Enzymatic transition state structures constrained by experimental kinetic isotope effects: Experimental measurement of transition state variability

An individual kinetic isotope effect (KIE) provides bond vibrational and geometric information for the differences in atomic environment between an atom in a reactant and its transition state. The magnitude of KIEs measured at every atom surrounding the sites of bond-making and bond-breaking in a reaction places tight experimental constraints on calculations to determine the geometry of the transition state structure. Interpretation of enzymatic KIEs into the transition state structure first requires quantitation of the extent to which non-chemical enzymatic steps suppress the chemical isotope effects. Experimental methods are now available to solve this problem for most enzymes. The experimental transition state structure that matches the family of intrinsic KIEs is located by a systematic search through reaction space of leaving-group and attacking-group bond orders. The variation of transition state structures through reaction space is estimated from ab initio optimizations of small model compounds. This approach has been used with several N-ribohydrolases and transferases. The molecular electrostatic potentials at the van der Waals surfaces for these transition state structures have been used to design transition state inhibitors. Novel transition state inhibitors with affinities up to 10⁶-fold greater than those for the substrates have been obtained using these methods. Comparison of solution and enzymatic transition state structures provides fundamental information on how the enzyme stabilizes the transition states. The uncatalyzed and enzymatic hydrolysis and thiolysis of nicotinamide from NAD⁺ are used as examples of the practice of enzymatic transition state analysis.