Figure 5.

Vector projections showing the normalized magnitude of piston-like motions (in Å) within α-helix 4 of pTsr bound to (A) (R)-DHMA and (B) (S)-DHMA with respect to the simulated time (in nanoseconds). The projection values plotted correspond to projected lengths, p_i, calculated using Eq. 2 and extracted every 1 ns. Solid lines correspond to Bezier curves fitted to projected lengths extracted every 0.1 ns. Blue, red, black, yellow, and pink data points and lines correspond to data extracted from the first, second, third, fourth, and fifth simulations, respectively, for each of the complexes. The differences in initial points are attributed to the initial structure corresponding to the binding mode identified by our docking-refinement protocol as well as the use of a short equilibration stage before the 100-ns MD simulations. To see this figure in color, go online.