Comparison and Possible Binding Orientations of SARS-CoV-2 Spike N-Terminal Domain for Gangliosides GM3 and GM1

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The Supporting Information is available free of charge at https://pubs.acs.org/doi/10.1021/acs.jpcb.3c02286.

• Data from the simulations conducted to assess the reproducibility of the results produced by simulations of two different NTD orientations in POPC/CHOL/GM1 and POPC/CHOL/GM3 membrane bilayers. Table S1–S4: The membrane lipid bilayer composition; area per lipid and bilayer thickness of the systems; contribution of the short-range Coulomb (Coul-SR) and Lenard Jones (LJ-SR) energies to the total interaction energy; lateral diffusion coefficient of different lipid components calculated from the independent simulations. Figure S1–S12: The superimposition of our starting conformation of the NTD on the PDB Id 6vsb crystal structure. The total potential energy of the system versus the equilibration time; independent trajectories snapshots showing the time evolution interactions of lipid bilayer ternary mixture with spike NTD receptor orientation I and II; time evolution series for the number of contacts; fractional occupancy of amino acid residues from orientation I and II of NTD around gangliosides GM1 and GM3; preferential partitioning matrix of the lipid bilayers; the density distribution of the angle for the receptor binding pocket vector to the membrane bilayer normal; time evolution RMSD series for backbone beads of NTD; RMSF per ganglioside’s glucose moiety; the center-of-mass (COM) distance between spike NTD receptor and gangliosides GM1 or GM3; radial distribution function g(r) of local GM1/GM3 around the NTD receptor orientation I and II; 2D normalized number density maps in the xy plane of the bilayer for gangliosides. (PDF)