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

Pallavi Banerjee,Reinhard Lipowsky,Mark Santer,Marko Wehle

doi:10.1039/c8cp04059a

Abstract

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.

Highlights

Glycosylphosphatidylinositols (GPIs) are complex glycolipids present in eukaryotic cells, typically covalently bound to the C-terminus of proteins via a phospho-ethanolamine unit.[1]They primarily serve to anchor proteins to the outer leaflet of the cell membrane, where a Mana(1-2)-Man-a(1-4)-GlcNa(1-6)-myo-inositol pseudopentasaccharide core bridges towards a lipid tail, which in turn is inserted into the plasma membrane
In discussing how the conformational preferences of the hybrid link Ino-POMe emerge, extensive use has been made of the fact that use of either GLYCAM06-type or AM1-BCC charges led to indistinguishable results, see e.g. Fig. S3 in the Electronic supplementary information (ESI).† That is, without seriously affecting aspects of molecular mechanics, the hybrid link to bridge GLYCAM06 and Lipid[14] domains of atom types may be viewed as a vehicle to test nonbonded interactions systematically for instance, by altering the charge scheme on the glycan moieties, exploring different vdW combination rules between carbohydrates and lipids,[55] etc
In the course of 1 ms long simulations for each bilayer system, the GPI core within 200–300 ns flops down onto the bilayer assuming a hook-like conformation reminiscent of the ‘‘diver’’, with the green fluorescent protein (GFP) barrel resting on the head group region with the long axis pointing along the bilayer surface, compare Fig. 11(a); the ‘‘flop down’’, remarkably, allows for a completely upright orientation conveyed by the PE linker (b)

Summary

Introduction

Glycosylphosphatidylinositols (GPIs) are complex glycolipids present in eukaryotic cells, typically covalently bound to the C-terminus of proteins via a phospho-ethanolamine unit.[1]They primarily serve to anchor proteins to the outer leaflet of the cell membrane, where a Mana(1-2)-Man-a(1-4)-GlcNa(1-6)-myo-inositol pseudopentasaccharide core bridges towards a lipid tail, which in turn is inserted into the plasma membrane.

Results

Conclusion