Paper Citing NAMD - Abstract
Lamoureux, Guillaume; Klein, Michael L.; Berneche, Simon
A stable water chain in the hydrophobic pore of the AmtB ammonium transporter
BIOPHYSICAL JOURNAL, 92:L82-L84, MAY 1 2007
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 (NH3) molecules diffusing in a single. le fashion. The probable presence of water molecules in the pore would influence the relative stability of NH3 and NH4+, and thus calls for a reassessment of the overall permeation mechanism in ammonium transporters.
