Decipher the Mechanisms of Protein Conformational Changes Induced by Nucleotide Binding through Free-Energy Landscape Analysis: ATP Binding to Hsp70
Figure 3
Comparison between the simulated and experimental distance distribution functions P(r) of Hsp70 s.
A: Distance distribution function P(r) of the ATP-bound (green lines) and ADP-bound (blue lines) of E. coli DnaK computed from MD simulations (solid lines) and computed from the experimental X-ray (PDB ID: 4BQ9) [69] and NMR-derived (PDB ID: 2KHO) [70] structures (dashed lines), respectively. B: Distance distribution function P(r) of the ATP-bound (green line) and ADP-bound (blue line) of bHsc70. The function P(r) of bHsc70 in the ATP and ADP states were digitized from Figure 4 of Ref. [82].