Decipher the Mechanisms of Protein Conformational Changes Induced by Nucleotide Binding through Free-Energy Landscape Analysis: ATP Binding to Hsp70
Figure 2
Cartoon representation of the representative structures obtained by MD simulations.
A: MD runs APO1 (red) and APO2 (firebrick). B: MD runs ADP1 (blue) and ADP2 (light blue). C: MD runs ATP1 (green) and ATP2 (pale green). The NMR-derived structure used as starting point for the MD simulations (PDB ID: 2KHO) [70] is shown in transparent gray. Representative structures are extracted from a dPCA on the CGDAs γ (see Methods section). These figures were prepared with PyMOL [http://www.pymol.org].