Dynamic Fluctuations Provide the Basis of a Conformational Switch Mechanism in Apo Cyclic AMP Receptor Protein
Figure 6
Ensemble of CRP conformations.
Ensemble of structures (dynamic states) are selected according to their dynamic behavior among the MD cluster best member structures with a cluster radius of 3.5 Å. The ribbon diagrams are color coded with the correlation values of the L134-D138 region (average) with the rest of the structure. The difference-correlations maps for each structure in the ensemble with respect to the holo CRP dimer are given: (A) The L134-D138 hinge of both subunits (A/a& B/b) displays apo-like behavior with relatively strong coupling with the DNA binding domain of its own subunit (higher positive values), relatively weak coupling with the L134-D138, K52-E58 and G173-V176 regions of the other subunit (higher negative values), and weak coupling between the K52-E58 and G173-V176 sites (higher negative values). (B) This structure is the one that displays the closest dynamic behavior in overall to the holo state with respect the both subunits (A/a&B/b); theL134-D138 hinge is not strongly correlated with the DNA binding domain of its own subunit (lower positive values), and not weakly correlated with the K52-E58 and G173-V176 sites (lower negative values) compared to (A). (C) Subunit A/a displays more holo-like behavior while subunit B/b assumes apo-like behavior following the L134-D138 hinge dynamics. See (B) for the dynamics of subunit A/a and see (A) for the dynamics of subunit B/b.