A network of molecular switches controls the activation of the two-component response regulator NtrC

Abstract

Recent successes in simulating protein structure and folding dynamics have demonstrated the power of molecular dynamics to predict the long timescale behaviour of proteins. Here, we extend and improve these methods to predict molecular switches that characterize conformational change pathways between the active and inactive state of nitrogen regulatory protein C (NtrC). By employing unbiased Markov state model-based molecular dynamics simulations, we construct a dynamic picture of the activation pathways of this key bacterial signalling protein that is consistent with experimental observations and predicts new mutants that could be used for validation of the mechanism. Moreover, these results suggest a novel mechanistic paradigm for conformational switching.

Protein Allostery and Conformational Dynamics

“…30–31,69 In these models, microstates are obtained by clustering snapshots according to structural similarity, and transition probabilities between microstates are estimated from molecular dynamics trajectories.…”

Optimized parameter selection reveals trends in Markov state models for protein folding

“…In this case, the similarity of structures is judged by their root-mean-square deviation (RMSD) of atomic distances. 14,19,20,30,33,34,36,[50][51][52][53] While this process does not explicitly extract "features," it can be interpreted as a replacement for explicit featurization.…”

“…The clustering step reduces the representation of each frame in the time-series to a single integer (the cluster assignment) and it is from this representation that the MSM is constructed. Commonly used clustering algorithms include k-centers, 16,21,30,35,36,38,39,65 k-medoids, 53 and k-means. 44,66,67 More sophisticated methods, such as Ward's method, 34,68,69 have also been used.…”

To ∼P or Not to ∼P? Non‐canonical activation by two‐component response regulators

“…In the presence of the HK or a small molecule phosphodonor such as acetyl phosphate or phosphoramidate, the threonine side‐chain moves to form a charge‐dipole interaction with the newly arrived phosphoryl moiety, a movement that is transmitted to the β4–α4 loop and is also tracked by the closely packed tyrosine side‐chain. This ‘aromatic switch’, where the tyrosine moves from an exposed to a buried position, may be a general mechanism for intramolecular signalling in many RR proteins (Lee et al ., ), although it does not appear to be valid for NtrC (Villali et al ., ; Pontiggia et al ., ; Vanatta et al ., ). What remains less clear at present is how this conformational change is propagated to the C‐terminal effector domain.…”