Minimum Free Energy Path of Ligand-Induced Transition in Adenylate Kinase
Figure 5
Committor tests characterizing the TSE.
(A) The binned distributions of the final structures after 10 ns unrestrained MD simulations (blue bars), assigned by index of the nearest MFEP image (i.e., classified by the Voronoi tessellation). The MD simulations were executed from different initial distributions (red bars) at , 33, and 34. (B) The average structures of the MFEP images at
(before the TSE), and 34 (after the TSE). The ligand and the residues of Thr31, Lys57, Arg88, Gly85, and Gln92 are represented by sticks. The hydrogen bonds are indicated by the dashed yellow lines.