50
3 Mechanism of Unidirectional Rotation of γ Subunit in F 1 -ATPase
water entropy already maximized as discussed in Sect. 3.4.2. The system free energy
decreases by ΔG ab and ΔG bc in state changes (a)→(b) and (b)→(c), respectively,
and ΔG ab + ΔG bc = ΔG ~ −20k B T (T = 298 K).
3.4.5 Effect of Electrostatic Attractive Interaction Between γ
and β Subunits
For a protein or protein complex, a decrease in intramolecular energy by van der
Waals and electrostatic attractive interactions is unavoidably accompanied by a loss
of protein-water van der Waals and electrostatic attractive interactions. The loss
causes an energy increase referred to as the energetic dehydration penalty explained
in Sect. 2.6. The decrease in the intramolecular energy, which is almost cancelled
out by the energetic dehydration penalty, cannot be a driving force of the rotation of
the γ subunit.
It was suggested that the rotation was induced by the electrostatic, attractive
interaction between positively charged residues (Arg and Lys) on the protruding
portion of the γ subunit and negatively charged residues (Asp (D) and Glu (E)) in the
so-called DELSEED motif of the β subunit (corresponding to Asp394−Asp400 in the
α 3 β 3 γ complex being considered) [27]. However, it was shown in later experimental
works [28, 29] that the rotation is not influenced by mutating each residue and all five
acidic residues in the DELSEED motif to Ala (the kinetic parameters are comparable
to those of the wild type), demonstrating that the electrostatic, attractive interaction
mentioned above plays no roles for the rotation.
3.5 Theoretical Analyses Based on Experimental
Observations for Yeast F 1 -ATPase
Unfortunately, no crystal structures have been reported for state (b) shown in
Fig. 3.16. Instead, crystal structures are available for the catalytic dwell state of
yeast F 1 -ATPase and the state after 16° rotation of γ subunit [30]. In the catalytic
dwell structure, AMP-PNP is bound to β DP and β TP and Pi is bound to β E as illustrated
in Fig. 3.19. The ATP hydrolysis does not occur in β DP during the 16° rotation, and
the rotation is triggered by the dissociation of Pi from β E .
We analyze the packing structures of the two crystal structures mentioned above
(see Fig. 3.19) and the packing efficiencies of the α−β, α−γ and β−γ interfaces.
AMP-PNP is replaced by ATP. Refer to our earlier publication for more details [31].
The purpose of these analyses is to investigate the effect of Pi bound to β E on the
packing structure of the α 3 β 3 γ complex. It is interesting to know whether the subtle
difference between the left and right states shown in Fig. 3.19 in the packing structure
can be reproduced.
3 Mechanism of Unidirectional Rotation of γ Subunit in F 1 -ATPase
water entropy already maximized as discussed in Sect. 3.4.2. The system free energy
decreases by ΔG ab and ΔG bc in state changes (a)→(b) and (b)→(c), respectively,
and ΔG ab + ΔG bc = ΔG ~ −20k B T (T = 298 K).
3.4.5 Effect of Electrostatic Attractive Interaction Between γ
and β Subunits
For a protein or protein complex, a decrease in intramolecular energy by van der
Waals and electrostatic attractive interactions is unavoidably accompanied by a loss
of protein-water van der Waals and electrostatic attractive interactions. The loss
causes an energy increase referred to as the energetic dehydration penalty explained
in Sect. 2.6. The decrease in the intramolecular energy, which is almost cancelled
out by the energetic dehydration penalty, cannot be a driving force of the rotation of
the γ subunit.
It was suggested that the rotation was induced by the electrostatic, attractive
interaction between positively charged residues (Arg and Lys) on the protruding
portion of the γ subunit and negatively charged residues (Asp (D) and Glu (E)) in the
so-called DELSEED motif of the β subunit (corresponding to Asp394−Asp400 in the
α 3 β 3 γ complex being considered) [27]. However, it was shown in later experimental
works [28, 29] that the rotation is not influenced by mutating each residue and all five
acidic residues in the DELSEED motif to Ala (the kinetic parameters are comparable
to those of the wild type), demonstrating that the electrostatic, attractive interaction
mentioned above plays no roles for the rotation.
3.5 Theoretical Analyses Based on Experimental
Observations for Yeast F 1 -ATPase
Unfortunately, no crystal structures have been reported for state (b) shown in
Fig. 3.16. Instead, crystal structures are available for the catalytic dwell state of
yeast F 1 -ATPase and the state after 16° rotation of γ subunit [30]. In the catalytic
dwell structure, AMP-PNP is bound to β DP and β TP and Pi is bound to β E as illustrated
in Fig. 3.19. The ATP hydrolysis does not occur in β DP during the 16° rotation, and
the rotation is triggered by the dissociation of Pi from β E .
We analyze the packing structures of the two crystal structures mentioned above
(see Fig. 3.19) and the packing efficiencies of the α−β, α−γ and β−γ interfaces.
AMP-PNP is replaced by ATP. Refer to our earlier publication for more details [31].
The purpose of these analyses is to investigate the effect of Pi bound to β E on the
packing structure of the α 3 β 3 γ complex. It is interesting to know whether the subtle
difference between the left and right states shown in Fig. 3.19 in the packing structure
can be reproduced.