We observed a stable water molecule in the site formed by the carbonyl group of the backbone of A461.45, G501.49, and G3267.47 (cluster 3, in pink) in the empty form and Sal-bound receptor.
We, therefore, study the dynamics of the available active state of β2AR in the empty form and in the presence of the biased agonists, hoping to capture characteristics of the β-arrestin active state.
Thus, we noted tightening of interactions between helices 1 and 2 as well as between helices 3 and 7 in the CPB-bound receptor, between helices 6 and 7 in the Sal-bound receptor, and between helices 2 and 7 in the empty form of the receptor (highlighted in bold in Table 4).
To further characterize the aMD simulated conformational ensembles of β2AR in the empty form and bound to biased agonists in a detail, we focus on the appearance or disappearance of interhelical interactions and water clusters in the simulation trajectories, which are distinctive for the crystal structures of the receptor in the inactive and active states.
As expected, the highest fluctuation of the residues is in the empty form (3.4 ± 0.4 Å).
Conformational dynamics of the β2AR active state in the empty form and bound to the agonists were explored using intensive cMD and aMD simulations, which are summarized in Table 1.
Hereby, we extend the simulations of β2AR in the empty form and bound to biased agonists by employing intensive conventional and accelerated MD simulations (cMD and aMD, respectively) to initiate understanding of functional selectivity at the molecular level.
Thus, the active state of the receptor in the empty form and bound with the agonists reaches the projections of the crystal structures of the inactive state along aMD simulations trajectories.
In particular, the transition of the active to inactive conformation requires 17 ± 4 ns in the receptor empty form, whereas the transition occurs in a longer time in the complexed receptor, that is, 156 ± 7 and 274 ± 8 ns bound to CPB and Sal, respectively.
In a recent detailed study of human ARF-6 [44], it was clearly shown that the mutant ARF-6/T27N, considered as a GDP-bound blocked form, was in reality an empty form devoid of nucleotide since the Threonine 27 interacted with both GDP and GTP.
