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Thermodynamics of Transport Through the Ammonium Transporter Amt‑1 Investigated with Free Energy Calculations
journal contribution
posted on 2016-02-20, 14:30 authored by R. Thomas Ullmann, Susana L. A. Andrade, G. Matthias UllmannAmt-1 from Archaeoglobus fulgidus (AfAmt-1) belongs to the Amt/Rh family of ammonium/ammonia transporting
membrane proteins. The transport mode and the precise microscopic
permeation mechanism utilized by these proteins are intensely debated.
Open questions concern the identity of the transported substrate (ammonia
and/or ammonium) and whether the transport is passive or active. To
address these questions, we studied the overall thermodynamics of
the different transport modes as a function of the environmental conditions.
Then, we investigated the thermodynamics of the underlying microscopic
transport mechanisms with free energy calculations within a continuum
electrostatics model. The formalism developed for this purpose is
of general utility in the calculation of binding free energies for
ligands with multiple protonation forms or other binding forms. The
results of our calculations are compared to the available experimental
and theoretical data on Amt/Rh proteins and discussed in light of
the current knowledge on the physiological conditions experienced
by microorganisms and plants. We found that microscopic models of
electroneutral and electrogenic transport modes are in principle thermodynamically
viable. However, only the electrogenic variants have a net thermodynamic
driving force under the physiological conditions experienced by microorganisms
and plants. Thus, the transport mechanism of AfAmt-1 is most likely
electrogenic.
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electrogenic variantsbinding formsArchaeoglobus fulgidusmembrane proteinscontinuum electrostatics modelpermeation mechanismtransport modeAmmonium Transportertransport mechanismtransport modesOpen questions concernelectrogenic transport modesenergy calculationstransport mechanismsprotonation formsFree Energy CalculationsAmt
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