Decipher the Mechanisms of Protein Conformational Changes Induced by Nucleotide Binding through Free-Energy Landscape Analysis: ATP Binding to Hsp70
Figure 10
Comparison between MD data and EPR experiments.
Histograms of the distance E430-R547 computed from the MD simulations in the APO state (panels A and C, red) and in the ATP-bound state (panels B and D, green). Panels A and B represent the distributions up to 20 Å, as in the EPR experiments and panels C and D represents the same distributions up to 40 Å. Each subpopulation in the distance distribution was fitted with a Gaussian function shown with black lines. The black arrows in panels A and B represent the experimental results from Ref. [81]. FEP V(γ504) computed from different subpopulations relative to the distance E430/R547 distribution function in the APO state (panel E) and in the ATP state (panel F). <d> represents the mean value of the Gaussian distributions shown in panel C for the APO-DnaK and D for the ATP-DnaK.