The structural differences between E. coli AmtB and the human RhCG as well as the Rh50 from Nitrosomonas europaea suggest different ammonia conduction mechanisms for the AmtB and the Rh proteins. This study investigates the mechanism differences by using molecular dynamics simulations on RhCG and Rh50NE structures. Unlike AmtB the Rh proteins lack the aromatic cage at the bottom of the periplasmic vestibule. This report establishes the periplasmic Glu residue as the NH+4？binding site for Rh proteins, and the two Phe residues at the entrance of the pore as the NH3 binding site. The？NH+4？molecule pushed by another ammonium releases one of its protons on its way to the phenyl gate. This study also discovers that, unlike AmtB, the Rh protein pores allow water molecules, which eventually facilitates the NH3 conduction from periplasm to cytoplasm.
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