Characterizing the Hydration Properties of Proton Binding Sites in the ATP Synthase c-Rings of Bacillus Species

The Journal of Physical Chemistry. B
Alexander KrahPeter J Bond

Abstract

The membrane-embedded domain of ATP synthases contains the c-ring, which translocates ions across the membrane, and its resultant rotation is coupled to ATP synthesis in the extramembranous domain. During rotation, the c-ring becomes accessible on both sides of the lipid bilayer to solvent via channels connected to the other membrane-embedded component, the a subunit, and thereby allows the ion to be released into the solvent environment. In recent times, many experimental structures of c-rings from different species have been solved. In some of these, a water molecule with a proposed "structural role" has been identified within the c-ring ion binding site, but in general, the requirement for high resolution to resolve specific water densities complicates their interpretation. In the present study, we use molecular dynamics (MD) simulations and rigorous free energy calculations to characterize the dynamics and energetics of a water molecule within the ion binding site of the c-ring from Bacillus pseudofirmus OF4, in its wild type (WT) and P51A mutant forms, along with the c-ring from thermophilic Bacillus PS3. Our data suggest that a water molecule stably binds to the P51A mutant, as well as helping to identify a bound water mo...Continue Reading

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Citations

Oct 19, 2020·Biochimica Et Biophysica Acta. General Subjects·Alexander KrahDuncan G G McMillan
Nov 13, 2020·The Journal of Physical Chemistry. B·Siewert J Marrink, Ilya Levental

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