Molecular determinants for binding of ammonium ion in the ammonia transporter AmtB-A quantum chemical analysis.

The transport of ammonium across the cell membrane represents an important biological process in all living organisms. The mechanisms for ammonium translocation were analyzed by computer simulations based on first principles. Intermolecular interaction energies between the differentially methylated ammonium and the ammonium channel protein AmtB were calculated by means of the supermolecular approach at the MP2/6-311+G* level based on the high-resolution crystal structures of ligand-bound protein complexes. Our analysis attributes the molecular determinants for protein-ligand recognition in ammonium transporter AmtB to the aromatic cage formed by three aromatic residues Phe103, Phe107, and Trp148, as well as Ser219. The former residues are involved in cation-pi interactions with the positively charged methylated ammoniums. The latter residue acts as a hydrogen bond acceptor to ammonium. Thus, this work provides directly the missing evidence for the hypothesized role played by the wider vestibule site of AmtB at the periplasmic side of the membrane in "recruiting" NH(4)(+) or methylammonium ions as proposed by Khademi et al. (Science 2004, 305, 1587). In addition, a hybrid quantum mechanics/molecular mechanics scheme was applied to optimize the structures of differentially methylated ammoniums in the AmtB protein, which generated structural and energetic data that provide a satisfactory explanation to the experimental observation that tetramethylammonium is not inhibitory to conducting ammonium and methylammonium in the ammonium transport channel.