Abstract
The mechanism by which proteins of the Amt/MEP/Rh family transport ammonium remains largely unknown. No convincing mechanistic picture has emerged yet as to whether it is an electroneutral NH3 transport or an electrogenic NH3/H+ co-transport. using free energy calculations with polarizable force fields and with hybrid QM/MM descriptions, we have investigated the binding of ammonium and its transport across the pore of Escherichia coli's AmtB protein. The simulations reveal a novel cotransport mechanism in which the NH4+ substrate binds deeply into the pore and translocates as separate NH3 and H+ fragments. Critical to the cotransport mechanism is a pair of highly-conserved histidine residues, that enhance NH4+ binding, form a “proton wire” for charge transfer, and provide a scaffold for a water chain in the pore lumen.
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