Probing the Flexibility of Large Conformational Changes in Protein Structures through Local Perturbations
For each graph, an experimental measure (grey) is compared to the flexibility calculated from a structure (labeled on the top left of graph) using RIP (blue), ANM (red) or CONCOORD (green). RMSDf is calculated as the mean of the Cα RMSD of the crystal structures if they are found in different states as shown in Figure 1. (A) Flexibility of TIM in the open conformation compared to the RMSDf. (B) Flexibility of TIM in the closed conformation. Flexibilities from the DHFR occluded structure, compared to (C) RMSDf, (D) S2 parameters and (E) Rex factors. (F) Flexibility of ER in the closed conformation compared to the RMSDf. (G) Flexibility of HSP90 compared to the RMSDf.