Molecular Dynamics Simulations of Transducin: Interdomain and Front to Back Communication in Activation and Nucleotide Exchange
The dynamic events that underlie the nucleotide exchange process for the GÎ± subunit of transducin (GÎ±t) were studied with nanosecond time-scale molecular dynamics simulations. The modeled systems include the active and inactive forms of the wild-type GÎ±t and three of its mutants (GDP-bound form only): F332A, A322S, and Q326A that are known to exhibit various degrees of enhancement of their basal and receptor-catalyzed rates of nucleotide exchange (150-fold, 70-fold and WT-like, respectively). The results of these computational experiments reveal a number of nucleotide-dependent structural and dynamic changes (involving the Î±B–Î±C loop, the inter-domain orientation of the helical and GTPase domains and the Î±5 helix) that were not observed in the various crystal structures of GÎ±t. Notably, the results show the existence of a front to back communication device (involving the Î²2–Î²3 hairpin, the Î±1 helix and the Î±5 helix), strategically located near all elements susceptible to be involved in receptor-mediated activation/nucleotide exchange. The wild-type simulations suggest that the dynamic interplay between the elements of this device would be critical for the activation of the GÎ±t subunit. This inference is confirmed by the results of the computational experiments on the mutants that show that even in their GDP-bound forms, the A322S and F332A mutants acquire an “active-like” structure and dynamics phenotype. The same is not true for the Q326A mutant whose structural and dynamic properties remain similar to those of the GDP-bound WT. Taken together the results suggest a nucleotide exchange mechanism, analogous to that found in the Arf family GTPases, in which a partially activated state, achievable from a receptor-mediated action of the front to back communication device either by displacement of the C-terminal Î±5 helix, of the N-terminal Î±N helix, or of the GÎ²Î³ subunit, could precede the dissociation of GDP from the native GÎ± subunit.