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Two mechanisms are proposed for the racemization reaction catalyzed by Aquifex pyrophillus glutamate racemase enzyme. The results have shown that the behavior of an enzyme depends on the ionization state of its active site residues and justifies the calculation of their ionization probabilities to understand the enzyme catalytic mechanism.

A fully microscopical simulation of the rate-limiting hydrogen abstraction catalyzed by soybean lipoxygenase-1 (SLO-1) was carried out and the rate constants and kinetic isotope effect (KIE) were calculated. The results show that the compression of the wild-type active site enzyme results in the huge contribution of tunneling to the rate of the hydrogen abstraction and the calculated KIE for the wild-type enzyme has an important dependence on the barrier width.

Computer simulations on a QM/MM potential energy surface are carried out to gain insights into the catalytic mechanism of glutamate racemase (Murl). Studies suggest two possible roles for Murl as a catalyst, which are achieved without resorting to covalent bond formulation between the enzyme or cofactor and the transition state.

Molecular dynamics umbrella-sampling simulations and ensemble-averaged variational transition state theory with multidimensional tunneling (EA-VTST/MT) is applied to explore the free energy surface, reaction paths, and dideuterium kinetic isotope effect (KIE) of the beta-oxidation of butyryl-coenzyme A by short-chain acyl-CoA dehydrogenase. There is a dip in the free energy profile between the proton-transfer barrier and the hybride-transfer barrier, and this dip may be too small to be observed.

Research has been conducted on the effects of quantum mechanics in enzyme kinetics. The topics of interest include atoms' electronic structure in the catalytic center, the nature of the quantum mechanical vibrational energies and the multidimensional tunneling.

The presence of a negative slope of the chemical shift as a function of the temperature can be used to identify hydrogen bonds as low-barrier hydrogen bonds in gas phase and even in inert solvents. This was gleaned from an analysis of the nuclear magnetic resonance chemical shifts of the proton involved in the intramolecular hydrogen bond in hexabenzyloxymethyl-XDK monoanion and hydrogen oxalate anion. It was found that the chemical shift decreases as the temperature rises for hexabenzyloxymethyl-XDK monoanion, while the opposite is true for the hydrogen oxalate anion.

Quantum mechanical and thermodynamic ab initio calculations were performed to characterize and compare the gas-phase properties of the intramolecular hydrogen bond in the maleic monoanion, otherwise known as hydrogen maleate anion, with hydrogen bonds in the monoanion of maleic monoamide. The results provided evidence concerning its status as a low-barrier hydrogen bond, one of which relates to the short distance between the hydrogen-donor and hydrogen-acceptor atoms.

Molecular Dynamics simulations with a Molecular Mechanics (MM) force field and the quantum mechanics (QM)/MM potential energy surfaces are preformed to analyze the D-glutamate -> L-glutamate reaction catalyzed by Bacillus subtilis glutamate racemase. The studies have shown that the whole process has involved four successive proton transfers occurring in three different steps.

4-Oxalocrotonate tautomerase enzyme (4-OT) has catalyzed the isomerization of 2-oxo-4-hexenedioate and the isomerization is studied by using the combined quantum mechanical and molecular mechanical method. The studies have shown that proton transfer process is coupled to a conformational change of the substrate and the conformation change is promoted by the changes in the electron distribution of the substrate taking place as the proton transfer has occurred.

A computational study of pyruvate to lactate transformation catalyzed by lactate dehydrogenase is performed. Results indicate that the two transfers take place in a single concerted process although the degree of asynchronicity may depend on the particular reaction path followed.

A theoretical study designed to examine the reliability of inferring the transition state structure for an enzyme-catalyzed hydride transfer reaction on the basis of an empirical criterion is presented. Results reveal that the donor carbon at the hydride transfer transition state resembles the reactant state more than the product state, whereas the acceptor carbon is more productlike, which is a symptom of transition state imbalance.

Reactive flux molecular dynamics simulations are carried out using a combined QM/MM potential to study the dynamics of the nucleophilic substitution reaction of dichloroethane by a carboxylate group in haloalkane dehalogenase and in water. It is found that protein dynamics accelerates the reaction rate by a factor of 2 over the uncatalyzed reaction.

Research shows that the M20 loop of Escherichia coli dihydrofolate reductase contributes to the electrostatic stabilization of the hydride transfer transition state during the transfer reaction from NADPH coenzyme to the substrate. Data indicate that the hydride transfer reaction becomes rate limiting at high pH as revealed by the kinetic isotopic effect.

The xylose isomerization is examined in terms of the classical/quantal dynamical simulations to understand metal motion. Research reveals that the average magnesium-magnesium distance increases monotonically from 3.6 angstrom to 3.9 angstrom with respect to the reaction coordinate. Data indicate that hydride-transfer reaction follows proton-transfer step during the isomerization.

Recent experimental results have challenged conventional views on the role metals play in the chemistry of protein kinases because it has been shown that (cAMP)-dependent protein kinase (PKA) is active in the presence of other divalent alkaline earth metal cations besides physiological Mg2+ ions. This has raised the important possibility that Ca2+ may also be a physiological cofactor of protein kinases. In this work, QM/MM calculations, at the DFT and MP2 levels for the QM part, on complete solvated models of PKAc–M2ATP–substrate ternary complexes, with PKAc as the catalytic subunit of PKA, M denoting Ca2+ or Sr2+ and substrate denoting SP20 or Kemptide, have been carried out for the overall phosphoryl transfer reaction. In accordance with the experimental data, our theoretical results show for the first time at the molecular level how the overall PKAc-catalyzed phosphorylation of SP20, via a dissociative mechanism, is plausible with Ca2+ and Sr2+. The viability of the catalytic reaction with Kemptide and Ca2+ is also verified here. The energy barrier of the rate-limiting phosphoryl-transfer step does not depend on different coordination environments of the alkaline earth metal cations whereas the proton-transfer step region is metal dependent making the global chemical process more exoergic on going from Mg2+ to Sr2+. This trend is in agreement with the less effective release of the phosphorylated product observed experimentally in the presence of Ca2+versus Mg2+, and would explain also the lower activity of PKAc with Ca2+, since phospho-substrate and ADP releases are rate limiting for catalytic turnover. For the same reason, we predict an even lower activity of PKAc with Sr2+. Moreover, the active sites of the in silico reactant and product complexes and the available X-ray crystallographic structures show good agreement. [ABSTRACT FROM AUTHOR]