Ligand binding reaction occupancy

Figure 3.4. Quantitative treatment of irreversible inhibition, a Starting assumptions and derived receptor occupancy. [RI] will depend on inhibitor concentration but also other things such as speed of reaction and of elimination. We assume that the reaction is complete and [RI] is stable when the ligand binds, b Plots of receptor occupancy vs agonist (L) concentration after exposure to different inhibitor concentrations. The binding equihbrium (K) for the agonist will be unchanged, bnt the maximum occupancy will be reduced in a dose-dependent fashion.

If the chemical reactions of the photoactivated intermediate were completely nonspecific, the thermodynamic dissociation constant, Kt, would be the primary consideration (assuming that the reactive intermediate has the same Ki), Since there may be highly reactive entities outside the site, such as other macromolecules or water, the rate of dissociation and the chemical half-life of the intermediate are also important. Further, noncovalently bound reaction products can prevent stoichiometric labeling by their occupancy of the ligand binding site. 

As with Mb/Hb, metHr is the thermodynamically stable form in aerobic solutions, and a metHr reductase has been reported. The rate of autoxidation of oxyHr decreases by approximately tenfold with a one-unit decrease in pH in the acidic region, consistent with reaction (6a). Certain exogenous anions, particularly azide, catalyze autoxidation of oxyHr by nucleophilic displacement of the peroxo ligand and/or by delivery of a proton to the coordinated peroxo. The slow rates of reactions (6a) and (6b) in the absence of these anions, however, indicate a substantial kinetic barrier to autoxidation. Presumably, autoxidation requires entry of solvent into the 02-binding pocket of oxyHr, i.e., transient, simultaneous occupancy of the pocket by both bound O2 and solvent. Consistent with this mechanism, the L98 variants of Hr in which either smaller or more polar side chains were substituted all led to significant increases in autoxidation rates.Thus, the main function of L98 and the other hydrophobic residues shown in Figure 17 may be as hydrophobic and steric barriers to solvent-induced autoxidation. 

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