Figure 6.

Conformational changes in the isolated ATP-bound and apo NBD. (A) RMSD of Cα atoms in the simulations of the isolated Sav1866 NBD monomer; ATP-bound (black), apo (red). (B) Projection of the ANM mode 1 on the Cα trajectory of the simulations of the isolated Sav1866 NBD monomer; ATP-bound (black), apo (red). Projection is in nanometres. (C) Comparison of rotation axes of the HD in the simulations and the ANM analysis. Stereo representation of the Sav1866 NBD with the HD depicted as the three differently shaded helices on the right side of each structure and the remainder of the NBD shaded differently, on the left and centre of each panel. The rotation axes of the HD are shown by long lines. The shorter lines connect the centre of mass of the rotating domain with the pivot point on the rotation axis. The pivot points are proximal to the loop joining the C-terminal of the HD to the core subdomain approximately at the bottom middle of the NBD. Principal component analysis of the Cα trajectories were performed and the hinge axes calculated between the maximum and minimum projection structures. ANM mode 1 (blue), apo NBD simulation 3B (purple), apo NBD simulation 2A (blue), apo NBD simulation 2A (green) (Color online.)