Dihydrofolate reductase as a model for studies of enzyme dynamics and catalysis.

Amnon Kohen

doi:10.12688/f1000research.6968.1

Abstract

Dihydrofolate reductase from Escherichia coli (ecDHFR) serves as a model system for investigating the role of protein dynamics in enzyme catalysis. We discuss calculations predicting a network of dynamic motions that is coupled to the chemical step catalyzed by this enzyme. Kinetic studies testing these predictions are presented, and their potential use in better understanding the role of these dynamics in enzyme catalysis is considered. The cumulative results implicate motions across the entire protein in catalysis.

Highlights

Enzymes are large and flexible proteins that catalyze most chemical reactions in life
We will present studies of E. coli dihydrofolate reductase, or DHFR, that focus on the role of dynamics across the protein in the chemical step catalyzed by this enzyme
Concluding remarks An important take-home message from the above studies is that observed rate constants and kinetic isotope effects (KIEs) should not be taken as a probe for a single kinetic step

Summary

Introduction

Enzymes are large and flexible proteins that catalyze most chemical reactions in life. Studies of mutants far from the active site indicate that double mutants have a non-additive effect that is much larger than their respective single mutants (ΔEa (H/T) double mutant A&B > ΔEa (H/T) mutant A + This finding supports the prediction that those residues are coupled to each other along the reaction coordinate for the hydride transfer in the wild-type enzyme. The observed rate constants and KIEs, and especially their temperature dependence (and their activation parameters) often reflect complex phenomena involving many microscopic rate constants This is unfortunate, as most calculations address only the barrier that is the chemical step, but not other steps affecting the experimental measurement. In accordance with predictions made by the calculations presented above, these findings indicate that several residues across the whole protein, including some far from the active site, are involved in a network of coupled motions that affect the chemical step catalyzed by DHFR from E. coli. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Kohen A

Cook PF

13. Northrop DB