Decipher the Mechanisms of Protein Conformational Changes Induced by Nucleotide Binding through Free-Energy Landscape Analysis: ATP Binding to Hsp70
Figure 4
Contact maps from ATP-bound and ADP-bound MD trajectories.
A: Interdomain interactions extracted from the contact map difference ATP/ADP (see text for details). Residues involved in the interdomain interactions are shown in stick representation. The color code is the same as in Fig. 1. B: Interactions between the ATP nucleotide and the NBD of DnaK from ATP-bound MD trajectories. C: Three-dimensional representation of the interactions between ATP and the NBD. Residues of the NBD in contact with ATP are shown in stick representation. The color code of the protein structure is the same as in Fig. 1. These figures were prepared with PyMOL [http://www.pymol.org].