8.4 ATP Synthase: The Twofold Rotary Protein Motor of Oxidative Phosphorylation
415
8.36, on the basis of
AGap,
one would expect the
y-rotor to orient with its most hydrophobic face
away from the two catalytic sites containing
ADP-AIF4 and therefore be directed toward
the pE catalytic site containing ADP-SO4. This
is the orientation of the y-rotor in the structure
in Figure 8.36. Before proceeding to the most
significant aspect of the structures in Figures
8.35 and 8.36, however, additional structures
with different p-subunit occupancies can be
examined to address the consistency of the
expectation that the orientation of hydropho-
bic face of the y-rotor would be toward the least
polar occupancy site.
8.4.4.8 Consistency of Least Apolar-Polar
Repulsion Positioning the Hydrophobic
Face with Three Additional and Different
Binding Site Occupancies
In addition to the structures in Figures 8.30^"*
and 8.36,^^ three more crystal structures of the
Fi-ATPase have been determined by the
Walker group. The first of the three involve
the occupancy states of ATP(A), ATP(B),
ATP(C), ADP(D), P04(E), and ATP(F) for the
protein structure listed in the Protein Data
Bank as Structure File 1H8H.^^ The second of
the three involve the occupancy states of
ANP(A), ANP(B), ANP(C), ADP(D), P04(E),
and ANP(F) where PNP may also be repre-
sented as AMPPNP, that is, a nitrogen replaces
the bridge oxygen of ATP between the p-
and y-phosphates; this structure, shown in
Figure 8.37, is listed in the Protein Data
Bank as Structure File lElQ.^^ The third of
the three additional structures involves occu-
pancy states of ANP(A), ANP(B), ANP(C),
ANP(D), empty(E), and ANP(F) and is listed
in the Protein Data Bank as Structure File
lOHH.^^ In each case the hydrophobic side of
the y-rotor faces the occupancy state of
chain E.
Certainly, the third structure holds the
hydrophobic side of the y-rotor most tena-
ciously at the p-empty catalytic site, even more
so than the structures in Figures 8.30 through
8.34, because all five additional sites are occu-
pied by the ATP equivalent, namely, ANP. The
other two structures depend on the relative
polarities of ADP(D) and P04(E) in their
respective positions of exposure to the y-rotor.
That the P-P04(E) is least polar from the per-
spective of the y-rotor becomes apparent from
the display of the second structure of the three
in Figure 8.37B, where the P-PO4 of chain E is
positioned so as to be sterically obscured from
the y-rotor. Accordingly, consistency holds for
all five structures of the Fi-ATPase; the most
hydrophobic side of the y-rotor is always found
opposite the least polar occupancy site, where
the apolar-polar repulsive free energy of
hydration, AGap, is the least.
8A.4.9 Role of ATP in the a-ATP
Subunits: Triangulation of
Repulsive Forces
When the p-ATP and a-ATP sites are diamet-
rically opposed, as in Figure 8.34C, the appear-
ance read in terms of AGap is that the P-ATP
site expresses slightly more apolar-polar repul-
sion than does the a-ATP site. From the point
of view of the hydrophobic consilient mecha-
nism, this suggests that the exposure of phos-
phates of the a-ATP sites through water to the
y-rotor is greater for the p-ATP sites. Figure
8.38 shows the exposure of the y-rotor to a-
ATP phosphates of chains A, B, and C of the
structures utilized in Figures 8.30 through 8.34.
In each of the a-ATP only a single oxygen of
the y-phosphate can be seen through a small
peephole. While exposure of the a-ATP phos-
phates to the y-rotor could be larger in the
dynamic functional state, this situation is com-
pared with a slightly greater exposure of the
phosphates of the P-ATP site immediately
below and to an analogue of the massively
greater exposure on hydrolysis to form ADP
plus Pi.
By the hydrophobic consilient mechanism,
the a-ATP sites provide a critical role of estab-
lishing a triangulation of repulsive forces that
serves to limit the hydrophobic associations
of the y-rotor. This triangulation of repulsive
forces prevents the occurrence of a frictional
drag on rotor rotation that would seriously
limit motor efficiency.