Unraveling the role of protein dynamics in dihydrofolate reductase catalysis

• Published in: Proceedings of the National Academy of Sciences - PNAS Vol. 110; no. 41; pp. 16344 - 16349
• Main Authors: Luk, Louis Y. P., Ruiz-Pernía, J. Javier, Dawson, William M., Roca, Maite, Loveridge, E. Joel, Glowacki, David R., Harvey, Jeremy N., Mulholland, Adrian J., Tuñón, Iñaki, Moliner, Vicent, Allemann, Rudolf K.
• Format: Journal Article
• Language: English
• Published: United States National Academy of Sciences 08.10.2013; NATIONAL ACADEMY OF SCIENCES; National Acad Sciences
• Subjects: Atoms; Biochemistry; Carbon Isotopes - metabolism; Catalysis; Chemical reactions; Coefficients; Comparative analysis; Coordinate systems; Enzymes; Escherichia coli - enzymology; Hydrides; Hydrogen; Kinetics; Models, Molecular; Molecular Dynamics Simulation; Nitrogen Isotopes - metabolism; Physical Sciences; Proteins; Proteins - metabolism; Quantum physics; Quantum tunneling; Simulation; Tetrahydrofolate Dehydrogenase - metabolism; Tritium - metabolism; quantum biology; computational chemistry; kinetics; biological chemistry; biophysics
• ISSN: 0027-8424; 1091-6490
• DOI: 10.1073/pnas.1312437110

Protein dynamics have controversially been proposed to be at the heart of enzyme catalysis, but identification and analysis of dynamical effects in enzyme-catalyzed reactions have proved very challenging. Here, we tackle this question by comparing an enzyme with its heavy (¹⁵N, ¹³C, ²H substituted) counterpart, providing a subtle probe of dynamics. The crucial hydride transfer step of the reaction (the chemical step) occurs more slowly in the heavy enzyme. A combination of experimental results, quantum mechanics/molecular mechanics simulations, and theoretical analyses identify the origins of the observed differences in reactivity. The generally slightly slower reaction in the heavy enzyme reflects differences in environmental coupling to the hydride transfer step. Importantly, the barrier and contribution of quantum tunneling are not affected, indicating no significant role for “promoting motions” in driving tunneling or modulating the barrier. The chemical step is slower in the heavy enzyme because protein motions coupled to the reaction coordinate are slower. The fact that the heavy enzyme is only slightly less active than its light counterpart shows that protein dynamics have a small, but measurable, effect on the chemical reaction rate.