jp0c03896_si_001.pdf (5.03 MB)
Characterizing the Hydration Properties of Proton Binding Sites in the ATP Synthase c‑Rings of Bacillus Species
journal contribution
posted on 2020-08-07, 11:34 authored by Alexander Krah, Jan K. Marzinek, Peter J. BondThe
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 molecule in Bacillus PS3 whose presence was previously overlooked due to the limited
resolution of the structural data. Sequence analysis further identifies
a novel conserved sequence motif that is likely required to harbor
a water molecule for stable ion coordination in the binding site of
such proteins.