The enzymatic activation of coenzyme B12

Green Molecular Transformation in Dual Catalysis: Photoredox Activation of Vitamin B12 Using Heterogeneous Photocatalyst

This concept focuses on dual-catalysis using metal complexes and heterogeneous photocatalysts. Vitamin B12 derivatives are sophisticated metal complexes that facilitate enzymatic reactions in the biological systems. The B12 enzymes inspired reactions catalytically proceed in dual-catalyst systems of B12 derivatives and heterogeneous photocatalysts, such as titanium oxide (TiO2) and metal-organic frameworks (MOFs), under light irradiation. The cobalt ions in B12 derivatives are effectively reduced by photoexcited photocatalysts, producing low-valent Co(I) species. The photoinduced nucleophilic Co(I) species react with an alkyl halide to form an organometallic complex with a Co-C bond. The Co-C bond dissociates during photolysis to generate alkyl radicals. Based on this mechanism, dual-catalysis effectively promotes various light-driven organic syntheses and light-driven dehalogenation reactions of toxic alkyl halides. The trends of the dual-catalyst system and recent progress in this field are discussed in this concept.

Effect of Macrocycles on the Photochemical and Electrochemical Properties of Cobalt-Dehydrocorrin Complex: Formation and Investigation of Co(I) Species

Co(II)-pyrocobester (P-Co(II)), a dehydrocorrin complex, was semisynthesized from vitamin B12 (cyanocobalamin), and its photochemical and electrochemical properties were investigated and compared to those of the cobester (C-Co(II)), the cobalt-corrin complex. The UV-vis absorptions of P-Co(II) in CH2Cl2, ascribed to the π-π* transition, were red-shifted compared to those of C-Co(II) due to the π-expansion of the macrocycle in the pyrocobester. The reversible redox couple of P-Co(II) was observed at E1/2 = -0.30 V vs Ag/AgCl in CH3CN, which was assigned to the Co(II)/Co(I) redox couple by UV-vis, ESR, and molecular orbital analysis. This redox couple was positively shifted by 0.28 V compared to that of C-Co(II). This is caused by the high electronegativity of the dehydrocorrin macrocycle, which was estimated by DFT calculations for the free-base ligands. The reactivity of the Co(I)-pyrocobester (P-Co(I)) was evaluated by the reaction with methyl iodide in CV and UV-vis to form a photosensitive Co(III)-CH3 complex (P-Co(III)-CH3). The properties of the excited state of P-Co(I), *Co(I), were also investigated by femtosecond transient absorption (TA) spectroscopy. The lifetime of *Co(I) was estimated to be 29 ps from the kinetic trace at 587 nm. The lifetime of *Co(I) became shorter in the presence of Ar-X, such as iodobenzonitrile (1a), bromobenzonitrile (1b), and chlorobenzonitrile (1c), and the rate constants of electron transfer (ET) between the *Co(I) and Ar-X were determined to be 2.9 × 1011 M-1 s-1, 4.9 × 1010 M-1 s-1, and 1.0 × 1010 M-1 s-1 for 1a, 1b, and 1c, respectively.

Cofactor Selectivity in Methylmalonyl Coenzyme A Mutase, a Model Cobamide-Dependent Enzyme

Cobamides, a uniquely diverse family of enzyme cofactors related to vitamin B12, are produced exclusively by bacteria and archaea but used in all domains of life. While it is widely accepted that cobamide-dependent organisms require specific cobamides for their metabolism, the biochemical mechanisms that make cobamides functionally distinct are largely unknown. Here, we examine the effects of cobamide structural variation on a model cobamide-dependent enzyme, methylmalonyl coenzyme A (CoA) mutase (MCM). The in vitro binding affinity of MCM for cobamides can be dramatically influenced by small changes in the structure of the lower ligand of the cobamide, and binding selectivity differs between bacterial orthologs of MCM. In contrast, variations in the lower ligand have minor effects on MCM catalysis. Bacterial growth assays demonstrate that cobamide requirements of MCM in vitro largely correlate with in vivo cobamide dependence. This result underscores the importance of enzyme selectivity in the cobamide-dependent physiology of bacteria.IMPORTANCE Cobamides, including vitamin B12, are enzyme cofactors used by organisms in all domains of life. Cobamides are structurally diverse, and microbial growth and metabolism vary based on cobamide structure. Understanding cobamide preference in microorganisms is important given that cobamides are widely used and appear to mediate microbial interactions in host-associated and aquatic environments. Until now, the biochemical basis for cobamide preferences was largely unknown. In this study, we analyzed the effects of the structural diversity of cobamides on a model cobamide-dependent enzyme, methylmalonyl-CoA mutase (MCM). We found that very small changes in cobamide structure could dramatically affect the binding affinity of cobamides to MCM. Strikingly, cobamide-dependent growth of a model bacterium, Sinorhizobium meliloti, largely correlated with the cofactor binding selectivity of S. meliloti MCM, emphasizing the importance of cobamide-dependent enzyme selectivity in bacterial growth and cobamide-mediated microbial interactions.

Modulating the cobalt redox potential through imidazole hydrogen bonding interactions in a supramolecular biomimetic protein-cofactor model

This paper describes a supramolecular biomimetic model of the “His-on” configuration and the charge relay system present in certain types of B₁₂-dependent enzymes.

A realistic model for the active site of histidine-on cobalamin@protein complexes is reported and studied under homogeneous and immobilized conditions. Analysis of lower ligand modulation and its influence on the properties of the biomimetic compound are presented. The cofactor attachment by a protein's histidine residue was imitated by covalently linking an artificial imidazole-containing linker to cobyric acid. The resulting intramolecular coordination complex is an excellent structural model of its natural archetype, according to 2D ¹H-NMR studies and molecular modeling. The effect of deprotonation of the axially coordinating imidazole ligand – as proposed for natural cofactor complexes – tunes significantly the position of the cathodic peak (ΔV = –203 mV) and stabilizes thereby the Co^III form. Partial deprotonation of the imidazole moiety through hydrogen bonding interactions was then achieved by immobilizing the biomimetic model on hydrophobic C18 silica, which yielded an unprecedented insight on how this class of Cbl-dependent proteins may fine-tune their properties in biological systems.

Intraprotein transmethylation via a CH3–Co(iii) species in myoglobin reconstituted with a cobalt corrinoid complex

A cobalt corrinoid complex bound in the myoglobin heme pocket demonstrates the formation of a CH₃–Co(iii) bond and subsequent transmethylation.

Elements in maternal blood and amniotic fluid determined by ICP-MS

OBJECTIVE

Knowledge about levels of toxic and non-toxic elements in amniotic fluid is limited. The aims of this study were: (1) to measure levels of trace elements Cu, Fe, Zn, B, Sr and Co in amniotic fluid and maternal serum during second trimester of pregnancy; and (2) to determine what correlations exists between elements levels in amniotic fluid and maternal serum.

METHODS

The levels of, iron, copper, zinc, cobalt, strontium and boron were measured in blood and amniotic fluid during genetic amniocentesis using inductively coupled plasma mass spectrometry (ICP-MS).

RESULTS

Concentrations of the elements: Fe, Cu, Zn, Co, Sr and B in amniotic fluid were significantly lower than in maternal blood. For iron, zinc, cobalt, strontium and boron there was a linear correlation between levels in amniotic fluid and maternal serum.

CONCLUSIONS

The concentration of trace elements in amniotic fluid was found to be lower than maternal serum and linearly correlated to its level.

Entropic origin of cobalt-carbon bond cleavage catalysis in adenosylcobalamin-dependent ethanolamine ammonia-lyase

Adenosylcobalamin-dependent enzymes accelerate the cleavage of the cobalt-carbon (Co-C) bond of the bound coenzyme by >10(10)-fold. The cleavage-generated 5'-deoxyadenosyl radical initiates the catalytic cycle by abstracting a hydrogen atom from substrate. Kinetic coupling of the Co-C bond cleavage and hydrogen-atom-transfer steps at ambient temperatures has interfered with past experimental attempts to directly address the factors that govern Co-C bond cleavage catalysis. Here, we use time-resolved, full-spectrum electron paramagnetic resonance spectroscopy, with temperature-step reaction initiation, starting from the enzyme-coenzyme-substrate ternary complex and (2)H-labeled substrate, to study radical pair generation in ethanolamine ammonia-lyase from Salmonella typhimurium at 234-248 K in a dimethylsulfoxide/water cryosolvent system. The monoexponential kinetics of formation of the (2)H- and (1)H-substituted substrate radicals are the same, indicating that Co-C bond cleavage rate-limits radical pair formation. Analysis of the kinetics by using a linear, three-state model allows extraction of the microscopic rate constant for Co-C bond cleavage. Eyring analysis reveals that the activation enthalpy for Co-C bond cleavage is 32 ± 1 kcal/mol, which is the same as for the cleavage reaction in solution. The origin of Co-C bond cleavage catalysis in the enzyme is, therefore, the large, favorable activation entropy of 61 ± 6 cal/(mol·K) (relative to 7 ± 1 cal/(mol·K) in solution). This represents a paradigm shift from traditional, enthalpy-based mechanisms that have been proposed for Co-C bond-breaking in B12 enzymes. The catalysis is proposed to arise from an increase in protein configurational entropy along the reaction coordinate.

Gold-containing indoles as anticancer agents that potentiate the cytotoxic effects of ionizing radiation

This report describes the design and application of several distinct gold-containing indoles as anticancer agents. When used individually, all gold-bearing compounds display cytostatic effects against leukemia and adherent cancer cell lines. However, two gold-bearing indoles show unique behavior by increasing the cytotoxic effects of clinically relevant levels of ionizing radiation. Quantifying the amount of DNA damage demonstrates that each gold-indole enhances apoptosis by inhibiting DNA repair. Both Au(I)-indoles were tested for inhibitory effects against various cellular targets including thioredoxin reductase, a known target of several gold compounds, and various ATP-dependent kinases. While neither compound significantly inhibits the activity of thioreoxin reductase, both showed inhibitory effects against several kinases associated with cancer initiation and progression. The inhibition of these kinases provides a possible mechanism for the ability of these Au(I)-indoles to potentiate the cytotoxic effects of ionizing radiation. Clinical applications of combining Au(I)-indoles with ionizing radiation are discussed as a new strategy to achieve chemosensitization of cancer cells.

4-[(4′-Chloromethyl-[1,1′-biphenyl]-4-yl)methyl]bis(dimethylglyoximato-κ2N,N′)(pyridine-κN)cobalt(III)

The title compound, [Co(C₁₄H₁₄Cl)(C₄H₆N₂O₂)₂(C₅H₅N)], is a model compound for the more complex cobalamines like vitamins B₁₂. The Co^III atom is coordinated by a (4′-chloro­methyl-[1,1′-biphen­yl]-4-yl)methyl group, an N-bonded pyridine and two N,N′-bidentate dimethyl­glyoximate ligands in a distorted octa­hedral geometry. The glyoximate ligands exhibit intra­molecular O—H⋯O hydrogen bonds, which is very common in cobaloxime derivatives.

Butyl-bis-(diphenyl-glyoximato)(pyridine-κN)-cobalt(III)

In the title compound, [Co(C₄H₉)(C₁₄H₁₁N₂O₂)₂(C₅H₅N)], the Co^III atom is coordinated by a butyl group, a nitro­gen-bonded pyridine and two N,N′-bidentate diphenyl­glyoximate ligands in a distorted octa­hedral geometry. The crystal structure features two short O—H⋯O bridges between the two chelating anions, with O⋯O distances less than 2.5 Å.

Internal Spin Trapping of Thiyl Radical during the Complexation and Reduction of Cobalamin with Glutathione and Dithiothrietol

The activation of cobalamin requires the reduction of Cbl(III) to Cbl(II). The reduction by glutathione and dithiothreitol was followed using visible spectroscopy and electron paramagnetic resonance. In addition the oxidation of glutathione was monitored. Glutathione first reacts with oxidized Cbl(III). The binding of a second glutathione required for the reduction to Cbl(II) is presumably located in the dimethyl benzimidazole ribonucleotide ligand cavity. The reduction of Cbl(III) by dithiothreitol, which contains two thiols, is much faster even though no stable Cbl(III) complex is formed. The reduction, by both thiol reagents, results in the formation of thiyl radicals, some of which are released to form oxidized thiol products and some of which remain associated with the reduced cobalamin. In the reduced state the intrinsic lower affinity for the benzimidazole base, coupled with a trans effect from the initial GSH bound to the β-axial site and a possible lowering of the pH results in an equilibrium between base-on and base-off complexes. The dissociation of the base facilitates a closer approach of the thiyl radical to the Co(II) α-axial site resulting in a complex with ferromagnetic exchange coupling between the metal ion and the thiyl radical. This is a unique example of 'internal spin trapping' of a thiyl radical formed during reduction. The finding that the reduction involves a peripheral site and that thiyl radicals produced during the reduction remain associated with the reduced cobalamin provide important new insights into our understanding of the formation and function of cobalamin enzymes.

Structural basis for adenosylcobalamin activation in AdoCbl-dependent ribonucleotide reductases

Class II ribonucleotide reductases (RNR) catalyze the formation of an essential thiyl radical by homolytic cleavage of the Co-C bond in their adenosylcobalamin (AdoCbl) cofactor. Several mechanisms for the dramatic acceleration of Co-C bond cleavage in AdoCbl-dependent enzymes have been advanced, but no consensus yet exists. We present the structure of the class II RNR from Thermotoga maritima in three complexes: (i) with allosteric effector dTTP, substrate GDP, and AdoCbl; (ii) with dTTP and AdoCbl; (iii) with dTTP, GDP, and adenosine. Comparison of these structures gives the deepest structural insights so far into the mechanism of radical generation and transfer for AdoCbl-dependent RNR. AdoCbl binds to the active site pocket, shielding the substrate, transient 5'-deoxyadenosyl radical and nascent thiyl radical from solution. The e-propionamide side chain of AdoCbl forms hydrogen bonds directly to the α-phosphate group of the substrate. This interaction appears to cause a "locking-in" of the cofactor, and it is the first observation of a direct cofactor-substrate interaction in an AdoCbl-dependent enzyme. The structures support an ordered sequential reaction mechanism with release or relaxation of AdoCbl on each catalytic cycle. A conformational change of the AdoCbl adenosyl ribose is required to allow hydrogen transfer to the catalytic thiol group. Previously proposed mechanisms for radical transfer in B12-dependent enzymes cannot fully explain the transfer in class II RNR, suggesting that it may form a separate class that differs from the well-characterized eliminases and mutases.

Continuous wave photolysis magnetic field effect investigations with free and protein-bound alkylcobalamins

The activation of the Co-C bond in adenosylcobalamin-dependent enzymes generates a singlet-born Co(II)-adenosyl radical pair. Two of the salient questions regarding this process are: (1) What is the origin of the considerable homolysis rate enhancement achieved by this class of enzyme? (2) Are the reaction dynamics of the resultant radical pair sensitive to the application of external magnetic fields? Here, we present continuous wave photolysis magnetic field effect (MFE) data that reveal the ethanolamine ammonia lyase (EAL) active site to be an ideal microreactor in which to observe enhanced magnetic field sensitivity in the adenosylcobalamin radical pair. The observed field dependence is in excellent agreement with that calculated from published hyperfine couplings for the constituent radicals, and the magnitude of the MFE (<18%) is almost identical to that observed in a solvent containing 67% glycerol. Similar augmentation is not observed, however, in the equivalent experiments with EAL-bound methylcobalamin, where all field sensitivity observed in the free cofactor is washed out completely. Parallels are drawn between the latter case and the loss of field sensitivity in the EAL holoenzyme upon substrate binding (Jones et al. J. Am. Chem. Soc. 2007, 129, 15718-15727). Both are attributed to the rapid removal of the alkyl radical immediately after homolysis, such that there is inadequate radical pair recombination for the observation of field effects. Taken together, these results support the notion that rapid radical quenching, through the coupling of homolysis and hydrogen abstraction steps, and subsequent radical pair stabilization make a contribution to the observed rate acceleration of Co-C bond homolysis in adenosylcobalamin-dependent enzymes.

Proteome of Salmonella Enterica Serotype Typhimurium Grown in a Low Mg/pH Medium

To determine the impact of a low Mg(2+)/pH defined growth medium (MgM) on the proteome of Salmonella enterica serotype Typhimurium, we cultured S. Typhimurium cells in the medium under two different conditions termed MgM Shock and MgM Dilution and then comparatively analyzed the bacterial cells harvested from these conditions by a global proteomic approach. Proteomic results showed that MgM Shock and MgM Dilution differentially affected the S. Typhimurium proteome. MgM Shock induced a group of proteins whose induction usually occurred at low O(2) level, while MgM Dilution induced those related to the type III secretion system (T3SS) of Salmonella Pathogenicity Island 2 (SPI2) and those involved in thiamine or biotin biosynthesis. The metabolic state of the S. Typhimurium cells grown under MgM Shock condition also differed significantly from that under MgM Dilution condition. Western blot analysis not only confirmed the proteomic results, but also showed that the abundances of SPI2-T3SS proteins SsaQ and SseE and biotin biosynthesis proteins BioB and BioD increased after S. Typhimurium infection of RAW 264.7 macrophages. Deletion of the gene encoding BioB reduced the bacterial ability to replicate inside the macrophages, suggesting a biotin-limited environment encountered by S. Typhimurium within RAW 264.7 macrophages.

DFT and ONIOM(DFT:MM) studies on Co-C bond cleavage and hydrogen transfer in B12-dependent methylmalonyl-CoA mutase. Stepwise or concerted mechanism?

The considerable protein effect on the homolytic Co-C bond cleavage to form the 5'-deoxyadenosyl (Ado) radical and cob(II)alamin and the subsequent hydrogen transfer from the methylmalonyl-CoA substrate to the Ado radical in the methylmalonyl-CoA mutase (MMCM) have been extensively studied by DFT and ONIOM(DFT/MM) methods. Several quantum models have been used to systematically study the protein effect. The calculations have shown that the Co-C bond dissociation energy is very much reduced in the protein, compared to that in the gas phase. The large protein effect can be decomposed into the cage effect, the effect of coenzyme geometrical distortion, and the protein MM effect. The largest contributor is the MM effect, which mainly consists of the interaction of the QM part of the coenzyme with the MM part of the coenzyme and the surrounding residues. In particular, Glu370 plays an important role in the Co-C bond cleavage process. These effects tremendously enhance the stability of the Co-C bond cleavage state in the protein. The initial Co-C bond cleavage and the subsequent hydrogen transfer were found to occur in a stepwise manner in the protein, although the concerted pathway for the Co-C bond cleavage coupled with the hydrogen transfer is more favored in the gas phase. The assumed concerted transition state in the protein has more deformation of the coenzyme and the substrate and has less interaction with the protein than the stepwise route. Key factors and residues in promoting the enzymatic reaction rate have been discussed in detail.

Computational Studies of Bioorganometallic Enzymes and Cofactors

Because of their complex geometric and electronic structures, the active sites and cofactors of bioorganometallic enzymes, which are characterized by their metal–carbon bonds, pose a major challenge for computational chemists. However, recent progress in computer technology and theoretical chemistry, along with insights gained from mechanistic, spectroscopic, and X-ray crystallographic studies, have established an excellent foundation for the successful completion of computational studies aimed at elucidating the electronic structures and catalytic cycles of these species. This chapter briefly reviews the most popular computational approaches employed in theoretical studies of bioorganometallic species and summarizes important information obtained from computational studies of (i) the enzymatic formation and cleavage of the Co–C bond of coenzyme B12; (ii) the catalytic cycle of methyl-coenzyme M reductase and its nickel-containing cofactor F430; (iii) the polynuclear active-site clusters of the bifunctional enzyme carbon monoxide dehydrogenase/acetyl-coenzyme A synthase; and (iv) the magnetic properties of the active-site cluster of Fe-only hydrogenases.

Chemoselective deprotection of alpha-indole and imidazole ribonucleosides

A series of 2 ',3 '-isopropylidene and 5 '-trityl-protected alpha-indole and alpha/beta-benzimidazole and imidazole ribonucleosides were deprotected with different acids. Selectivity was achieved for 5 '-versus 2 ',3 '- deprotection by using formic acid in the alpha-indole ribonucleoside series. Treatment of alpha-indole ribonucleosides with a mixture of formic acid and ether at room temperature afforded 2 ',3 '-deprotected alpha-ribonucleosides, whereas treatment of the alpha-benzimidazole ribonucleosides with the same acid afforded the 5 '-deprotected ribonucleoside without any 2 ', 3 '-deprotected products. The structures of these ribonucleosides were elucidated with 2D (NOESY, COSY, and HMQC) NMR spectroscopy.

NMR observations of 13C-enriched coenzyme B12 bound to the ribonucleotide reductase from Lactobacillus leichmannii

The 13C NMR resonance and one-bond 1H-13C coupling constants of coenzyme B12 enriched in 13C in the cobalt-bound carbon have been observed in the complex of the coenzyme with the B12-dependent ribonucleotide reductase from Lactobacillus leichmannii. Neither the 13C NMR chemical shift nor the 1H-13C coupling constants are significantly altered by binding of the coenzyme to the enzyme. The results suggest that ground-state Co-C bond distortion is not utilized by this enzyme to activate coenzyme B12 for C-Co bond homolysis.