Significance: The role of protein dynamics in enzyme catalysis remains a topic of considerable debate. Here, we use a combination of experimental and computational methods to identify the origins of the observed changes in reactivity on isotopic substitution of dihydrofolate reductase fromEscherichia coli. Isotopic substitution causes differences in environmental coupling to the hydride transfer step and protein dynamics have therefore a small but measurable effect on the chemical reaction rate.

While the full catalytic power of dihydrofolate reductase depends on finely tuning protein motions in each step of the catalytic cycle, dynamic coupling to the actual chemical step is detrimental to catalysis.

Isotopic substitution (¹⁵N, ¹³C, ²H) of a catalytically compromised variant of Escherichia coli dihydrofolate reductase, EcDHFR-N23PP/S148A, has been used to investigate the effect of these mutations on catalysis. The reduction of the rate constant of the chemical step in the EcDHFR-N23PP/S148A catalyzed reaction is essentially a consequence of an increase of the quasi-classical free energy barrier and to a minor extent of an increased number of recrossing trajectories on the transition state dividing surface. Since the variant enzyme is less well set up to catalyze the reaction, a higher degree of active site reorganization is needed to reach the TS. Although millisecond active site motions are lost in the variant, there is greater flexibility on the femtosecond time scale. The “dynamic knockout” EcDHFR-N23PP/S148A is therefore a “dynamic knock-in” at the level of the chemical step, and the increased dynamic coupling to the chemical coordinate is in fact detrimental to catalysis. This finding is most likely applicable not just to hydrogen transfer in EcDHFR but also to other enzymatic systems.