Do Dynamic Effects Play a Significant Role in Enzymatic Catalysis? A Theoretical Analysis of Formate Dehydrogenase

Abstract

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Unraveling the role of protein dynamics in dihydrofolate reductase catalysis

“…γ(T) can be estimated from molecular dynamics (MD) trajectories starting from the TS with a thermal distribution of velocities. Recent studies on several enzyme-catalyzed reactions (11)(12)(13)(14) suggest that recrossing coefficients tend to be somewhat closer to unity than the corresponding counterpart reactions in solution. In general, κ(T) ≥ 1, with values larger than unity when quantum tunneling is important (41,42).…”

“…Exactly how γ(T) and κ(T) contribute to Γ(T), and in particular how these are affected by protein dynamics, remains a fundamental and hotly debated question with important consequences for understanding enzyme catalysis. Using a combination of experiment, theory, and computation, we analyze dynamical effects by comparing the rate coefficients for hydride transfer in NADPH catalyzed by both "heavy" ( 15 N, 13 C, 2 H isotopically substituted) and "light" (natural isotopic abundance) EcDHFR. We have measured, analyzed, and simulated the temperature dependence of the EcDHFR-catalyzed hydride transfer from NADPH to H 2 F in the heavy and light enzymes.…”

“…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.…”

“…However, a connection between promoting motions and potential energy barrier modulation has never been demonstrated directly, and recent work has shown that the temperature dependence of kinetic isotope effects can be accounted for by conformational effects for a number of enzymes (5). Whereas some authors postulate dynamics as a key driving force in catalysis (1)(2)(3)(4), others have performed analyses showing activation free-energy reduction, which is an equilibrium property, to be the source of catalysis (6)(7)(8)(9)(10)(11)(12)(13)(14). Enzyme reactions, and particularly their dynamics, present formidable challenges for study, and progress requires a combination of theoretical, experimental, and computational approaches (5,(15)(16)(17)(18) (20).…”

“Eppur si muove” (yet it moves)

“…However, the most intriguing question is probably whether the dynamics of the protein structural fluctuations are on the same timescale as the chemical step, and therefore coupled to the reaction coordinate and influencing chemical catalysis. In this regard, the role of protein motions in enzyme catalysis has been the topic of many experimental and theoretical studies in recent years, with no consensus of whether they can be considered crucial for the catalysis (1)(2)(3)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15)(16)(17)(18)(19). Thus, the key question would be on quantifying the contribution of "protein-promoting vibrations" (18) (Fig.…”