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We present a computational model of glycosylphosphatidyl-inositol (GPI) anchors for molecular dynamics studies. The model is based on state-of-the-art biomolecular force fields from the AMBER family, employing GLYCAM06 for carbohydrates and Lipid14 to represent fatty acid tails. We construct an adapted glycero-phosphatidyl-inositol unit to establish a seamless transition between the two domains of atom types. This link can readily be extended into a broad variety of GPI variants by applying either domain's building block scheme. As test cases, selected GPI fragments inserted into DMPC and POPC bilayer patches are considered. Our results suggest that the glycan part of the GPI anchor interacts strongly with the lipid head groups, partially embedding the carbohydrate moieties. This behaviour is supported by the conformational preferences of the GPI anchor, which in particular are conveyed by the strong interactions between the proximal amine and phosphate groups. In a similar way we can conclude that the extension of the anchor away from the lipid bilayer surface that could prevent the contact of the membrane with an attached protein ("lollipop picture") is quite unfavorable. Indeed, when attaching green fluorescent protein to the GPI anchor, it is found to reside close to bilayer surface all the time, and the rather flexible phosphoethanolamine linker governs the extent to which the protein directly interacts not only with the head groups, but also with its own GPI core.

A molecular dynamics model for glycosylphosphatidyl-inositol anchors: “flop down” or “lollipop”?