Fig. 6: Predicted lipid interactions and K33ASSP stabilization of JUNV GPC TM regions.
From: Molecular organization of the New World arenavirus spike glycoprotein complex
a, Membrane-embedded JUNV GPC used for molecular dynamics (MD) simulations. MD simulations were performed in triplicate (n = 3). See Extended Data Fig. 7 for additional information. b, JUNV GPC A33SSP and neighbouring residues in the cryo-EM structure. Relevant distances are shown as dashed lines. c, JUNV GPC A33SSP in a representative frame focused on a pocket at the SSP-GP2 interface at the end of the MD simulation. POPC, phosphatidylcholine. d, Top view of the JUNV GPC A33SSP GPC TM helices in a representative frame at the end of the simulation. In addition to the POPC tail occupying one of the pockets, the other pockets are occupied by a second POPC and a palmitoylsphingomyelin (PSM) tail. e,f, Structure of A33SSP JUNV GPC showing lipid-like cryo-EM density occupying the pocket in a side (e) or top view (f). Part of a lipid tail is modelled (yellow sticks) for illustrative purposes. g, WT JUNV GPC (K33SSP, modelled in silico) and neighbouring hydrophobic residues. Relevant distances are shown as dashed lines. h, JUNV GPC K33SSP in a representative frame focused on the pocket at the end of the MD simulation. The pocket is occupied by a POPC lipid tail. i, Top view of the JUNV GPC K33SSP TM helices in a representative frame at the end of the simulation. In addition to the POPC lipid tail occupying one of the pockets, the two other pockets are occupied by 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoserine (POPS) lipid tails. j, JUNV GPC SSP with dashed boxes serving as points of reference for plots shown in k. k, RMSF plots for the SSP chains. l, GP2 TM α-helix (residues 420–442). m, RMSF plots for the GP2 TM (α6) helices (residues 420–442). n,o, Mean RMSF values during MD simulations for the SSP protomers (n) or the GP2 TM α-helices (o) plotted for the WT (K33SSP) and A33SSP JUNV GPC. Error bars represent standard errors. In n and o, comparison between two groups was performed using an unpaired, two-tailed Student’s t-test. **P = 0.003, ****P < 0.0001.
