(A) Definition of displacements (denoted by ) and angles. Longitudinal (), normal (), and transverse () displacements of the central -sheet are shown. Displacements of , Q320 of , and are similarly defined. For orientation, forward tilt (), transverse tilt (), and azimuthal () angles of the central -sheet were measured. For , the angle is relative to the transverse direction. For , the transverse tilt () and azimuthal () angles were measured. (B–G) Average and RMSD of the measured quantities relative to the first frame of ATP during the last 500 ns of each simulation. (B–E) Translation, (F,G) Rotation. In (B), translation of was measured using Q320 on its C-terminal end. Notable differences between pre- and post-stroke states are summarized in Figure 3A,B. In (F), the sign of is inverted for the plot. It increases in the pre-stroke state, similar to in (G). (H) Water density map (blue) near and MT. Last 500 ns of ATP was used for calculation. A density cutoff of 0.033 Å(bulk density) was used for visualizing the map. Compare with Figure 3C. (I–K) Decomposition of the binding energy between kinesin and tubulin (in kcal/mol units). (I) Combined electrostatic interaction and the generalized-Born solvation free energy. (J) van der Waals energy, (K) Nonpolar energy, which approximately follows the van der Waals profile. (L) The net binding energy (sum of the energies in (I–K)) between kinesin and -tubulin (triangle), -tubulin (square), and together (solid circle). More negative energy indicates stronger binding. Note that conformational entropy is not included in the energy calculation.