Figure 5
Proposed conformations of naturally isopeptide-linked Ub2s originating from non-canonical Lys11- (colored in red, left), and Lys27-linkage (colored in blue, right). These two structures have been obtained from an ensemble of simulated Ub2 conformations lowest in free energy by using a combination of the experimental and simulated data presented in this study. The proximal Ub2 moieties are colored in light gray whereas the distal moieties are colored in red (in case of Lys11-linkage) and in blue (in case of Lys27-linkage), respectively. Individual R2/R1 values obtained for the proximal Ub2 moieties (Figs. S13C, S14B) indicating backbone dynamics on the fast NMR time scale are shown in putty mode. Values lower than the 10% trimmed mean are shown in thick mode, values larger than the 10% trimmed mean are shown in thin mode in respective proximal moieties (continuous scale). Chemical shift perturbations shown in Fig. 1C are highlighted by using violet color for Δω values larger the mean and dark purple color for Δω values larger the mean plus one standard deviation. The conformational space covered by the distal Ub2 moiety obtained from MD simulations is illustrated in mesh mode and is based on four representative structures of the dominant minima in free energy found in the coarse grained simulations. The configuration of Ub2 that fits best to the experimentally obtained NMR data is highlighted by presenting the distal moiety in cartoon mode. The structures have been created by using the PyMOL Molecular Graphics System, Version 2.4.0a0, Schrödinger, LCC (www.pymol.org).
