AGha calculating

Coherence Between AG p and AGha Calculated Using Different Experimental Data Demonstrates Presence and Dominance of the Consilient Mechanism in Model Proteins... 

Different Estimates of Transition Temperature Used in Calculating the Gibbs Free Energy for Hydrophobic Association, AGha, by Equation (5.10a)... 

For the following estimates, Tb values are available for guest amino acid residues without functional groups. With Equation (5.10b), the calculated values for the residues more hydrophobic than glycine (Gly, G), that is, AGha(GGGVP —> GXGVP) substitutions, in... 

Figure 5.10. An embodiment of the comprehensive hydrophobic effect in terms of a plot of the temperature for the onset of phase separation for hydrophobic association, Tb, versus AGha. the Gibbs free energy of hydrophobic association for the amino acid residues, calculated by means of Equation (5.10b) using the heats of the phase (inverse temperature) transition (AH,). Values were taken from Table 5.3. Tb and T, were determined from the onset of the phase separation as defined in Figure 5.1C,B, respectively. The estimates of AGha utilized the AH, data listed in Table 5.1 for fx = 0.2 but extrapolated to fx = 1, and the Gly (G) residue was taken as the...

Calculation of AGha for a Change in the State of Bound Biologically Relevant Functional Groups... 

Using AT, Due to Addition of Salts to Calculate Change in Free Energy (AGha) for Hydrophobic Association of Neutral Poly(GVGVP)... 

Figure 5.11. Dependences of T,-values for poly(GVGVP) as a function of salt concentration, (A) and of organic solvents and solutes (B). These data are used in Table 5.4 on a per mole (normality) basis to calculate the AGHA(solute) in terms of kcal/mole solute. (Adapted with permission from Urry. )...

Several points require consideration on identification of AH,(CH2) - T,(GVGIP)AS,(CH2) as -AGha(CH2). The points include the separability assumption of Equations (5.3) and (5.4), the relevance of the model protein to such identification, and the choice of reference state in order that the nonlinearity of hydrophobic-induced pKa shifts be included. From the data of Butler, the separability is reasonable for a simple CH group, but examination of the calculated result is required to be satisfied whether or not extension to more complex substituents is warranted. As the inverse temperature transition of (GVGVP) has been experimentally shown to involve no Raman detectable changes in secondary structure, the elastic-contractile model proteins of focus here reasonably represent the best known model available for such an effort. It should be noted, however, that NMR studies on the temperature and solvent dependence of peptide NH and... 

Calculations of the surface AGha values are necessarily very gross until they are given per nanometer squared and until a set of rules are developed to take into consideration the extent of residue exposure to the surface and especially the exposure of the charged or polar component of the functional side chain to the surface. 

Thus, values of AGha should be recognized as the net result of a transition dominated by the endothermic conversion of hydrophobic hydration to bulk water attending hydrophobic association with a lesser contribution due to the exothermic association of the model protein molecules, resulting from van der Waals interactions usually calculated using the Lennard-... 

As calculated and discussed in section S.3.4.4.4, the AGha(P04") due to phosphorylation of poly[30(GVGIP)(GRGDSP)] at the Ser (S) residue raises the value of T, to an extent that the calculated increase in free energy for hydrophobic association becomes about... 

Figure 8.15. By the use of white for charged residues and gray to black for increasingly hydrophobic residues, it becomes apparent by inspection of the involved surface areas, without calculation of the Gibbs free energy for hydrophobic association, AGha, that the Q site is much more hydrophobic than the cytochrome Ci site. The hydrophobicity of the globular component of the RIP that associates with either the Qo site or the cytochrome Ci site is even more apparent. The very dark tip, shown in end view and in side view in Figures 8.16A,B, respectively, makes clear that the interaction of the FeS center with the Qo site would clearly be dominated by hydrophobic association.

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. 

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. 

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