Coarse-Grained Molecular Model for the Glycosylphosphatidylinositol Anchor with and without Protein.

Pallavi Banerjee,Reinhard Lipowsky,Mark Santer

doi:10.1021/acs.jctc.0c00056

Abstract

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.

Highlights

The plasma membrane of eukaryotic cells contains a large variety of functionally active proteins, such as transmembrane proteins acting as ion channels or RAS proteins which have a simple fatty acid tail tethering them to the plasma membrane
We developed a coarse-grained model of simple sugars− glucose, sucrose, and trehalose−, GPI and GPI-anchored green fluorescent protein (GFP)
The interaction potentials of lipid−lipid, sugar−lipid, and protein−lipid were retained from the MARTINI polarizable force field, but the potentials describing sugar−sugar and sugar−protein were altered by scaling down the amplitudes εijs of the Lennard-Jones potentials to match the experimental and atomistic behavior

Summary

Introduction

The plasma membrane of eukaryotic cells contains a large variety of functionally active proteins, such as transmembrane proteins acting as ion channels or RAS proteins which have a simple fatty acid tail tethering them to the plasma membrane. The so-called glycosylphosphatidylinositols (GPIs) provide a intriguing anchoring mechanism. They are covalently added to the C-terminus of proteins through posttranslational modification in the endoplasmic reticulum. The structure of GPI consists of a highly conserved pseudopentasaccharide glycan core Man-α(1→2)-Man-α(1→6)-Manα(1→4)-GlcN-α(1→6)-myo-inositol that is further connected to a lipid tail which inserts into the plasma membrane. In spite of the conserved core, GPIs are of heterogeneous structure through various types of sugar side branches, the composition of which can vary even with the very same protein (microheterogeneity)

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