Transient kinetic studies of substrate inhibition in the horse liver alcohol dehydrogenase reaction

Substrate inhibition by the blockage of product release and its control by tunnel engineering

Substrate inhibition is the most common deviation from Michaelis-Menten kinetics, occurring in approximately 25% of known enzymes. It is generally attributed to the formation of an unproductive enzyme-substrate complex after the simultaneous binding of two or more substrate molecules to the active site. Here, we show that a single point mutation (L177W) in the haloalkane dehalogenase LinB causes strong substrate inhibition. Surprisingly, a global kinetic analysis suggested that this inhibition is caused by binding of the substrate to the enzyme-product complex. Molecular dynamics simulations clarified the details of this unusual mechanism of substrate inhibition: Markov state models indicated that the substrate prevents the exit of the halide product by direct blockage and/or restricting conformational flexibility. The contributions of three residues forming the possible substrate inhibition site (W140A, F143L and I211L) to the observed inhibition were studied by mutagenesis. An unusual synergy giving rise to high catalytic efficiency and reduced substrate inhibition was observed between residues L177W and I211L, which are located in different access tunnels of the protein. These results show that substrate inhibition can be caused by substrate binding to the enzyme-product complex and can be controlled rationally by targeted amino acid substitutions in enzyme access tunnels.

Substitutions of Amino Acid Residues in the Substrate Binding Site of Horse Liver Alcohol Dehydrogenase Have Small Effects on the Structures but Significantly Affect Catalysis of Hydrogen Transfer

Previous studies showed that the L57F and F93W alcohol dehydrogenases catalyze the oxidation of benzyl alcohol with some quantum mechanical hydrogen tunneling, whereas the V203A enzyme has diminished tunneling. Here, steady-state kinetics for the L57F and F93W enzymes were studied, and microscopic rate constants for the ordered bi-bi mechanism were estimated from simulations of transient kinetics for the S48T, F93A, S48T/F93A, F93W, and L57F enzymes. Catalytic efficiencies for benzyl alcohol oxidation (V₁/E_tK_b) vary over a range of ∼100-fold for the less active enzymes up to the L57F enzyme and are mostly associated with the binding of alcohol rather than the rate constants for hydride transfer. In contrast, catalytic efficiencies for benzaldehyde reduction (V₂/E_tK_p) are ∼500-fold higher for the L57F enzyme than for the less active enzymes and are mostly associated with the rate constants for hydride transfer. Atomic-resolution structures (1.1 Å) for the F93W and L57F enzymes complexed with NAD⁺ and 2,3,4,5,6-pentafluorobenzyl alcohol or 2,2,2-trifluoroethanol are almost identical to previous structures for the wild-type, S48T, and V203A enzymes. Least-squares refinement with SHELXL shows that the nicotinamide ring is slightly strained in all complexes and that the apparent donor-acceptor distances from C4N of NAD to C7 of pentafluorobenzyl alcohol range from 3.28 to 3.49 Å (±0.02 Å) and are not correlated with the rate constants for hydride transfer or hydrogen tunneling. How the substitutions affect the dynamics of reorganization during hydrogen transfer and the extent of tunneling remain to be determined.

Metabolic methanol: molecular pathways and physiological roles

Methanol has been historically considered an exogenous product that leads only to pathological changes in the human body when consumed. However, in normal, healthy individuals, methanol and its short-lived oxidized product, formaldehyde, are naturally occurring compounds whose functions and origins have received limited attention. There are several sources of human physiological methanol. Fruits, vegetables, and alcoholic beverages are likely the main sources of exogenous methanol in the healthy human body. Metabolic methanol may occur as a result of fermentation by gut bacteria and metabolic processes involving S-adenosyl methionine. Regardless of its source, low levels of methanol in the body are maintained by physiological and metabolic clearance mechanisms. Although human blood contains small amounts of methanol and formaldehyde, the content of these molecules increases sharply after receiving even methanol-free ethanol, indicating an endogenous source of the metabolic methanol present at low levels in the blood regulated by a cluster of genes. Recent studies of the pathogenesis of neurological disorders indicate metabolic formaldehyde as a putative causative agent. The detection of increased formaldehyde content in the blood of both neurological patients and the elderly indicates the important role of genetic and biochemical mechanisms of maintaining low levels of methanol and formaldehyde.

Alternative pathways and reactions of benzyl alcohol and benzaldehyde with horse liver alcohol dehydrogenase

Liver alcohol dehydrogenase catalyzes the reaction of NAD+ and benzyl alcohol to form NADH and benzaldehyde by a predominantly ordered reaction. However, enzyme-alcohol binary and abortive ternary complexes form at high concentrations of benzyl alcohol, and benzaldehyde is slowly oxidized to benzoic acid. Steady-state and transient kinetic studies, equilibrium spectrophotometric measurements, product analysis, and kinetic simulations provide estimates of rate constants for a complete mechanism with the following reactions: (1) E<-->E-NAD+<-->E-NAD(+)-RCH2OH<-->E-NADH-RCHO<-->E-NADH<-->E ; (2) E-NADH<-->E-NADH-RCH2OH<-->E-RCH2OH<-->E; (3) E-NAD+<-->E-NAD(+)-RCHO-->E- NADH-RCOOH<-->E-NADH. The internal equilibrium constant for hydrogen transfer determined at 30 degrees C and pH 7 is about 5:1 in favor of E-NAD(+)-RCH2OH and has a complex pH dependence. Benzyl alcohol binds weakly to free enzyme (Kd = 7 mM) and significantly decreases the rates of binding of NAD+ and NADH. The reaction of NAD+ and benzyl alcohol is therefore kinetically ordered, not random. High concentrations of benzyl alcohol (> 1 mM) inhibit turnover by formation of the abortive E-NADH-RCH2-OH complex, which dissociates at 0.3 s-1 as compared to 6.3 s-1 for E-NADH. The oxidation of benzaldehyde by E-NAD+ (Km = 15 mM, V/E = 0.4 s-1) is inefficient relative to the oxidation of benzyl alcohol (Km = 28 microM, V/E = 3.1 s-1) and leads to a dismutation (2RCHO-->RCH2OH + RCOOH) as E-NADH reduces benzaldehyde. The results provide a description of final product distributions for the alternative reactions catalyzed by the multifunctional enzyme.

Characterization of the general anion-binding site in glutamate dehydrogenase-NADPH complex

The reductive amination of alpha-ketoglutarate, catalyzed by bovine liver glutamate dehydrogenase, is inhibited by various anions. Formate and acetate ions are competitive with alpha-ketoglutarate. The pH dependence of the pKi profiles for these anions reveals that they bind to the enzyme-NADPH complex only when an enzymatic residue of pK 8.0 +/- 0.1 in the binary complex is protonated. The ionization of this residue has a delta Hion of 15 +/- 4 kcal/mol. These pK and delta Hion values are not significantly different from those observed in the same complex for the enzyme group which binds the gamma-CO2- of alpha-ketoglutarate and oxalylglycine. It is concluded that formate and acetate also bind to the gamma-carboxylate site in enzyme-NADPH. The Ki values for formate and acetate in a buffer containing 0.1 M phosphate are 20 +/- 4 and 32 +/- 5 mM, respectively, when the pK 8.0 group is fully protonated. Phosphate and trifluoroacetate also show an inhibitory effect, while valerate and sulfate have little effect on the reductive amination rates. The results suggest that specific anions can bind to the gamma-carboxylate site by ionic interactions and alter the kinetic and thermodynamic parameters of the glutamate dehydrogenase-NADPH complex in significant ways.

Kinetics and mechanism of methanol and formaldehyde interconversion and formaldehyde oxidation catalyzed by liver alcohol dehydrogenase

It has been shown that the hydrophobic interaction in the active-site plays a fundamental role in substrate binding. Proper molecular orientation is required for hydride transfer (Dalziel and Dickinson, 1967). For methanol, the binding is unfavored due to the lack of a hydrophobic chain. In the enzyme-coenzyme-substrate complex, the small methyl group of the substrate is not held in a fixed position, resulting in a low hydride transfer rate. The binding of NAD+ to the enzyme does not exhibit a significant effect on the binding of methanol, nor does methanol affect NAD+ binding. In the presence of LADH, methanol is oxidized by NAD+ to formaldehyde, while formaldehyde can be oxidized by NAD+ to formate ion or reduced by NADH to methanol. These reactions follow a rapid equilibrium random mechanism. Among these three reactions, the reduction of formaldehyde is the most rapid. The rate of formaldehyde oxidation is faster than the oxidation of methanol. Our study with these non-hydrophobic substrates provides an important bridge between the bioinorganic activation of zinc-bound water and the bioorganic oxidation of ethanol. Furthermore, it furnishes some insight into an enzymatic system that is so highly sensitive to small changes in substrate chain length that it can magnify the consequence of a modest change in substrate hydrophobicity.

Influence of anions and pH on the conformational change of horse liver alcohol dehydrogenase induced by binding of oxidized nicotinamide adenine dinucleotide: binding of chloride to the catalytic metal ion

The conformational change of horse liver alcohol dehydrogenase induced by binding of NAD+ was studied by electronic absorption spectroscopy using cobalt as a spectroscopic probe in the active site. The complex of the enzyme with NAD+ exists in an acidic and an alkaline form. The transition between the two forms proceeds through several intermediates and is controlled by an apparent pKa of 6.9. Only at pH values below this pKa can a complex between enzyme, NAD+, and Cl- be formed. The spectral changes indicate that chloride displaces the cobalt-bound water molecule in a tetracoordinate structure. We conclude that a negative charge at the active site is necessary to stabilize the closed conformation of the enzyme in the presence of NAD+. Spectral correlations are given which strongly support the postulation of a metal-bound alkoxide in the closed structure of the enzyme as an essential feature of the catalytic mechanism of horse liver alcohol dehydrogenase.

Anion effects on the liver alcohol dehydrogenase reaction

The effects of various anions on the rate constant for dissociation of NADH from a binary complex with horse liver alcohol dehydrogenase were evaluated. Phosphate, sulfate, and fluoride had no effect, while nitrate and the other halide ions caused a three- to fourfold increase in the rate constant for NADH dissociation. These results indicate that a ternary enzyme-NADH-anion complex is formed, and from the anion concentration dependence the relative affinities are iodide greater than nitrate and bromide greater than chloride. At high salt concentrations, above 0.2 M, the rate constants for NADH dissociation decreased, which was attributed to a decrease in the activity coefficient of the reactants or "salting in." The rate constant for NADH dissociation from ternary complex with imidazole, which crystallizes in an orthorhombic form rather than triclinic, was also substantially enhanced by anions. This provides an indication that the enhancement is independent of the conformational state of the enzyme complex. Thus, the most likely explanation for the observed enhancement of NADH dissociation is anion interference with binding of the coenzyme pyrophosphate group, which does not occur with larger anions such as phosphate or sulfate. Since NADH dissociation partially limits the turnover of the enzyme, the effect of nitrate on steady-state turnover was determined. A twofold increase was observed at optimal levels of nitrate, at both substrate inhibitory and noninhibitory concentrations of ethanol.

Synergism between coenzyme and alcohol binding to liver alcohol dehydrogenase

Heterotropic cooperativity effects in the binding of alcohols and NAD+ or NADH to liver alcohol dehydrogenase have been examined by equilibrium measurements and stopped-flow kinetic studies. Equilibrium data are reported for benzyl alcohol, 2-chloroethanol, 2,2-dichloroethanol, and trifluoroethanol binding to free enzyme over the pH range 6-10. Binary-complex formation between enzyme and alcohols leads to inner-sphere coordination of the alcohol to catalytic zinc and shows a pH dependence reflecting the ionization states of zinc-bound water and the zinc-bound alcohol. The affinity of the binding protonation state of the enzyme for unionized alcohols increases approximately by a factor of 10 on complex formation between enzyme and NAD+ or NADH. The rate and kinetic cooperativity with coenzyme binding of the alcohol association step indicates that enzyme-bound alcohols participate in hydrogen bonding interactions which affect the rates of alcohol and coenzyme equilibration with the enzyme without providing any pronounced contribution to the net energetics of alcohol binding. The pKa values determined for alcohol deprotonation at the binary-complex level are linearly dependent on those of the free alcohols, and can be readily reconciled with the pKa values attributed to ionization of zinc-bound water. Alcohol coordination to catalytic zinc provides a major contribution to the pKa shift which ensures that the substrate is bound predominantly as an alcoholate ion in the catalytically productive ternary complex at physiological pH. The additional pKa shift contributed by NAD+ binding is less pronounced, but may be of particular mechanistic interest since it increases the acidity of zinc-bound alcohols relatively to that of zinc-bound water.