Unraveling the role of protein dynamics in dihydrofolate reductase catalysis.
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 ((15)N, (13)C, (2)H 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.
School of Chemistry and Cardiff Catalysis Institute, Cardiff University, Cardiff CF10 3AT, United Kingdom.
Louis Y P
LY
Luk
J
J
Javier Ruiz-Pernía
William M
WM
Dawson
Maite
M
Roca
E Joel
EJ
Loveridge
David R
DR
Glowacki
Jeremy N
JN
Harvey
Adrian J
AJ
Mulholland
Iñaki
I
Tuñón
Vicent
V
Moliner
Rudolf K
RK
Allemann
D002247:Carbon Isotopes / Q000378:metabolism; D002384:Catalysis; D004926:Escherichia coli / Q000201:enzymology*; D007700:Kinetics; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D009587:Nitrogen Isotopes / Q000378:metabolism; D011506:Proteins / Q000378:metabolism*; D013762:Tetrahydrofolate Dehydrogenase / Q000378:metabolism*; D014316:Tritium / Q000378:metabolism
D002247:Carbon Isotopes; D009587:Nitrogen Isotopes; D011506:Proteins; D014316:Tritium; D013762:Tetrahydrofolate Dehydrogenase
biological chemistry; biophysics; computational chemistry; kinetics; quantum biology