Figure 7
(a) Root Mean Square Deviation (RMSD) for the C-alpha atoms is shown for both VcHutB (blue) and VcFhuD (green) for the full simulation range. (b) The Root Mean Square Fluctuation (RMSF) of the Cα atoms was calculated from the simulation trajectories and then converted into the B-factor of the Cα atoms. VcHutB protein is clearly showing more fluctuations than VcFhuD. Visualization of (c) VcFhuD and (d) VcHutB, as predicted by PCA. The conformations are aligned with respect to the N-lobe to show the inter-domain movement. (e) Snapshots of MD trajectories of VcFhuD are superimposed to show the dynamics of the residues at the binding site. (f) Superposition of ferri-desferal bound VcFhuD structure on that of EcFhuD to show the spatial disposition of different important residues at the binding site. (g) Docking of ferri-enterobactin at the ligand binding pocket of VcFhuD. (h) Superposition of the snapshots of MD simulation trajectories to show the movement of Y65 and H164 in VcHutB. (i) MD simulations show the dynamics of the substrate binding region between the N and C-lobes of VcHutB. The distance between the Cα atoms of Y65 and H164 is shown against the simulation time (inset).
