Protein conformational heterogeneity and dynamics are known to play an important role in enzyme catalysis, but their influence has been difficult to observe directly. We have studied the effects of heterogeneity in the catalytic reaction of pig heart lactate dehydrogenase using isotope edited infrared spectroscopy, laser-induced temperature jump relaxation, and kinetic modeling. The isotope edited infrared spectrum reveals the presence of multiple reactive conformations of pyruvate bound to the enzyme, with three major reactive populations having substrate C2 carbonyl stretches at 1686, 1679, and 1674 cm−1, respectively. The temperature jump relaxation measurements and kinetic modeling indicate that these substates form a heterogeneous branched reaction pathway, and each substate catalyzes the conversion of pyruvate to lactate with a different rate. Furthermore, the rate of hydride transfer is inversely correlated with the frequency of the C2 carbonyl stretch (the rate increases as the frequency decreases), consistent with the relationship between the frequency of this mode and the polarization of the bond, which determines its reactivity toward hydride transfer. The enzyme does not appear to be optimized to use the fastest pathway preferentially but rather accesses multiple pathways in a search process that often selects slower ones. These results provide further support for a dynamic view of enzyme catalysis where the role of the enzyme is not just to bring reactants together but also to guide the conformational search for chemically competent interactions.

Lactate dehydrogenase (LDH) catalyzes the interconversion between pyruvate and lactate with nicotinamide adenine dinucleotide (NAD) as a cofactor. Using isotope-edited difference Fourier transform infrared spectroscopy on the “live” reaction mixture (LDH·NADH·pyruvate ⇌ LDH·NAD+·lactate) for the wild-type protein and a mutant with an impaired catalytic efficiency, a set of interconverting conformational substates within the pyruvate side of the Michaelis complex tied to chemical activity is revealed. The important structural features of these substates include (1) electronic orbital overlap between pyruvate’s C2=O bond and the nicotinamide ring of NADH, as shown from the observation of a delocalized vibrational mode involving motions from both moieties, and (2) a characteristic hydrogen bond distance between the pyruvate C2=O group and active site residues, as shown by the observation of at least four C2=O stretch bands indicating varying degrees of C2=O bond polarization. These structural features form a critical part of the expected reaction coordinate along the reaction path, and the ability to quantitatively determine them as well as the substate population ratios in the Michaelis complex provides a unique opportunity to probe the structure–activity relationship in LDH catalysis. The various substates have a strong variance in their propensity toward on enzyme chemistry. Our results suggest a physical mechanism for understanding the LDH-catalyzed chemistry in which the bulk of the rate enhancement can be viewed as arising from a stochastic search through an available phase space that, in the enzyme system, involves a restricted ensemble of more reactive conformational substates as compared to the same chemistry in solution.

The photochemistry of 2-naphthoyl azide was studied in various solvents by femtosecond time-resolved transient absorption spectroscopy with IR and UV-vis detection. The experimental findings were interpreted with the aid of computational studies. Using polar and nonpolar solvents, the formation and decay of the first singlet excited state (S(1)) was observed by both time-resolved techniques. Three processes are involved in the decay of the S(1) excited state of 2-naphthoyl azide: intersystem crossing, singlet nitrene formation, and isocyanate formation. The lifetime of the S(1) state decreases significantly as the solvent polarity increases. In all solvents studied, isocyanate formation correlates with the decay of the azide S(1) state. Nitrene formation correlates with the decay of the relaxed S(1) state only upon 350 nm excitation (S(0) → S(1) excitation). When S(n) (n ≥ 2) states are populated upon excitation (λ(ex) = 270 nm), most nitrene formation takes place within a few picoseconds through the hot S(1) and higher singlet excited states (S(n)) of 2-naphthoyl azide. The data correlate with the results of electron density difference calculations that predict nitrene formation from the higher-energy singlet excited states, in addition to the S(1) state. For all of these experiments, no recovery of the ground state was observed up to 3 ns after photolysis, which indicates that both internal conversion and fluorescence have very low efficiencies.

The photochemistry of three carbonyl azides was studied by ultrafast time-resolved IR spectroscopy. Benzoyl, 2-naphthoyl, and pivavoyl azides are promoted to upper excited states S(n) with 270 nm excitation in chloroform. The S(n) states decay in 300 fs to form both the carbonylnitrenes and the S(1) excited states. The decay of the S(1) states of the carbonyl azides correlates with the growth of isocyanates. Formation of carbonylnitrene from S(1) is at most a minor process if it happens at all. The quantum yields of azide decomposition of these azides with 270 nm light are close to unity in chloroform.