Fig. 5.

Time evolution of various structural descriptors, following trans-to-cis ligand-switching of PDZ2. Shown are means (blue) and rmsd (orange) of ${\mathrm{C}}_{\alpha }$ distances $d_{\mathrm{20,71}}$ (A) and $d_{\mathrm{4,55}}$ (B), as well as populations of conformational states (C, D, and F). For easier representation, all MD data were smoothed. Starting at time $t\hspace{0.17em}=\hspace{0.17em}0$ almost completely in state 1, we compare results from the nonequilibrium MD simulations (C) with the corresponding predictions of an MSM (D). (E) Network representation of the MSM. The size of the states indicate their population, the thickness of the arrows and numbers indicate the transition times (in microseconds). For clarity, we discard transitions that take longer than 2.5 μs. (F) MSM simulations of the trans-to-cis transition, using trans equilibrium initial conditions.