title: A stable water chain in the hydrophobic pore of the AmtB ammonium transporter.
abstract: The accessibility of water molecules to the pore of the AmtB ammonium transporter is studied using molecular dynamics simulations. Free energy calculations show that the so-called hydrophobic pore can stabilize a chain of water molecules in a well of a few kcal/mol, using a favorable electrostatic binding pocket as an anchoring point. Moreover, the structure of the water chain matches precisely the electronic density maxima observed in x-ray diffraction experiments. This result questions the general assumption that the AmtB pore only contains ammonia (NH(3)) molecules diffusing in a single file fashion. The probable presence of water molecules in the pore would influence the relative stability of NH(3) and NH(4)(+), and thus calls for a reassessment of the overall permeation mechanism in ammonium transporters.
authors.affiliation: Center for Molecular Modeling, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, USA. lamourgu@cmm.upenn.edu
authors.forename: Guillaume
authors.initials: G
authors.lastname: Lamoureux
authors.forename: Michael L
authors.initials: ML
authors.lastname: Klein
authors.forename: Simon
authors.initials: S
authors.lastname: Bernèche
mesh_terms: D027682:Cation Transport Proteins / Q000737:chemistry* / Q000648:ultrastructure*; D003198:Computer Simulation; D029968:Escherichia coli Proteins / Q000737:chemistry* / Q000648:ultrastructure*; D057927:Hydrophobic and Hydrophilic Interactions; D015640:Ion Channel Gating; D008956:Models, Chemical; D008958:Models, Molecular; D016062:Porosity; D011487:Protein Conformation; D000644:Quaternary Ammonium Compounds / Q000737:chemistry*; D012995:Solubility; D013329:Structure-Activity Relationship; D014867:Water / Q000737:chemistry*
chemical_list: C111096:AmtB protein, E coli; D027682:Cation Transport Proteins; D029968:Escherichia coli Proteins; D000644:Quaternary Ammonium Compounds; D014867:Water