Figure 5: 1D Potential of mean force of the swiveling motion of the CD with the distance H456Cα − H565Cα used as a reaction coordinate.
From: Structural intermediates and directionality of the swiveling motion of Pyruvate Phosphate Dikinase
Results for the non-phosphorylated state are depicted in (a–c), those for the state with phosphorylated H456 in (d–f). (a,d) depict results obtained with open NBD, (b,e) those with a simultaneous opening-closing of the NBD, and (c,f) with closed NBD. At the top, schematic representations of each state at the respective endpoints of a PMF are shown. In the middle row, sampled conformations are projected onto distanceCD–PBD and distanceNBD1 − NBD3 (Supplementary Fig. 4c), with each color representing one MD simulation with an umbrella potential applied at a given value of distanceCD–PBD. The PMFs are depicted in the bottom row. The diamonds show projections of PPDK crystal structures in conformational states marked by Roman numbers (Fig. 4a) onto the plane spanned by the two reaction coordinates (using for each organism the corresponding residues to evaluate the reaction coordinates (Supplementary Tab. 1))
