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. 2020 Jun 9;16(6):3889-3903.
doi: 10.1021/acs.jctc.0c00056. Epub 2020 May 26.

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

Pallavi Banerjee  1   2 , Reinhard Lipowsky  1   2 , Mark Santer  1
Affiliations

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

Pallavi Banerjee et al. J Chem Theory Comput. .

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.

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Conflict of interest statement

The authors declare no competing financial interest.

Figures

Figure 1
Figure 1
Chemical structure of a GPI anchor. The GPI core consists of Man3-Man2-Man1-GlcN-Ino. The core is connected to a phosphoglycerol (PGL) head which further connects to the lipid tail. A phosphoethanolamine linker (EtNP) attaches the protein to GPI. Ino+PGL are shown in blue to indicate the transition between the two force-field domains of GLYCAM06h (black) and Lipid14 (orange) that have been merged to provide a molecular model of the full structure.
Figure 2
Figure 2
Mapping scheme for coarse-graining sugars: (a) glucose, (b) sucrose, and (c) trehalose. The colors of the coarse-grained beads encode the mapped groups of the atomistic molecules.
Figure 3
Figure 3
Mapping of GPI anchor from atomistic to coarse-grained representation.
Figure 4
Figure 4
Free energy profiles ΔG as a function of the coupling parameter λ for (a) glucose, (b) sucrose, and (c) trehalose obtained from the thermodynamic integration of one sugar molecule in water (black) and in water-saturated octanol (red) separately.
Figure 5
Figure 5
(a) All-atom representation of EtNP linker. (b) Mapping of the all-atom model in (a) to a coarse-grained parametrization consisting of beads, with the green beads representing the amino-acid residues in the following order: THR-ILE-GLY-T, starting from the linkage at L1. BB beads are backbone beads, and SC are side chain beads. The yellow beads make up the EtNP linker, and the blue beads represent GPI’s last two mannose residues. Beads are shown with their bead names.
Figure 6
Figure 6
Coarse-grained representation of GFP (a) without and (b) with elastic bonds. The black mesh in (b) depicts the elastic network imposed on the backbone beads of GFP. The chromophore is shown as brown beads in the center of the barrel.
Figure 7
Figure 7
(a) Root-mean-square deviation (RMSD) of coarse-grained GFP compared to the crystal structure. (b) Comparison of root-mean-square fluctuation (RMSF) of the all-atom (black) and coarse-grained (red) GFPs in water.
Figure 8
Figure 8
Radius of gyration Rg for GFP as obtained with the atomistic (AA) (black) and coarse-grained (CG) (red) models.
Figure 9
Figure 9
Sugar–sugar radial distribution functions (RDFs) g(r) as a function of distance r averaged over all 200 ns segments and corresponding B22 vs r profiles of all 200 ns segments put together for solutions of glucose, sucrose, and trehalose. In the B22 plots, the dotted lines come from the 200 ns intervals, and the solid line is the averaged profile over all the intervals. Profiles from unscaled γ = 1 are shown in red, and profiles from scaled γ = 0.85 are shown in green. The averaged constant value at the far end (at 5 nm) is the reported B22 value.
Figure 10
Figure 10
Snapshots taken at the end of 1 μs long simulations of five GPI glycans in water modeled with (a) unscaled MARTINI at γ = 1 and (b) scaled MARTINI at γ = 0.85. Each GPI molecule has a different color.
Figure 11
Figure 11
Comparison of distributions of number of contacts made within a radius of 0.6 nm between GFP and GPI glycan between four different all-atom (AA) trajectories (black, red, green, blue) and coarse-grained (CG) trajectories (magenta for the unscaled and orange for the scaled force field). The plots show running averages over five neighboring data points to enhance legibility.
Figure 12
Figure 12
Comparison of structural properties (a) end-to-end distance Ree and (b) radius of gyration Rg between the all-atom (black) and coarse-grained (red) representations of a single GPI core in water.
Figure 13
Figure 13
Comparison of structural properties (a) end-to-end distance, Ree, and (b) radius of gyration, Rg, between all-atom and coarse-grained GPIs in a pure DMPC bilayer. Part (c) shows the description of tilt angle θz of the GPI core, and its corresponding distribution profiles are displayed in (d). Profiles of all-atom GPI in the top leaflet are shown in black, in the bottom leaflet is shown in red, the coarse-grained GPI in the top leaflet is shown in green, and in the bottom leaflet it is shown in blue.
Figure 14
Figure 14
Snapshots at the end of 1 μs long simulations of GPIs in DMPC bilayers for (a) the all-atom and (b) the coarse-grained model.
Figure 15
Figure 15
Hydration ratios for each carbohydrate residue of the GPI in the (a) all-atom and (b) coarse-grained system.
Figure 16
Figure 16
Comparison of density distributions of each residue of the GPI away from the bilayer center along the bilayer normal between the (a) all-atom and (b) coarse-grained systems.
Figure 17
Figure 17
Comparison of end-to-end (Ree) distance and radius of gyration (Rg) of GFP-attached-GPI between four different 1 μs long all-atom (black, red, green, blue) and a 4 μs long coarse-grained (orange) trajectories.
Figure 18
Figure 18
Comparison of tilt angle of (a) GFP and (d) GPI between four independent all-atom (black, red, green, blue) and coarse-grained (orange) systems. Parts (b) and (c) show tilt angles of GFP, and parts (e) and (f) show tilt angles of GPI. Tilt angle ϕz of GFP is defined as the angle between the bilayer normal (z axis) and the vector connecting the purple residues (glutamine and histidine). (d) Tilt angle ξz of GPI is defined in the same way as in Figure 13c.
Figure 19
Figure 19
GFP-GPI inserted into DMPC lipid bilayers at atomistic and coarse-grained resolutions in (a) and (b), respectively.
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