Decipher the Mechanisms of Protein Conformational Changes Induced by Nucleotide Binding through Free-Energy Landscape Analysis: ATP Binding to Hsp70
Figure 9
Analysis of the FEL of ATP-bound DnaK.
A: FES generated from dPCA of MD run ATP1. Minima and saddle points are shown with gray (green for the most probable one) and red diamonds, respectively. The PME is represented by the red line. B: Free-energy VPME along the PME for the transition A1→A2→A3→A4→A5. C: Results of the clustering along the PME. Each frame is represented at the corresponding time t observed in the MD trajectory.