Minimum Free Energy Path of Ligand-Induced Transition in Adenylate Kinase
Figure 4
Two-dimensional PMF surface of the motion of the ligand along the MFEP.
(A) PMF is projected onto the MFEP images and onto the 1st PC of the xyz-coordinates of the mass center of the AMP adenine. The PMF is represented by the colored contour lines. (B) Tens of the MD snapshots are superimposed at (left image), and 4 snapshots shows the misbinding between the AMP ribose and Asp84 at
(right image). The hydrogen bonds are indicated by the dashed yellow lines.