The transmembrane protein AmtB has an important role in ammonium transport, especially at low external ammonium concentrations.  However, whether AmtB is just a channel that permeates NH3 or a co-transporter that transports NH3 and H+ at the same time is still a question. To study the mechanism of ammonium transport through AmtB, an extensive series of hybrid Quantum Mechanical(QM)/Molecular Mechanical(MM) simulations has been performed. Emphasis has been placed on the deprotonation mechanism of ammonium. Results of Constraint Dynamics simulations have been combined to obtain the Potentials of Mean Force for two possible deprotonation paths: One through protein side chains and the other through solvents. A comparison of the energy barriers reveals the more possible pathway. Statistical results on the solvent and ammonium distribution inside the pore is also shown and the possible mechanisms of ammonia re-protonation and how side chains return back to original state are also presented.

Computational study of the ammonium transport mechanism in AmtB: NH3 permeation vs. NH3/H+ Co-transport

240th National Meeting (2010)

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