Towards the unification of coenzyme B12-dependent diol dehydratase stereochemical and model studies: The bound radical mechanism

Radical enzymes in anaerobes

This review describes enzymes that contain radicals and/or catalyze reactions with radical intermediates. Because radicals irreversibly react with dioxygen, most of these enzymes occur in anaerobic bacteria and archaea. Exceptions are the families of coenzyme B(12)- and S-adenosylmethionine (SAM)-dependent radical enzymes, of which some members also occur in aerobes. Especially oxygen-sensitive radical enzymes are the glycyl radical enzymes and 2-hydroxyacyl-CoA dehydratases. The latter are activated by an ATP-dependent one-electron transfer and act via a ketyl radical anion mechanism. Related enzymes are the ATP-dependent benzoyl-CoA reductase and the ATP-independent 4-hydroxybenzoyl-CoA reductase. Ketyl radical anions may also be generated by one-electron oxidation as shown by the flavin-adenine-dinucleotide (FAD)- and [4Fe-4S]-containing 4-hydroxybutyryl-CoA dehydratase. Finally, two radical enzymes are discussed, pyruvate:ferredoxin oxidoreductase and methane-forming methyl-CoM reductase, which catalyze their main reaction in two-electron steps, but subsequent electron transfers proceed via radicals.

Electron-Transfer Oxidation of Coenzyme B12 Model Compounds and Facile Cleavage of the Cobalt(IV)−Carbon Bond via Charge-Transfer Complexes with Bases. A Negative Temperature Dependence of the Rates

The electron-transfer oxidation and subsequent cobalt-carbon bond cleavage of vitamin B12 model complexes were investigated using cobaloximes, (DH)2Co(III)(R)(L), where DH- = the anion of dimethylglyoxime, R = Me, Et, Ph, PhCH2, and PhCH(CH3), and L = a substituted pyridine, as coenzyme B12 model complexes and [Fe(bpy)3](PF6)3 or [Ru(bpy)3](PF6)3 (bpy = 2,2'-bipyridine) as a one-electron oxidant. The rapid one-electron oxidation of (DH)2Co(III)(Me)(py) (py = pyridine) with the oxidant gives the corresponding Co(IV) complexes, [(DH)2Co(IV)(Me)(py)]+, which were well identified by the ESR spectra. The reorganization energy (lambda) for the electron-transfer oxidation of (DH)2Co(Me)(py) was determined from the ESR line broadening of [(DH)2Co(Me)(py)]+ caused by the electron exchange with (DH)2Co(Me)(py). The lambda value is applied to evaluate the rate constants of photoinduced electron transfer from (DH)2Co(Me)(py) to photosensitizers in light of the Marcus theory of electron transfer. The Co(IV)-C bond cleavage of [(DH)2Co(Me)(py)]+ is accelerated significantly by the reaction with a base. The overall activation energy for the second-order rate constants of Co(IV)-C bond cleavage of [(DH)2Co(IV)(Me)(py)]+ in the presence of a base is decreased by charge-transfer complex formation with a base, which leads to a negative activation energy for the Co(IV)-C cleavage when either 2-methoxypyridine or 2,6-dimethoxypyridine is used as the base.

Kinetic and thermodynamic studies on ligand substitution reactions and base-on/base-off equilibria of cyanoimidazolylcobamide, a vitamin B12 analog with an imidazole axial nucleoside

Ligand substitution reactions of the vitamin B12 analog cyanoimidazolylcobamide, CN(Im)Cbl, with cyanide were studied. Cyanide substitutes imidazole (Im) in the alpha-position more slowly than it substitutes dimethylbenzimidazole in cyanocobalamin (vitamin B12). The kinetics of the displacement of Im by CN- showed saturation behaviour at high cyanide concentration; the limiting rate constant was found to be 0.0264 s(-1) at 25 degrees C and is characterized by the activation parameters: DeltaH(not =) = 111 +/- 2 kJ mol(-1), DeltaS(not =) = +97 +/- 6 J K(-1) mol(-1), and DeltaV(not =) = +9.3 +/- 0.3 cm3 mol(-1). These parameters are interpreted in terms of an I(d) mechanism. The equilibrium constant for the reaction of CN(Im)Cbl with CN- was found to be 861 +/- 75 M(-1), which is significantly less than that obtained for the reaction of cyanocobalamin with CN- (viz. 10(4) M(-1)). pKbase-off for the base-on/base-off equilibrium was determined spectrophotometrically and found to be 0.99 +/- 0.05, which is about 0.9 pH units higher than that obtained previously in the case of cyanocobalamin. In addition, the kinetics of the base-on/base-off reaction was studied using a pH-jump technique and the data obtained revealed evidence for an acid catalyzed reaction path. The results obtained in this study are discussed in reference to those reported previously for cyanocobalamin.

Co-C bond dissociation energy and reaction volume change of 2',5'-dideoxyadenosylcobalamin studied by laser-induced time-resolved photoacoustic calorimetry

Time resolved photoacoustic calorimetry (PAC) was applied to a study of the photolysis of a coenzyme B(12) analog 2',5'-dideoxyadenosylcobalamin, which lacks an -OH group at the 2' position of ribofuranose ring. In aqueous solution, we report for the first time the quantum yield Phi(d) (0.25+/-0.02), Co-C bond dissociation energy (BDE; 31.8+/-2.5 kcal mol(-1)) and reaction volume change deltaV(R) (6.5+/-0.5 ml mol(-1)) due to conformation changes of the corrin ring and its side chains accompanying the cleavage of the Co-C bond. These values for the analog are very similar to those for the natural cofactor. Based our results and previous studies, a possible explanation for the similarity in their structure and properties versus the large difference in their enzymatic activity is discussed.

Substituent effects on the ionization reaction of beta-mesylate phenethyl radicals

A series of beta-methanesulfonate phenethyl radicals bearing a range of electron donating and withdrawing aromatic substituents were generated and studied in a variety of solvent mixtures using nanosecond laser flash photolysis. Rate constants for the formation of the corresponding styrene radical cation via heterolytic loss of the beta-mesylate leaving group were measured using time-resolved absorption spectroscopy. The ionization reaction was investigated in a variety of solvents and solvent mixtures including 1,1,1,3,3,3-hexafluoro-2-propanol, 2,2,2-trifluoroethanol, acetonitrile, methanol and water. The influence of substituent electronic effect and solvent polarity on the kinetics of the beta-heterolysis reaction are discussed and assessed using the sigma+ Hammett parameter and Y(OMs) values, respectively. The small magnitude of m calculated for the formation of the 4-methoxystyrene radical cation by ionization of the mesylate group (m = 0.33) in aqueous methanol mixtures is compared to values obtained for the formation of the same radical cation via loss of chloride and bromide where m = 0.56 and m = 0.45, respectively.

Steric control of organic transformation by a dendrimer cage: organocobalt dendrimer porphyrins as novel coenzyme B(12) mimics

Cobalt(II) complexes of poly(aryl ester) dendrimer porphyrins (m-[Gn]TPP)Co(II) and (p-[Gn]TPP)Co(II) (n = 0-3) underwent AIBN-initiated alkylation (AIBN = 2,2'-azobis(isobutyronitrile)) at the metal center with propargyl alcohol in CDCl(3) at 60 degrees C, where the dendritic substituents did not affect the overall conversion rate but selectivity of the alkylation. With the largest (m-[G3]TPP)Co(II), a single organocobalt(III) species (Co(III)-C(=CH(2))CH(2)OH, 4) was selectively formed in 91% yield, due to a steric protection of 4 by the large dendrimer cage from the access of another molecule of cobalt porphyrin species. In contrast, with other cobalt(II) porphyrins, isomerized compounds such as Co(III)-C(CH(3))=CHOH (5) and Co(III)-CH(CH(3))CHO (6) were formed in addition to 4. A stereochemical investigation with (m-[G3]TPP)Co(II) using AIBN-d(12), in place of nondeuterated AIBN, demonstrated that the alkylation (cobalt(III) hydride addition to propargyl alcohol) is selective to a trans adduct. Results also indicated that this addition step does not involve external activation of propargyl alcohol.

Computational exploration of rearrangements related to the vitamin B12-dependent ethanolamine ammonia lyase catalyzed transformation

DFT (B3LYP/6-31G) and ab initio molecular orbital theory (QCISD/cc-pVDZ) are used to investigate several possible mechanisms involving free radical intermediates as well as their protonated forms for processes related to the coenzyme B(12)-dependent rearrangement catalyzed by ethanolamine ammonia lyase. Two major types of rearrangements are discussed in detail, intramolecular migration and dissociation of the amine/ammonia groups, for both of which several scenarios are considered. According to the calculations, the complete dissociation of the migrating group and its subsequent association constitute an unlikely route for both the protonated and the unprotonated reactant because of the high-energy barriers (more than 23 kcal/mol) involved in these steps. Direct migration of the protonated amine group is far more favorable (10.4 kcal/mol) and therefore presents the most likely candidate for the actual enzymatic reaction. The calculations further imply that the direct loss of an ammonium cation (10.6 kcal/mol) represents a feasible pathway as well. Comparing the rearrangements for the aminoethanol radical and its protonated counterpart, in line with previous findings reported by Golding, Radom, and co-workers, we find that the migration of a protonated group is in general associated with lower energy barriers, suggesting that the actual enzyme substrate quite likely corresponds to (partially) protonated aminoethanol. As the extent of the substrate protonation/deprotonation by the active site of the enzyme may vary, the actual energy barriers are expected to range between the values calculated for the two extreme cases of a substrate, that is, the aminoethanol radical 2 and its fully protonated form 6.

Mechanism of anaerobic ether cleavage: conversion of 2-phenoxyethanol to phenol and acetaldehyde by Acetobacterium sp

2-Phenoxyethanol is converted into phenol and acetate by a strictly anaerobic Gram-positive bacterium, Acetobacterium strain LuPhet1. Acetate results from oxidation of acetaldehyde that is the early product of the biodegradation process (Frings, J., and Schink, B. (1994) Arch. Microbiol. 162, 199-204). Feeding experiments with resting cell suspensions and 2-phenoxyethanol bearing two deuterium atoms at either carbon of the glycolic moiety as substrate demonstrated that the carbonyl group of the acetate derives from the alcoholic function and the methyl group derives from the adjacent carbon. A concomitant migration of a deuterium atom from C-1 to C-2 was observed. These findings were confirmed by NMR analysis of the acetate obtained by fermentation of 2-phenoxy-[2-(13)C,1-(2)H(2)]ethanol, 2-phenoxy-[1-(13)C,1-(2)H(2)]ethanol, and 2-phenoxy-[1,2-(13)C(2),1-(2)H(2)]ethanol. During the course of the biotransformation process, the molecular integrity of the glycolic unit was completely retained, no loss of the migrating deuterium occurred by exchange with the medium, and the 1,2-deuterium shift was intramolecular. A diol dehydratase-like mechanism could explain the enzymatic cleavage of the ether bond of 2-phenoxyethanol, provided that an intramolecular H/OC(6)H(5) exchange is assumed, giving rise to the hemiacetal precursor of acetaldehyde. However, an alternative mechanism is proposed that is supported by the well recognized propensity of alpha-hydroxyradical and of its conjugate base (ketyl anion) to eliminate a beta-positioned leaving group.

Understanding the mechanism of B(12)-dependent diol dehydratase: a synergistic retro-push--pull proposal

Ab initio molecular orbital theory is used to investigate the coenzyme B(12)-dependent reactions catalyzed by diol dehydratase. The key step in such reactions is believed to be a 1,2-hydroxyl migration, which occurs within free-radical intermediates. The barrier for this migration, if unassisted, is calculated to be too high to be consistent with the observed reaction rate. However, we find that "pushing" the migrating hydroxyl, through interaction with a suitable acid, is able to provide significant catalysis. This is denoted retro-push catalysis, the retro prefix signifying that the motion of the migrating group is in the direction opposite to the electron motion. Similarly, the "pulling" of the migrating group, through interaction of the spectator hydroxyl with an appropriate base, is found to substantially reduce the rearrangement barrier. Importantly, the combination of these two effects results in a barrier reduction that is notably greater than additive. This synergistic interplay of the push and the pull provides an attractive means of catalysis. Our proposed retro-push--pull mechanism leads to results that are consistent with isotope-labeling experiments, with experimental rate data, and with the crystal structure of the enzyme.

Synthesis and Electrochemical Reactivity of sigma-Bonded and N-Substituted Cobalt Porphycenes

The first synthesis and characterization of sigma-bonded and N-substituted cobalt porphycenes is reported. The investigated compounds are represented as (Pc)Co(R) and (N-CH(3)OEPc)CoCl, where R is CH(3) or C(6)H(5), Pc is the dianion of 2,3,6,7,12,13,16,17-octaethylporphycene (OEPc), 2,7,12,17-tetrapropylporphycene (TPrPc), or 2,7,12,17-tetraethyl-3,6,13,16-tetramethylporphycene (EtioPc), N-CH(3)OEPc is the monoanion of N-methyl-2,3,6,7,12,13,16,17-octaethylporphycene. Each sigma-bonded (Pc)Co(R) derivative can be reversibly reduced or oxidized by two electrons, but a slow migration of the sigma-bonded R group occurs following electrogeneration of [(Pc)Co(R)](+)()(*)() leading, as a final product, to an N-substituted cobalt(II) porphycene which is also electroactive and undergoes two reductions in PhCN. The singly reduced product of this reaction is formulated as a Co(II) pi-anion radical which undergoes a slow "back-migration" of the CH(3) group to regenerate (OEPc)Co(CH(3)).

Mössbauer study of 4-hydroxybutyryl-CoA dehydratase--probing the role of an iron-sulfur cluster in an overall non-redox reaction

4-Hydroxybutyryl-CoA dehydratase from Clostridium aminobutyricum catalyzes the dehydration of 4-hydroxybutyryl-CoA to crotonyl-CoA. Although dehydration is an overall non-redox reaction, the enzyme contains FAD and Fe-S clusters. Previous work has shown that the Fe-S clusters are difficult to reduce and therefore unlikely to be redox-active in catalysis. Here, Mössbauer spectroscopy has been used to characterise the Fe-S clusters in active as well as in air-inactivated enzyme. In zero magnetic field at 80 K and 4.2 K, the spectra of active dehydratase consisted mainly of one species (95%) with quadrupole splitting, deltaE(Q) = 1.00 mm s(-1) and isomer shift, delta = 0.43 mm s(-1). Magnetically perturbed Mössbauer spectra indicated a spin of zero. In the presence of 6 mM crotonyl-CoA, the spectra remained unchanged. Taken together, the data show that there are [4Fe-4S]2+ in the enzyme, most probably two clusters/homotetramer, that the four iron atoms in each cluster are coordinated in an identical fashion, and that there is no direct interaction with substrates. We therefore infer that the Fe-S clusters serve a structural rather than a catalytic role in 4-hydroxybutyryl-CoA dehydratase. In air-inactivated enzyme (10% residual activity), a new doublet appeared (58%) with deltaE(Q) = 0.72 mm s(-1), delta = 0.32 mm s(-1) and S = 0. The assignment of this subspectrum to [3Fe-4S]+ clusters, based on the typical Mössbauer parameters, is contradicted by the finding of spin zero for the species. One possible explanation could be spin-coupling of two [3Fe-4S]+ clusters in close proximity.

Mechanisms of Reactions of (*)NO with Complexes with Metal-Carbon sigma-Bonds and with Aliphatic Radicals

The competition kinetics between metal complexes and (*)NO for aliphatic radicals is a convenient technique for determining the rate constants of the reactions of (*)NO with aliphatic radicals. Thus, the rate constants of (*)CH(3) and (*)CH(2)OH with (*)NO were determined to be (3.4 +/- 1.1) x 10(9) and (5.9 +/- 0.5) x 10(9) M(-)(1) s(-)(1), respectively. The same rate constants can be determined, in several systems, from the decrease in the half-life of transient complexes with metal-carbon sigma-bonds which decompose homolytically. In the presence of (*)NO, the half-life of these transient complexes decreases, and their decomposition turns from second-order to first-order processes. From the dependence of the observed first-order rate constant on (*)NO and on the metal complex concentrations, it is concluded that the mechanism of the decomposition of these transients in the presence of (*)NO involves the reaction of (*)NO with the carbon-centered radicals as well as with the transient with the metal-carbon sigma-bonds to form the same products. The rate constants of the reactions of (*)NO with (cyclam)(H(2)O)Ni(III)CH(3)(2+) and (nta)Co(III)CH(2)OH(H(2)O)(-) were determined to be (1.5 +/- 0.2) x 10(5) and (3.6 +/- 0.4) x 10(8) M(-)(1) s(-)(1), respectively. The reactions of (*)NO with complexes with metal-carbon sigma-bonds are analogous to those of aliphatic radicals and dioxygen with the same complexes. This is not surprising as (*)NO is a radical. The biological implications of these results are discussed.

Molecular design and catalytic function of a B12-enzyme mimetic

Developing artificial holoenzymes requires attention to the molecular design, not only of the active site, but also of its microenvironment, which in the naturally occurring enzyme is provided by the apoprotein. Microenvironmental effects play a major role in determining the catalytic performance of an enzyme. Using the development of a B12-dependent holoenzyme mimetic as an example, the important factors and concepts underlying the approaches to developing an artificial holoenzyme are discussed.