible time scales are now at least an order of magnitude larger than for the all-atom system. This is particularly important for fine-tuning the mutual interactions of lipids, carbohydrates, and amino acids when comparing to experimental results. We discuss the prospective use of the coarse-grained GPI model for studying protein-sorting and trafficking in membrane models.
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eukaryotic cellsmodeling carbohydratesGPI-anchored proteinProtein Glycosylphosphatidylinositolmembrane modelsGPI structureapolar phasesCoarse-Grained Molecular Modelall-atom computer simulationsMARTINI force fieldplasma membranesGPI-APcoarse-grained modelnonbonded interactionscoarse-grained GPI modelpartitioningtime scalesSimplified atomistic modelsvirial coefficientsall-atom systemextracellular leafletGPI anchorGlycosylphosphatidylinositol Anchortraffickinglipid bilayer patches