Extended Data Fig. 8: MACV GPC MD simulations and JUNV GPC K33 position during MD simulations.
From: Molecular organization of the New World arenavirus spike glycoprotein complex
a, Membrane-embedded MACV GPC used for MD simulations performed in triplicate (n = 3). b, A33SSP in the MACV GPC structure. Relevant distances are shown as dashed lines. c, A hydrophobic pocket near A33SSP is occupied by a phosphatidylethanolamine (POPE) lipid tail at the end of the simulation. A representative frame is shown. d, Top view of GPC TM helices at the end of the MD simulation. In addition to the POPE tail occupying one of the pockets, the other pockets are occupied by a palmitoylsphingomyelin (PSM) tail and a phosphatidylcholine (POPC) tail partially occupies another pocket. e,f, Structure of A33SSP MACV GPC showing lipid-like cryo-EM density occupying the pocket in a side view (e) or a top view (f). Part of a lipid tail is modeled (yellow sticks). g, WT MACV GPC (K33SSP, modeled in silico) and neighboring residues. h,i, Representative frames after MD simulation of WT (K33SSP) MACV GPC. A POPE tail is in the pocket. A side view (h) or a top view showing the three binding sites (i) are provided. j–n, Frames from the MD simulations showing the lack of a conserved contacts K33SSP. K33SSP from different SSP protomers are shown. See Fig. 6h for a related frame (SSPA at 500 ns). o,p, RMSF curves for MD simulations of A33SSP (cryo-EM structure) of K33SSP (mutated in silico) for JUNV (u) or MACV (v) GPC. Three thin lines represent individual MD runs, and a thick line represents averaged RMSF values. q, MACV GPC SSP with dashed boxes as reference for the RMSF plots shown in (k). r, RMSF plots for the three MACV GPC SSP chains. s, GP2 TM (α6) TM helix (residues 430–456). t, RMSF plots for the three GP2 TM α-helices. u,v, Mean RMSF values calculated during MD simulations for the SSP protomers (n) or the GP2 TM helices (o). In (n) and (o), comparison between two groups was performed using an unpaired, two-tailed Student’s t-test. Error bars represent standard errors. ****P < 0.0001.
