title: Detailed mechanism for AmtB conducting NH4+/NH3: molecular dynamics simulations.
abstract: The mechanism by which the ammonium transporter, AmtB, conducts NH4+/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.
authors.affiliation: Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Science and Graduate School, Chinese Academy of Sciences, Shanghai 201203, China.
authors.forename: Huaiyu
authors.initials: H
authors.lastname: Yang
authors.forename: Yechun
authors.initials: Y
authors.lastname: Xu
authors.forename: Weiliang
authors.initials: W
authors.lastname: Zhu
authors.forename: Kaixian
authors.initials: K
authors.lastname: Chen
authors.forename: Hualiang
authors.initials: H
authors.lastname: Jiang
mesh_terms: D027682:Cation Transport Proteins / Q000737:chemistry* / Q000648:ultrastructure*; D002462:Cell Membrane / Q000737:chemistry*; D003198:Computer Simulation; D029968:Escherichia coli Proteins / Q000737:chemistry* / Q000648:ultrastructure*; D015640:Ion Channel Gating; D007700:Kinetics; D008956:Models, Chemical; D008958:Models, Molecular; D011487:Protein Conformation; D000644:Quaternary Ammonium Compounds / Q000737:chemistry*
chemical_list: C111096:AmtB protein, E coli; D027682:Cation Transport Proteins; D029968:Escherichia coli Proteins; D000644:Quaternary Ammonium Compounds