Transition-state configuration

P-site ligands inhibit adenylyl cyclases by a noncompetitive, dead-end- (post-transition-state) mechanism (cf. Fig. 6). Typically this is observed when reactions are conducted with Mn2+ or Mg2+ on forskolin- or hormone-activated adenylyl cyclases. However, under- some circumstances, uncompetitive inhibition has been noted. This is typically observed with enzyme that has been stably activated with GTPyS, with Mg2+ as cation. That this is the mechanism of P-site inhibition was most clearly demonstrated with expressed chimeric adenylyl cyclase studied by the reverse reaction. Under these conditions, inhibition by 2 -d-3 -AMP was competitive with cAMP. That is, the P-site is not a site per se, but rather an enzyme configuration and these ligands bind to the post-transition-state configuration from which product has left, but before the enzyme cycles to accept new substrate. Consequently, as post-transition-state inhibitors, P-site ligands are remarkably potent and specific inhibitors of adenylyl cyclases and have been used in many studies of tissue and cell function to suppress cAMP formation. 

Figure 1.13 Transition-state configuration of methane activation on Ru(1120) surface bond (eo) ...

Class II dependence for the activation of a chemical bond as a function of surface metal atom coordinative unsaturation is typically found for chemical bonds of a character, such as the CH or C-C bond in an alkane. Activation of such bonds usually occurs atop of a metal atom. The transition-state configuration for methane on a Ru surface illustrates this (Figure 1.13). 

When one looks at the general reaction systems from the standpoint of the kineticist, species YNX1At would represent the transition state configuration. In this case equation 7.4.2 indicates that... 

While the collision theory of reactions is intuitive, and the calculation of encounter rates is relatively straightforward, the calculation of the cross-sections, especially the steric requirements, from such a dynamic model is difficult. A very different and less detailed approach was begun in the 1930s that sidesteps some of the difficulties. Variously known as absolute rate theory, activated complex theory, and transition state theory (TST), this class of model ignores the rates at which molecules encounter each other, and instead lets thermodynamic/statistical considerations predict how many combinations of reactants are in the transition-state configuration under reaction conditions. 

In terms of enzyme catalysis, the following factors are likely to influence the magnitude of the rate enhancement in enzymatic processes (a) proximity and orientation effects (b) electrostatic complementarity of the enzyme s active site with respect to the reactant s stabilized transition state configuration (c) enzyme-bound metal ions that serve as template, that alter pK s of catalytic groups, that facilitate nucleophilic attack, and that have... 

HIV protease inhibitors are transition-state analogs (Chapter 9, Section 9.2.6) HIV protease binds them much more tightly than the natural substrate because the substrate must be distorted to assume its transition-state configuration. Thus, HIV protease inhibitors are competitive enzyme inhibitors and thereby prevent the maturation and infectivity of the viral particle. They offer advantages over RTIs with respect to efficacy, safety, and occurrence of resistance. However, just like RTIs, HIV protease inhibitors are most often offered in combination with therapies based on another mode of action. Structures and data for the five approved HIV protease inhibitors are shown in Figure 13.14 and in Table 13.5. 

The inner-sphere component of the reorganization energy represents the minimum energy required to change the internal structure of the redox center to its nuclear transition state configuration. Equation (2.3) is derived from the classical harmonic oscillator model and is an expression of the free energy associated with... 

Figure 2. Schematic representation of the free energy changes in an enzyme-catalyzed reaction where the enzyme is complementary to either the substrate (broken lines) or to its transition state configuration (solid lines).

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