Importance of Protein Dynamics during Enzymatic C–H Bond Cleavage Catalysis

Abstract

Quantum tunneling and protein dynamics have emerged as important components of enzyme function. This review focuses on soybean lipoxygenase-1, to illustrate how the properties of enzymatic C–H bond activation link protein motions to the fundamental bond making–breaking processes.

Mediation of donor–acceptor distance in an enzymatic methyl transfer reaction

“…The central role of H-nuclear tunneling in the latter case indicates that catalysis requires a close approach between the H-donor and acceptor, estimated to be reduced by 0.3-0.6 Å from donor-acceptor van der Waals distances. For native and optimized enzymes, reduced distances are attributed to a stochastic search among protein ground states that leads to short, tunneling-ready donor-acceptor configurations (25). Significantly, the present work also uncovers a ground state compaction in an activated, substrate-ionized ground state that correlates with very high turnover rates for COMT (compare Fig.…”

“…Models for catalysis that depend on such protein motions have been particularly important in the area of C-H activation, where the transfer of hydrogen by tunneling mechanisms implicates a critical dependence of the reaction rate on barrier width, and not just barrier height (23,24). Achievement of the tunneling-ready state requires a transient sampling of enzymatic ground states that achieves a reduced distance between the H-donor and acceptor (25). This feature raises the question of whether the reported inverse KIE in COMT could result from ground state interactions that bring about catalytically relevant changes in the reactants' geometry and distance (26).…”

Kinetic Deuterium Isotope Effects in Cytochrome P450 Reactions

“…Some of the approaches to studying tunneling are technically difficult, but there are probably some good candidates. Archebacterial P450s would seem to be good candidates because of their broader temperature range for comparing activation energies for protiated and deuterated substrates (Klinman, 2013), although only limited information is available regarding their substrates and redox partners.…”

Resolution and Characterization of Chemical Steps in Enzyme Catalytic Sequences by Using Low-Temperature and Time-Resolved, Full-Spectrum EPR Spectroscopy in Fluid Cryosolvent and Frozen Solution Systems

“…There have also been proposals for roles of protein conformational dynamics in steps that bracket (precede, follow) the chemical steps in enzyme reactions (Boehr, McElheny, Dyson, & Wright, 2006; Henzler-Wildman, Lei, et al, 2007; Henzler-Wildman, Thai, et al, 2007; Whitford, Onuchic, & Wolynes, 2008), including setting the stage for reaction coordinate-specific vibrations (S. Hay, Johannissen, Sutcliffe, & Scrutton, 2010; Nunez, Antoniou, Schramm, & Schwartz, 2004; Pudney et al, 2013), as summarized by (Benkovic, Hammes, & Hammes-Schiffer, 2008; Boehr et al, 2006; Klinman, 2013). Some of these proposals have been criticized, on the basis that they are not true catalyic effects ( i.e ., relative to a solution reference reaction), or that they are not rigorously defined ( i.e ., in terms of an energy surface description) (Kamerlin & Warshel, 2011; Olsson, Parson, & Warshel, 2006).…”