A stable water chain in the hydrophobic pore of the AmtB ammonium transporter.
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.
Lamoureux
Guillaume
G
Center for Molecular Modeling, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, USA. lamourgu@cmm.upenn.edu
Klein
Michael L
ML
Bernèche
Simon
S
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*
C111096:AmtB protein, E coli; D027682:Cation Transport Proteins; D029968:Escherichia coli Proteins; D000644:Quaternary Ammonium Compounds; D014867:Water