Rotors hydrophobic face

Demonstrations of these predictions constitute the message of this section 8.4, and its success introduces the perspective of a conjoined hydrophobic elastic consilient mechanism. With the values in Table 5.3 and the crystal structure with three different states of occupancy, empty, ATP, and ADP, the three sides of the rotor can be identified and the respective Gibbs free energies of hydrophobic association, AGha, have been estimated to be -20, 0, and +9kcal/mole. The most hydrophobic face associates with the empty site, the neutral face with the ATP bound site, and the most polar face with the ADP site which in the synthesis mode would be in position to add Pj. As expected from the magnitude of the resulting AG,p for a series of crystal structures wherein the least polar occupancy state for the catalytic site could be defined, the most hydrophobic side of the rotor resides in apposition to the least polar site. 

Prediction and Demonstration That the Most Hydrophobic Face of the Rotor Hydrophobically Associates with the Most Hydrophobic State of the Housing... 

Figure 8.31. J-(Empty) face of the y-rotor of ATP synthase identified as the very hydrophobic face by the calculation shown of Table 8.2 to give 5AGHA(empty face) = -20kcal/mole. Shown at right are the a-ATP and )-ADP ligands, at left the a-ATP...

This configuration, which for simplicity may be designated as EGC, makes a profound statement. As shown in Figure 8.34A, the association between the P-empty subunit and the y-rotor is profoundly hydrophobic at the levels of both the nucleotide sites and the interaction as the y-rotor enters the (aP)s construct. The most hydrophobic face of the y-rotor hydrophobi-cally associates extensively with the P-empty subunit. Interestingly, except at the very tip of the y-rotor, there is no interaction with the a-ATP(C) subimit instead, there is an aqueous chasm separating G from C down to but not including the tip of the y-rotor. It is difficult to... 

Figure 8.36. (A) Hydrophobic face of the y-rotor of ATP synthase 2AGHA(opposite pair of very polar ADP-AIF) = -20kcal/mole. With the most polar ADP-AIF4 at rear sides and with one ADP at rear and three in front, AG p would place the hydrophobic face at front. F250 identifies the hydrophobic side of the y-rotor, again to show the orientation effect of AG,p. The neutral residues are light gray, the aro-...

S.4.5.2 Binding of ATP Exhibits Negative Cooperativity Due to Increases in AGap with Increasingly Hydrophobic Faces of the y-Rotor... 

Furthermore, the most hydrophobic face of the y-rotor functions as such it associates hydrophobically with the P-empty subunit, which becomes the most hydrophobic P-subunit due to the absence of polar (charged) nucleotides. 

In the extramembrane component the y-rotor forms the stem and core of an orangeshaped structure comprised of six sections, three a-subunits and three P-subunits, arranged as threefold symmetrical (aP) pairs, designated as (aP)3. The key element of the consilient mechanism applied to ATP synthase is that the y-rotor exhibits three faces of very different hydrophobicity. In our view, rotation of the y-rotor by the Fo-motor causes the very hydrophobic side of the rotor to be spatially opposed, through a water-filled cleft, to the catalytic site containing the most charged state. 

Figure 2.13. Shown is one complete cycle of the Fj-motor of ATP synthase on filling all catalytic sites with nucleotide and with a y-rotor that has three faces of very different hydrophobicities, that is, of very different oil-like character. As discussed in Chapter 8, the relative oil-like character of the three faces compare as -20kcal/mol-face for the most oillike, -i-Okcal/mol-face for an essentially neutral face, and h-9 kcal/mol-face for the least oil-like face. The least oil-like face would allow ADP and Pi to enter the catalytic site. As the Fo-motor rotates the darkened, oil-like face of the rotor toward the catalytic site containing ADP plus Pi, the repulsion between...

Hie hydrophobicity scale in Table 5.3 lists the contribution of each amino add residue to the Gibbs free energy of hydrophobic association, AGha- Table 5.3 also provides the information required to calculate numbers for the relative hydrophobidties of the faces of the y-rotor. The resulting numbers are tabulated and summed in Table 8.2, where the LAGHA(P-empty face) = -20 kcal/mole. This is indeed a very hydrophobic value. 

S.4.4.3.4 An Additional Point About the Relative Hydrophobicities of the Faces of the y-rotor... 

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 represented 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 occupancy 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 In each case the hydrophobic side of the y-rotor faces the occupancy state of chain E. 

As required for the hydrophobic consilient mechanism to be operative for an ATP synthase/Fi-ATPase protein-based machine, the three faces of the y-rotor exhibit very different hydrophobicities, that is, different AGha values, namely, approximately -20,0, and +9kcal/mole. 

In the eighth point of correlation of the hydrophobic elastic consilient mechanism given above, the maximal stage of apolar-polar repulsion occurred when the most polar occupancy state, ADP Mg plus HPOJ", faced off against the most hydrophobic side of the y-rotor to provide the thrust for a counterclockwise... 

Prediction 1 The rotor must be hydrophobi-cally asymmetric. Because the catalytic housing of the Fi-ATPase is essentially threefold symmetric but with different occupancies in the three p-catalytic subunits, three different faces of the y-rotor are identified from the crystal structure with different occupancies of the three catalytic subunits. Indeed, the three faces are calculated to have very different Gibbs free energies for hydrophobic association, AGha, namely, -20, 0, and +9kcal/mole in order of decreasing hydrophobicity. Thus, the prediction of a rotor with hydrophobic asymmetry is strikingly borne out. Tbe order of hydrophobicity, when considered in terms of the apolar-polar repulsion between occupancy and direction of rotation, makes sense with respect to mechanism. 

Prediction 2 In the static state the most hydrophobic side of the rotor faces the least polar side of the motor housing. Examination of five crystal structures with different... 

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