Case Study Catalytic Mechanism of Yeast Enolase

5 Case Study Catalytic Mechanism of Yeast Enolase 

Synopsis of Alhambra et al. (1999) Quantum Mechanical Dynamical Effects in an Enzyme-catalyzed Proton Transfer Reaction . 

Alhambra and co-workers adopted a QM/MM strategy to better understand quantum mechanical effects, and particularly the influence of tunneling, on the observed primary kinetic isotope effect of 3.3 in this system (that is, the reaction proceeds 3.3 times more slowly when the hydrogen isotope at C-2 is deuterium instead of protium). In order to carry out their analysis they combined fully classical MD trajectories with QM/MM modeling and analysis using variational transition-state theory. Kinetic isotope effects (KIEs), tunneling, and variational transition state theory are discussed in detail in Chapter 15 - we will not explore these topics in any particular depth in this case study, but will focus primarily on the QM/MM protocol. 

Having successfully matched the several experimental observables available for the enolase system, Alhambra and co-workers then examine the reaction coordinate to better understand the factors discriminating H from D reactivity. They discover that the TS for the reaction of H is much later than that for reaction of D, because the rapidly increasing zero-point energy of the N-H bond compared to the N-D bond offsets the drop in reaction coordinate potential energy and moves the free-energy bottleneck for H further towards products. 

The authors finish by predicting a quantity that has not yet been measured, the secondary KIE that would be obtained with -ND2 in place of -NI Q as the reactive base. They also note the critical role of the Mg counterions in facilitating the reaction. The binding to the two cations of the phosphoenolpyruvate tetraanion compared to the reactant trianion is predicted to be increased by some 240 kcal mol this offsets the highly unfavorable pKa of the C-2 proton sufficiently to render the overall reaction thermochemistry only 2.8 kcal mol endergonic. 

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CASE STUDY CATALYTIC MECHANISM OF YEAST ENOLASE... 

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