Decipher the Mechanisms of Protein Conformational Changes Induced by Nucleotide Binding through Free-Energy Landscape Analysis: ATP Binding to Hsp70
Figure 1
Nucleotide-dependent conformational states of Hsp70 s.
A: Cartoon diagram of the experimental NMR structure of E. coli ADP-Hsp70 (PDB ID: 2KHO) [70] used as input structure for the MD simulations. B: Cartoon diagram of the experimental X-ray structure of E. coli ATP-Hsp70 (PDB ID: 4B9Q) [69]. C: Schematic representation of the conformational transition as expected from experimental data and observed in MD simulations of ATP-Hsp70, starting from the closed conformation of Hsp70. The color code is the following: NBD-IA (residues 4–37, 112–182 and 363–383; red), NBD-IB (residues 38–111; green), NBD-IIA (residues 183–227 and 311–362; blue), NBD-IIB (residues 228–310; yellow), linker (residues 384–393; black), SBD-β (residues 394–502; magenta) and SBD-α (residues 503–603; cyan). These figures were prepared with PyMOL [http://www.pymol.org].