Simulations of Ammonium Transport in the AmtB Protein

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IBI SEMINAR SERIES
Simulations of Ammonium Transport in the AmtB
Protein Guillaume Lamoureux Assistant
Professor Department of Chemistry and
Biochemistry, Concordia University Montreal,
Quebec Friday November 7, 2008 1200
Noon Biological Sciences 211 University of
Calgary Host Sergei Noskov
Abstract Bacteria, yeast and plants under low
ammonium concentrations express proteins from the
Amt/MEP family that have a high affinity for
ammonium and facilitate its transport across the
membrane. Despite a number of x-ray structures of
Amt/MEP proteins now available, the nature of the
chemical species found along the permeation
pathway remains highly ambiguous. Experiments in
bacteria suggest a net transport of NH3, but
experiments in plants suggest a net transport of
NH4. Using molecular dynamics simulations, we
examine the relative stabilities of various
conformations of water, ammonia (NH3) and
ammonium (NH4) in the pore of Escherichia coli's
AmtB. We re-assess some of the currently accepted
views on the transport mechanism in AmtB, and put
forward new mechanisms that are compatible with a
net charge transporteither in the form of a NH4
transport or of a NH3/H co-transport. On a more
technical note We account for the high
cooperativity of cation-pi interactions between
NH4 and the aromatic residues lining the AmtB
pore by using a polarizable force field based on
classical Drude oscillators. The talk will also
cover our recent developments on the molecular
mechanics models of aromatic compounds and
cation-pi systems.
Pizza and pop will be provided