Utilization of Cofactor Binding Energy for Enzyme Catalysis: Formate Dehydrogenase-Catalyzed Reactions of the Whole NAD Cofactor and Cofactor Pieces.

The pressure to optimize enzymatic rate accelerations has driven the evolution of the induced-fit mechanism for enzyme catalysts where the binding interactions of nonreacting phosphodianion or adenosyl substrate pieces drive enzyme conformational changes to form protein substrate cages that are activated for catalysis. We report the results of experiments to test the hypothesis that utilization of the binding energy of the adenosine 5'-diphosphate ribose (ADP-ribose) fragment of the NAD cofactor to drive a protein conformational change activates Candida boidinii formate dehydrogenase (CbFDH) for catalysis of hydride transfer from formate to NAD+. The ADP-ribose fragment provides a >14 kcal/mol stabilization of the transition state for CbFDH-catalyzed hydride transfer from formate to NAD+. This is larger than the ca. 6 kcal/mol stabilization of the ground-state Michaelis complex between CbFDH and NAD+ (KNAD = 0.032 mM). The ADP, AMP, and ribose 5'-phosphate fragments of NAD+ activate CbFDH for catalysis of hydride transfer from formate to nicotinamide riboside (NR). At a 1.0 M standard state, these activators stabilize the hydride transfer transition states by ≈5.5 (ADP), 5.5 (AMP), and 4.4 (ribose 5'-phosphate) kcal/mol. We propose that activation by these cofactor fragments is partly or entirely due to the ion-pair interaction between the guanidino side chain cation of R174 and the activator phosphate anion. This substitutes for the interaction between the α-adenosyl pyrophosphate anion of the whole NAD+ cofactor that holds CbFDH in the catalytically active closed conformation.

Phosphodianion Activation of Enzymes for Catalysis of Central Metabolic Reactions.

The activation barriers ΔG⧧ for kcat/Km for the reactions of whole substrates catalyzed by 6-phosphogluconate dehydrogenase, glucose 6-phosphate dehydrogenase, and glucose 6-phosphate isomerase are reduced by 11-13 kcal/mol by interactions between the protein and the substrate phosphodianion. Between 4 and 6 kcal/mol of this dianion binding energy is expressed at the transition state for phosphite dianion activation of the respective enzyme-catalyzed reactions of truncated substrates d-xylonate or d-xylose. These and earlier results from studies on ß-phosphoglucomutase, triosephosphate isomerase, and glycerol 3-phosphate dehydrogenase define a cluster of six enzymes that catalyze reactions in glycolysis or of glycolytic intermediates, and which utilize substrate dianion binding energy for enzyme activation. Dianion-driven conformational changes, which convert flexible open proteins to tight protein cages for the phosphorylated substrate, have been thoroughly documented for five of these six enzymes. The clustering of metabolic enzymes which couple phosphodianion-driven conformational changes to enzyme activation suggests that this catalytic motif has been widely propagated in the proteome.

N-(Hydroxybenzyl)benzamide Derivatives: Aqueous pH-Dependent Kinetics and Mechanistic Implications for the Aqueous Reactivity of Carbinolamides.

The rate constants for the aqueous reaction, between pH 0 and 14, have been determined for a series of amide substituted N-(hydroxybenzyl)benzamide derivatives, in H2O, at 25 °C, I = 1.0 M (KCl). The N-(hydroxybenzyl)benzamide derivatives were found to react via three distinct mechanisms with the kinetically dominant mechanism being dependent on the pH of the reaction solution. It has been shown that the carbinolamides react via a specific-base-catalyzed mechanism (E1cB-like) under basic and pH neutral conditions. At lower pH values, an acid-catalyzed mechanism was kinetically dominant and, last, a water reaction was postulated at pH values where neither the hydroxide-dependent nor the general-acid-catalyzed mechanism was dominant. Contrary to earlier studies with N-(hydroxymethyl)benzamide compounds, no evidence for mechanistic variation based upon the nature of the amidic substituent was observed for any of the N-(hydroxybenzyl)benzamide derivatives studied between pH values of 0-14. The rate for the acid-catalyzed reaction (kH, ρ = -1.17), the apparent second-order hydroxide rate constant (k1', ρ = 0.87), the hydroxide-independent rate (k1, ρ = 0.65), and the pKa's of the hydroxyl group of the carbinolamide (ρ = 0.23) are reported.

Determination of the pKa of cyclobutanone: Brønsted correlation of the general base-catalyzed enolization in aqueous solution and the effect of ring strain.

The induction of strain in carbocycles, thereby increasing the amount of s-character in the C-H bonds and the acidity of these protons, has been probed with regard to its effect on the rate constants for the enolization of cyclobutanone. The second-order rate constants for the general base-catalyzed enolization of cyclobutanone have been determined for a series of 3-substituted quinuclidine buffers in D(2)O at 25 °C, I = 1.0 M (KCl). The rate constants for enolization were determined by following the extent of deuterium incorporation (up to ∼30% of the first α-proton) into the α-position, as a function of time. The observed pseudo-first-order rate constants correlated to the [basic form] of the buffer and yielded the second-order rate constants for the general base-catalyzed enolization of cyclobutanone for four tertiary amine buffers. A Brønsted ß-value of 0.59 was determined from the second-order rate constants determined. Comparison of the results for cyclobutanone to those previously reported for acetone and a 1-phenylacetone derivative, under similar conditions, indicated that the ring strain of the carbocycle appeared to have only a small effect on the general base-catalyzed rate constants for enolization. The similarity of the rate constants for the general base-catalyzed enolization of cyclobutanone to those determined for acetone allowed for an estimation of the limits of the rate constant for protonation of the enolate intermediate of cyclobutanone by the conjugate acid of 3-quinuclidinone (k(BH) = 5 × 10(8) - 2 × 10(9) M(-1) s(-1)). Combining the rate constants for deprotonation of cyclobutanone (k(B)) and protonation of the enolate of cyclobutanone (k(BH)) by 3-quinuclidinone and its conjugate acid, the pK(a) of the α-protons of cyclobutanone has been estimated to be pK(a) = 19.7-20.2.

Amidates as leaving groups: structure/reactivity correlation of the hydroxide-dependent E1cB-like breakdown of carbinolamides in aqueous solution.

The kinetic study of the aqueous reaction, between pH 10 and 14, of eight N-(hydroxymethyl)benzamide derivatives in water at 25 degrees C, I = 1.0 M (KCl), has been performed. In all cases, the reaction proceeds via a specific-base-catalyzed deprotonation of the hydroxyl group followed by rate-limiting breakdown of the alkoxide to form aldehyde and amidate (E1cB-like). Such a mechanism was supported by the lack of general buffer catalysis and the first-order dependence of the rate of reaction at low hydroxide concentrations and the transition to zero-order dependence on hydroxide at high concentration. A rho-value of 0.67 was found for the Hammett correlation between the maximum rate for the hydroxide independent breakdown of the deprotonated carbinolamide (k1) and the substituent on the aromatic ring of the title compounds. Conversely, the substituents on the aromatic ring of the amide portion of the carbinolamide had only a small effect on the Ka of the hydroxyl group indicating that the amide group does not strongly transmit the electronic information of the substituents. These observations led to the conclusion that the major effect of electronic changes on the amide of carbinolamides is reflected in the nucleofugality of the amidate once the alkoxide is formed and not in the pKa of the hydroxyl group of the carbinolamide.

Ring strain and its effect on the rate of the general-base catalyzed enolization of cyclobutanone.

[reaction: see text] The 3-quinuclidinone-catalyzed (pK(BH) = 7.5) enolization of cyclobutanone (1) in D(2)O at 25 degrees C, I = 1.0 (KCl) was followed by deuterium incorporation, which was determined by (1)H NMR. The second-order rate constant for the buffer-catalyzed deprotonation of 1 was found to be k(B) = 3.3 x 10(-4) M(-1) s(-1), which is compared to rates for acetone and 2-(2'-oxopropyl)benzaldehyde under similar conditions. The data shows that ring strain has very little effect on the energy barrier to deprotonation of 1 vs the unstrained systems.