Critical role of substrate conformational change in the proton transfer process catalyzed by 4-oxalocrotonate tautomerase

Protein Dynamics and Enzymatic Catalysis

This Perspective presents a review of our work and that of others in the highly controversial topic of the coupling of protein dynamics to reaction in enzymes. We have been involved in studying this topic for many years. Thus, this perspective will naturally present our own views, but it also is designed to present an overview of the variety of viewpoints of this topic, both experimental and theoretical. This is obviously a large and contentious topic.

Solvation Induction of Free Energy Barriers of Decarboxylation Reactions in Aqueous Solution from Dual-Level QM/MM Simulations

Carbon dioxide capture, corresponding to the recombination process of decarboxylation reactions of organic acids, is typically barrierless in the gas phase and has a relatively low barrier in aprotic solvents. However, these processes often encounter significant solvent-reorganization-induced barriers in aqueous solution if the decarboxylation product is not immediately protonated. Both the intrinsic stereoelectronic effects and solute-solvent interactions play critical roles in determining the overall decarboxylation equilibrium and free energy barrier. An understanding of the interplay of these factors is important for designing novel materials applied to greenhouse gas capture and storage as well as for unraveling the catalytic mechanisms of a range of carboxy lyases in biological CO₂ production. A range of decarboxylation reactions of organic acids with rates spanning nearly 30 orders of magnitude have been examined through dual-level combined quantum mechanical and molecular mechanical simulations to help elucidate the origin of solvation-induced free energy barriers for decarboxylation and the reverse carboxylation reactions in water.

Variational transition state theory: theoretical framework and recent developments

This article reviews the fundamentals of variational transition state theory (VTST), its recent theoretical development, and some modern applications.

Transition state theory for enzyme kinetics

This article is an essay that discusses the concepts underlying the application of modern transition state theory to reactions in enzymes. Issues covered include the potential of mean force, the quantization of vibrations, the free energy of activation, and transmission coefficients to account for nonequilibrium effect, recrossing, and tunneling.

The importance of ensemble averaging in enzyme kinetics

The active site of an enzyme is surrounded by a fluctuating environment of protein and solvent conformational states, and a realistic calculation of chemical reaction rates and kinetic isotope effects of enzyme-catalyzed reactions must take account of this environmental diversity. Ensemble-averaged variational transition state theory with multidimensional tunneling (EA-VTST/MT) was developed as a way to carry out such calculations. This theory incorporates ensemble averaging, quantized vibrational energies, energy, tunneling, and recrossing of transition state dividing surfaces in a systematic way. It has been applied successfully to a number of hydrogen-, proton-, and hydride-transfer reactions. The theory also exposes the set of effects that should be considered in reliable rate constants calculations.

We first review the basic theory and the steps in the calculation. A key role is played by the generalized free energy of activation profile, which is obtained by quantizing the classical potential of mean force as a function of a reaction coordinate because the one-way flux through the transition state dividing surface can be written in terms of the generalized free energy of activation. A recrossing transmission coefficient accounts for the difference between the one-way flux through the chosen transition state dividing surface and the net flux, and a tunneling transmission coefficient converts classical motion along the reaction coordinate to quantum mechanical motion. The tunneling calculation is multidimensional, accounting for the change in vibrational frequencies along the tunneling path and shortening of the tunneling path with respect to the minimum energy path (MEP), as promoted by reaction-path curvature. The generalized free energy of activation and the transmission coefficients both involve averaging over an ensemble of reaction paths and conformations, and this includes the coupling of protein motions to the rearrangement of chemical bonds in a statistical mechanically correct way. The standard deviations of the transmissions coefficients provide information on the diversity of the distribution of reaction paths, barriers, and protein conformations along the members of an ensemble of reaction paths passing through the transition state.

We first illustrate the theory by discussing the application to both wild-type and mutant Escherichia coli dihydrofolate reductase and hyperthermophilic Thermotoga maritima dihydrofolate reductase (DHFR); DHFR is of special interest because the protein conformational changes have been widely studied. Then we present shorter discussions of several other applications of EA-VTST/MT to transfer of protons, hydrogen atoms, and hydride ions and their deuterated analogs. Systems discussed include hydride transfer in alcohol dehydrogenase, xylose isomerase, and thymidylate synthase, proton transfer in methylamine dehydrogenase, hydrogen atom transfer in methylmalonyl-CoA mutase, and nucleophilic substitution in haloalkane dehalogenase and two-dimensional potentials of mean force for potentially coupled proton and hydride transfer in the β-oxidation of butyryl-coenzyme A catalyzed by short-chain acyl-CoA dehydrogenase and in the pyruvate to lactate transformation catalyzed by lactate dehydrogenase.

A Benchmark Test Suite for Proton Transfer Energies and its Use to Test Electronic Structure Model Chemistries

We present benchmark calculations of nine selected points on potential energy surfaces describing proton transfer process in three model systems, H(5)O(2) (+), CH(3)OH…H(+)…OH(2), and CH(3)COOH…OH(2). The calculated relative energies of these geometries are compared to those calculated by various wave function and density functional methods, including the polarized molecular orbital (PMO) model recently developed in our research group and other semiempirical molecular orbital methods. We found that the SCC-DFTB and PMO methods (the latter available so far only for molecules consisting of only O and H and therefore only for the first of the three model systems) give results that are, on average, within 2 kcal/mol of the benchmark results. Other semiempirical molecular orbital methods have mean unsigned errors (MUEs) of 3 to 8 kcal/mol, local density functionals have MUEs in the range 0.7 to 3.7 kcal/mol, and hybrid density functionals have MUEs of only 0.3 to 1.0 kcal/mol, with the best density functional performance obtained by hybrid meta-GGAs, especially M06 and PW6B95.

Catalytic mechanism of 4-oxalocrotonate tautomerase: significances of protein-protein interactions on proton transfer pathways

4-Oxalocrotonate tautomerase (4-OT), a member of tautomerase superfamily, is an essential enzyme in the degradative metabolism pathway occurring in the Krebs cycle. The proton transfer process catalyzed by 4-OT has been explored previously using both experimental and theoretical methods; however, the elaborate catalytic mechanism of 4-OT still remains unsettled. By combining classical molecular mechanics with quantum mechanics, our results demonstrate that the native hexametric 4-OT enzyme, including six protein monomers, must be employed to simulate the proton transfer process in 4-OT due to protein-protein steric and electrostatic interactions. As a consequence, only three out of the six active sites in the 4-OT hexamer are observed to be occupied by three 2-oxo-4-hexenedioates (2o4hex), i.e., half-of-the-sites occupation. This agrees with experimental observations on negative cooperative effect between two adjacent substrates. Two sequential proton transfers occur: one proton from the C3 position of 2o4hex is initially transferred to the nitrogen atom of the general base, Pro1. Subsequently, the same proton is shuttled back to the position C5 of 2o4hex to complete the proton transfer process in 4-OT. During the catalytic reaction, conformational changes (i.e., 1-carboxyl group rotation) of 2o4hex may occur in the 4-OT dimer model but cannot proceed in the hexametric structure. We further explained that the docking process of 2o4hex can influence the specific reactant conformations and an alternative substrate (2-hydroxymuconate) may serve as reactant under a different reaction mechanism than 2o4hex.