Minimum Free Energy Path of Ligand-Induced Transition in Adenylate Kinase
Figure 3
PMFs of the domain motions and the RMSF along the MFEP.
(Top) PMF along the MFEP as a function of the inter-domain distances between (A) the LID-CORE and (B) AMPbd-CORE domains. The blue and red curves illustrate the results for apo-AK and holo-AK, respectively. The error bars are the statistical uncertainties relative to the PMF minimum. Note that the uncertainties are small because the domains were restricted to the regions around the MFEP. (Bottom) The RMSF of the atoms along the MFEP is shown as a function of the MFEP images for (C) apo and (D) holo-AK. The “cracked” regions with large RMSF values, around the LID-CORE hinge and P-loop, are encircled.