Allostery and folding of the N-terminal receiver domain of protein NtrC

The N-terminal receiver domain of protein NtrC (NtrC(r)) exhibits allosteric transitions between the inactive (unphosphorylated) and active (phosphorylated) state on the microsecond time scale. Using a coarse-grained variational model with coupled energy basins, we illustrate that significant loss of conformational flexibility is the key determinant of the inactive (I) → active (A) state transition mechanism of NtrC(r). In particular, our results reveal that the rearrangements of the native contacts involving the regulatory helix-α4 and the flexible β3-α3 loop upon activation play a crucial role in the activation mechanism. Interestingly, we find that the β3-α3 loop exhibits a gradual decrease in flexibility throughout the activation transition, while helix-α4, in contrast, becomes more rigid abruptly near the free energy barrier separating the two states. To gain further insight into role these flexible regions play in the transition mechanism, we consider folding of NtrC(r) to both states using a similar model. Our calculated folding routes suggest that helix-α4 becomes structured later when folding to the I state compared to folding of the A state, a result consistent with it is relative conformational flexibility in the two states. Finally, we find a good qualitative agreement between our predicted I → A transition mechanism and the measured backbone dynamics from nuclear magnetic resonance experiments.