Minimum Free Energy Path of Ligand-Induced Transition in Adenylate Kinase

doi:10.1371/journal.pcbi.1002555

Minimum Free Energy Path of Ligand-Induced Transition in Adenylate Kinase

Figure 6

Dehydration of an occluded water around the P-loop.

The isosurface representation of the 3D distribution function of water oxygen (red) and hydrogen (white) around the P-loop at (A) , (B) 41, and (C) 42. The surfaces show the areas in which the atoms are distributed four times as probably as in the bulk phase. For comparison, the oxygens of crystal waters are shown for (D) the open (PDBid: 4ake) and (E) closed conformations (PDBid: 1ake). An occluded water molecule at and the corresponding crystal water of the open form are indicated by the circles. (F) Two-dimensional PMF surface as a function of the MFEP images and the distances of the LID-CORE domains. The PMF is represented by the colored contour lines. Regions of physical events (AMP-binding and dehydration) are encircled.

doi: https://doi.org/10.1371/journal.pcbi.1002555.g006