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Originally published as Biophys J. BioFAST on March 9, 2007.
doi:10.1529/biophysj.106.102756
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Biophysical Journal 92:L82-L84 (2007)
© 2007 The Biophysical Society

A Stable Water Chain in the Hydrophobic Pore of the AmtB Ammonium Transporter

Guillaume Lamoureux *, Michael L. Klein * and Simon Bernèche {dagger}

* Center for Molecular Modeling, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania; and {dagger} Biozentrum, University of Basel, Basel, Switzerland

Correspondence: Address reprint requests and inquiries to Guillaume Lamoureux, E-mail: lamourgu{at}cmm.upenn.edu; or Simon Bernèche, E-mail: simon.berneche{at}unibas.ch.

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 file fashion. The probable presence of water molecules in the pore would influence the relative stability of NH3 and Formula and thus calls for a reassessment of the overall permeation mechanism in ammonium transporters.




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