Minimum Free Energy Path of Ligand-Induced Transition in Adenylate Kinase
Figure 2
PMF along the strings and the corresponding domain motions.
(Top) PMFs along the snapshots of the strings for (A) apo and (B) holo-AK at t = 0 (initial path), 2, 4, 6, 8, 10, 12 (MFEP) ns. The indices of string images are numbered from the open (PDBid: 4ake) to closed crystal structures (PDBid: 1ake). Partially-closed state of apo-AK and a substantial PMF barrier of holo-AK are encircled. (Bottom) Projections of MFEP onto the space defined by the distances of mass centers between the LID-CORE and AMPbd-CORE domains, for (C) apo and (D) holo-AK. The black curves indicate the initial paths (t = 0), and the red curves are the MFEPs (t = 12 ns). The PMF is visualized by the colored contour lines (delineating regions of low energy (blue) to regions of high energy (red)).