Unidirectional Mechanistic Valved Mechanisms for Ammonia Transport in GatCAB KangJiyoung KuroyanagiShigehide AkisadaTomohiro HagiwaraYohsuke TatenoMasaru 2012 Glutamine amidotransferase CAB (GatCAB), a crucial enzyme involved in translational fidelity, catalyzes three reactions: (i) the glutaminase reaction to yield ammonia (NH<sub>3</sub> or NH<sub>4</sub><sup>+</sup>) from glutamine, (ii) the phosphorylation of Glu-tRNA<sup>Gln</sup>, and (iii) the transamidase reaction to convert the phosphorylated Glu-tRNA<sup>Gln</sup> to Gln-tRNA<sup>Gln</sup>. In the crystal structure of GatCAB, the two catalytic centers are far apart, and the presence of a hydrophilic channel to transport the molecules produced by the reaction (i) was proposed. We investigated the transport mechanisms of GatCAB by molecular dynamics (MD) simulations and free energy (PMF) calculations. In the MD simulations (in total ∼1.1 μs), the entrance of the previously proposed channel is closed, as observed in the crystal structure. Instead, a novel hydrophobic channel has been identified in this study: Since the newly identified entrance opened and closed repeatedly in the MD simulations, it may act as a gate. The calculated free energy difference revealed the significant preference of the newly identified gate/channel for NH<sub>3</sub> transport (∼10<sup>4</sup>-fold). In contrast, with respect to NH<sub>4</sub><sup>+</sup>, the free energy barriers are significantly increased for both channels due to tight hydrogen-bonding with hydrophilic residues, which hinders efficient transport. The opening of the newly identified gate is modulated by Phe206, which acts as a “valve”. For the backward flow of NH<sub>3</sub>, our PMF calculation revealed that the opening of the gate is hindered by Ala207, which acts as a mechanistic “stopper” against the motion of the “valve” (Phe206). This is the first report to elucidate the detailed mechanisms of unidirectional mechanistic valved transport inside proteins.