Detailed mechanism for AmtB conducting NH₄⁺/NH ₃: Molecular dynamics simulations

The mechanism by which the ammonium transporter, AmtB, conducts NH ₄⁺/NH₃ into the cytoplasm was investigated using conventional molecular dynamics (MD) simulations. These simulations revealed that the neutral molecule, NH₃, passes automatically through the channel upon its arrival at the Am2 site and that the function of the channel as a one-way valve for passage of NH₃ is not determined by the cytoplasmic exit gate but, rather, by the periplasmic entrance gate of the channel. The NH₃, produced by deprotonation of NH₄ ⁺ at the entrance gate, is spontaneously conveyed to the central region of the channel via a hydrogen-bond network comprising His-168, His-318, Tyr-32, and the NH₃ molecule. Finally, the NH₃ molecule exits the channel through the exit gate formed by Phe-31, Ile-266, Val-314, and His-318. In addition, Ser-263 is shown to play a critical role in the final stages, acting as a pivoting arm to shunt the NH₃ molecule from the cytoplasmic exit gate of the channel out into the cytoplasm. This finding is further supported by another simulation which shows that NH₃ fails to be translocated through the channel formed by the Ser-263-Ala mutation. Thus, this study casts new insights on the mechanism of AmtB-mediated passage of NH₃ across cellular membranes.