Fig. 4: With only one hRpn13, ENT remains bound to Pru-A or Pru-B following MD but loses its U-shape.

a Positioning of ENT in the crystal structure (0 ns, T_{0 ns}) and after 100 ns (T_{100 ns}) of MD simulation for Pru-A (purple) or Pru-B (blue). Cartoon representations are displayed with coloring of Fig. 2a for T_{100 ns} and with hRpn13 and ENT in gray for (T_{0 ns}) starting crystal structure. b Plot for the distance between the Cβ atom of non-native ^bP and Cα atom of native T3 throughout a 100 ns MD simulation performed with Pru-A (purple), Pru-B (blue) or all three (orange) hRpn13 Pru molecules. c) An expanded view of Pru-A with ENT (colored as in a) after 100 ns of MD simulation highlights interactions between M1 and P40, S90, and W108. d Enlarged view of hRpn13 Pru bound to ENT to highlight the atom-to-atom distances plotted in panels (e, f). These distances are between hRpn13 Pru-A M1 Cγ, S, or Cβ and P40 Cβ, S90 Oγ, or W108 Cε3, respectively and between P40 Cβ and ^dS Cβ⊡ e, f) Plots (n = 1001) of Pru-A:ENT pairwise distances as a function of time (e) or violin plot (f) throughout 100 ns of molecular dynamics for the atom-atom pairs shown in panel (d). The median value is represented by a dashed line, and the first/third quartiles are represented by dotted lines. g An expanded view of Pru-B with ENT after 100 ns of MD simulation highlights interactions between D78, D79 and K99 with ^aG, ^cG, and ^dS, respectively. h Enlarged view of hRpn13 Pru-B bound to ENT to highlight the atom-to-atom distances plotted in panels (i, j). These distances are between hRpn13 Pru-B F76 Cε2 to M1 Cε, D78 Cγ to ^aG or ^cG backbone nitrogen, D79 Cγ to ^dS backbone nitrogen, and K99 sidechain Nζ to carbonyl of ^aG or ^bP. i, j Plots (n = 1001) of Pru-B:ENT pairwise distances as a function of time (i) and violin plots (j) throughout 100 ns of molecular dynamics for the atom-atom pairs shown in panel (h). Median values are represented by dashed lines, and the first/third quartiles are represented by dotted lines. Source data for (b, e, f, i and j) are provided in the Source Data file.