Origins of Enzyme Catalysis: Experimental Findings for C–H Activation, New Models, and Their Relevance to Prevailing Theoretical Constructs

Abstract

The physical basis for enzymatic rate accelerations is a subject of great fundamental interest and of direct relevance to areas that include the de novo design of green catalysts and the pursuit of new drug regimens. Extensive investigations of C-H activating systems have provided considerable insight into the relationship between an enzyme's overall structure and the catalytic chemistry at its active site. This Perspective highlights recent experimental data for two members of distinct, yet iconic C-H activation enzyme classes, lipoxygenases and prokaryotic alcohol dehydrogenases. The data necessitate a reformulation of the dominant textbook definition of biological catalysis. A multidimensional model emerges that incorporates a range of protein motions that can be parsed into a combination of global stochastic conformational thermal fluctuations and local donor-acceptor distance sampling. These motions are needed to achieve a high degree of precision with regard to internuclear distances, geometries, and charges within the active site. The available model also suggests a physical framework for understanding the empirical enthalpic barrier in enzyme-catalyzed processes. We conclude by addressing the often conflicting interface between computational and experimental chemists, emphasizing the need for computation to predict experimental results in advance of their measurement.

Equatorial Active Site Compaction and Electrostatic Reorganization in Catechol-O-methyltransferase

“…This description is couched within the framework of the “promoting vibration” hypothesis, which has been used to interpret isotope effects on H-transfer reactions. 14−16 The unusual deuterium KIE on the COMT reaction has also received much attention from the computational community, with a number of proposals put forward to describe catalysis by COMT. Ground state near attack conformers (NACs) have been proposed by Bruice, 17,18 whereas Warshel has recently argued against compaction and NACs in favor of electrostatic preorganization.…”

A Biophysical Perspective on Enzyme Catalysis

“…In the hypothesized model of enzymes ( Figure 1 and Figure 4) the energy is collected by fast motions of the surface protein residues through thermo-dynamical coupling with the solvent. 31,[89][90][91] This energy is transferred to the intermediate motions and eventually fed to the slow protein motions, which are coupled to the reaction. 12 Note that this process is not dissipative (that is energy is not lost by random collisions) but rather leads to directed flow of energy through discovered networks of coupled motions.…”

Fatty Acid Allosteric Regulation of C-H Activation in Plant and Animal Lipoxygenases

“…The extraction of a secondary KIE from the synthesis of a monodeuterated 11S-D1 labeled LA exhibited a modest secondary isotope effect of ~1.2 for the non-transferred hydrogen [90]. There are several important implications of hydrogen tunneling towards enzyme catalysis [59]. First is the breakdown of semi-classical transition state theory (over-the-barrier) view of catalysis.…”

“…There are several important implications of hydrogen tunneling towards enzyme catalysis [59]. First is the breakdown of semi-classical transition state theory (over-the-barrier) view of catalysis.…”

“…The initial and often rate-limiting step for the oxidation of fatty acids by lipoxygenases is a C-H activation (C-H bond cleavage) step ( Scheme 1 ) [ 59 ]. This process occurs by proton-coupled electron transfer (PCET) in which the proton is transferred to the metal-bound hydroxide and the electron is accepted by the metal center, converting it from the +3- to the +2-oxidation state [ 30 , 60 ].…”