Stabilisation of Methylene Radicals by Cob(II)alamin in Coenzyme B12 Dependent Mutases

Coenzyme B₁₂ initiates radical chemistry in two types of enzymatic reactions, the irreversible eliminases (e.g., diol dehydratases) and the reversible mutases (e.g., methylmalonyl‐CoA mutase). Whereas eliminases that use radical generators other than coenzyme B₁₂ are known, no alternative coenzyme B₁₂ independent mutases have been detected for substrates in which a methyl group is reversibly converted to a methylene radical. We predict that such mutases do not exist. However, coenzyme B₁₂ independent pathways have been detected that circumvent the need for glutamate, β‐lysine or methylmalonyl‐CoA mutases by proceeding via different intermediates. In humans the methylcitrate cycle, which is ostensibly an alternative to the coenzyme B₁₂ dependent methylmalonyl‐CoA pathway for propionate oxidation, is not used because it would interfere with the Krebs cycle and thereby compromise the high‐energy requirement of the nervous system. In the diol dehydratases the 5′‐deoxyadenosyl radical generated by homolysis of the carbon–cobalt bond of coenzyme B₁₂ moves about 10 Å away from the cobalt atom in cob(II )alamin. The substrate and product radicals are generated at a similar distance from cob(II )alamin, which acts solely as spectator of the catalysis. In glutamate and methylmalonyl‐CoA mutases the 5′‐deoxyadenosyl radical remains within 3–4 Å of the cobalt atom, with the substrate and product radicals approximately 3 Å further away. It is suggested that cob(II )alamin acts as a conductor by stabilising both the 5′‐deoxyadenosyl radical and the product‐related methylene radicals.     

Direct Participation of a Peripheral Side Chain of a Corrin Ring in Coenzyme B12 Catalysis

The crystal structures of the B₁₂‐dependent isomerases (eliminating) diol dehydratase and ethanolamine ammonia‐lyase complexed with adenosylcobalamin were solved with and without substrates. The structures revealed that the peripheral a‐acetamide side chain of the corrin ring directly interacts with the adenosyl group to maintain the group in the catalytic position, and that this side chain swings between the original and catalytic positions in a synchronized manner with the radical shuttling between the coenzyme and substrate/product. Mutations involving key residues that cooperatively participate in the positioning of the adenosyl group, directly or indirectly through the interaction with the a‐side chain, decreased the turnover rate and increased the relative rate of irreversible inactivation caused by undesirable side reactions. These findings guide the engineering of enzymes for improved catalysis and producing useful chemicals by utilizing the high reactivity of radical species.     

Glycerol as a Substrate and Inactivator of Coenzyme B12-Dependent Diol Dehydratase

Diol dehydratase, dependent on coenzyme B₁₂ (B₁₂-dDDH), displays a peculiar feature of being inactivated by its native substrate glycerol (GOL). Surprisingly, the isofunctional enzyme, B₁₂-independent glycerol dehydratase (B₁₂-iGDH), does not undergo suicide inactivation by GOL. Herein we present a series of QM/MM and MD calculations aimed at understanding the mechanisms of substrate-induced suicide inactivation in B₁₂-dDDH and that of resistance of B₁₂-iGDH to inactivation. We show that the first step in the enzymatic transformation of GOL, hydrogen abstraction, can occur from both ends of the substrate (either C1 or C3 of GOL). Whereas C1 abstraction in both enzymes leads to product formation, C3 abstraction in B₁₂-dDDH results in the formation of a low energy radical intermediate, which is effectively trapped within a deep well on the potential energy surface. The long lifetime of this radical intermediate likely enables its side reactions, leading to inactivation. In B₁₂-iGDH, by comparison, C3 abstraction is an endothermic step; consequently, the resultant radical intermediate is not of low energy, and the reverse process of reforming the reactant is possible.     

Stereochemistry of the Methyl Group in (R)‐3‐Methylitaconate Derived by Rearrangement of 2‐Methylideneglutarate Catalysed by a Coenzyme B12‐Dependent Mutase

2‐Methylideneglutarate mutase is an adenosylcobalamin (coenzyme B₁₂)‐dependent enzyme that catalyses the equilibration of 2‐methylideneglutarate with (R)‐3‐methylitaconate. This reaction is believed to occur via protein‐bound free radicals derived from substrate and product. The stereochemistry of the formation of the methyl group of 3‐methylitaconate has been probed using a `chiral methyl group'. The methyl group in 3‐([²H₁,³H]methyl)itaconate derived from either (R)‐ or (S)‐2‐methylidene[3‐²H₁,3‐³H₁]glutarate was a 50 : 50 mixture of (R)‐ and (S)‐forms. It is concluded that the barrier to rotation about the C−C bond between the methylene radical centre and adjacent C‐atom in the product‐related radical [^.CH₂CH(⁻O₂CC=CH₂)CO₂⁻] is relatively low, and that the interaction of the radical with cob(II)alamin is minimal. Hence, cob(II)alamin is a spectator of the molecular rearrangement of the substrate radical to product radical.     

Linking Phospholipase Mobility to Activity by Single‐Molecule Wide‐Field Microscopy

Many of the biological processes taking place in cells are mediated by enzymatic reactions occurring in the cell membrane. Understanding interfacial enzymatic catalysis is therefore crucial to the understanding of cellular function. Unfortunately, a full picture of the overall mechanism of interfacial enzymatic catalysis, and particularly the important diffusion processes therein, remains unresolved. Herein we demonstrate that single‐molecule wide‐field fluorescence microscopy can yield important new information on these processes. We image phospholipase enzymes acting upon bilayers of their natural phospholipid substrate, tracking the diffusion of thousands of individual enzymes while simultaneously visualising local structural changes to the substrate layer. We study several enzyme types with different affinities and catalytic activities towards the substrate. Analysis of the trajectories of each enzyme type allows us successfully to correlate the mobility of phospholipase with its catalytic activity at the substrate. The methods introduced herein represent a promising new approach to the study of interfacial/heterogeneous catalysis systems.     

Mechanistic Insights into the Radical S‐adenosyl‐l‐methionine Enzyme NosL From a Substrate Analogue and the Shunt Products

The radical S‐adenosyl‐l ‐methionine (SAM) enzyme NosL catalyzes the transformation of l ‐tryptophan into 3‐methyl‐2‐indolic acid (MIA), which is a key intermediate in the biosynthesis of a clinically interesting antibiotic nosiheptide. NosL catalysis was investigated by using the substrate analogue 2‐methyl‐3‐(indol‐3‐yl)propanoic acid (MIPA), which can be converted into MIA by NosL. Biochemical assays with different MIPA isotopomers in D₂O and H₂O unambiguously indicated that the 5′‐deoxyadenosyl (dAdo)‐radical‐mediated hydrogen abstraction is from the amino group of l ‐tryptophan and not a protein residue. Surprisingly, the dAdo‐radical‐mediated hydrogen abstraction occurs at two different sites of MIPA, thereby partitioning the substrate into different reaction pathways. Together with identification of an α,β‐unsaturated ketone shunt product, our study provides valuable mechanistic insight into NosL catalysis and highlights the remarkable catalytic flexibility of radical SAM enzymes.     

Probing Reversible Chemistry in Coenzyme B12‐Dependent Ethanolamine Ammonia Lyase with Kinetic Isotope Effects

Coenzyme B₁₂‐dependent enzymes such as ethanolamine ammonia lyase have remarkable catalytic power and some unique properties that enable detailed analysis of the reaction chemistry and associated dynamics. By selectively deuterating the substrate (ethanolamine) and/or the β‐carbon of the 5′‐deoxyadenosyl moiety of the intrinsic coenzyme B₁₂, it was possible to experimentally probe both the forward and reverse hydrogen atom transfers between the 5′‐deoxyadenosyl radical and substrate during single‐turnover stopped‐flow measurements. These data are interpreted within the context of a kinetic model where the 5′‐deoxyadenosyl radical intermediate may be quasi‐stable and rearrangement of the substrate radical is essentially irreversible. Global fitting of these data allows estimation of the intrinsic rate constants associated with Co?C homolysis and initial H‐abstraction steps. In contrast to previous stopped‐flow studies, the apparent kinetic isotope effects are found to be relatively small.     

Selective Enzymatic Oxidation of Silanes to Silanols

Compared to the biological world's rich chemistry for functionalizing carbon, enzymatic transformations of the heavier homologue silicon are rare. We report that a wild‐type cytochrome P450 monooxygenase (P450_BM3 from Bacillus megaterium, CYP102A1) has promiscuous activity for oxidation of hydrosilanes to give silanols. Directed evolution was applied to enhance this non‐native activity and create a highly efficient catalyst for selective silane oxidation under mild conditions with oxygen as the terminal oxidant. The evolved enzyme leaves C?H bonds present in the silane substrates untouched, and this biotransformation does not lead to disiloxane formation, a common problem in silanol syntheses. Computational studies reveal that catalysis proceeds through hydrogen atom abstraction followed by radical rebound, as observed in the native C?H hydroxylation mechanism of the P450 enzyme. This enzymatic silane oxidation extends nature's impressive catalytic repertoire.     

Does Hydrogen‐Bonding Donation to Manganese(IV)–Oxo and Iron(IV)–Oxo Oxidants Affect the Oxygen‐Atom Transfer Ability? A Computational Study

Iron(IV)–oxo intermediates are involved in oxidations catalyzed by heme and nonheme iron enzymes, including the cytochromes P450. At the distal site of the heme in P450 Compound I (Fe^IV–oxo bound to porphyrin radical), the oxo group is involved in several hydrogen‐bonding interactions with the protein, but their role in catalysis is currently unknown. In this work, we investigate the effects of hydrogen bonding on the reactivity of high‐valent metal–oxo moiety in a nonheme iron biomimetic model complex with trigonal bipyramidal symmetry that has three hydrogen‐bond donors directed toward a metal(IV)–oxo group. We show these interactions lower the oxidative power of the oxidant in reactions with dehydroanthracene and cyclohexadiene dramatically as they decrease the strength of the O? H bond (BDE_OH) in the resulting metal(III)–hydroxo complex. Furthermore, the distal hydrogen‐bonding effects cause stereochemical repulsions with the approaching substrate and force a sideways attack rather than a more favorable attack from the top. The calculations, therefore, give important new insights into distal hydrogen bonding, and show that in biomimetic, and, by extension, enzymatic systems, the hydrogen bond may be important for proton‐relay mechanisms involved in the formation of the metal–oxo intermediates, but the enzyme pays the price for this by reduced hydrogen atom abstraction ability of the intermediate. Indeed, in nonheme iron enzymes, where no proton relay takes place, there generally is no donating hydrogen bond to the iron(IV)–oxo moiety.     

A Mass Spectrometric Approach for Probing the Stability of Bioorganic Radicals

Glycyl radicals are important bioorganic radical species involved in enzymatic catalysis. Herein, we demonstrate that the stability of glycyl‐type radicals (X‐^.CH‐Y) can be tuned on a molecular level by varying the X and Y substituents and experimentally probed by mass spectrometry. This approach is based on the gas‐phase dissociation of cysteine sulfinyl radical (X‐Cys‐Y) ions through homolysis of a C_α? C_β bond. This fragmentation produces a glycyl‐type radical upon losing CH₂SO, and the degree of this loss is closely tied to the stability of the as‐formed radical. Theoretical calculations indicate that the energy of the C_α? C_β bond homolysis is predominantly affected by the stability of the glycyl radical product through the captodative effect, rather than that of the parent sulfinyl radical. This finding suggests a novel experimental method to probe the stability of bioorganic radicals, which can potentially broaden our understanding of these important reactive intermediates.     

Substrate‐Tuned Catalysis of the Radical S‐Adenosyl‐L‐Methionine Enzyme NosL Involved in Nosiheptide Biosynthesis

NosL is a radical S‐adenosyl‐L ‐methionine (SAM) enzyme that converts L ‐Trp to 3‐methyl‐2‐indolic acid, a key intermediate in the biosynthesis of a thiopeptide antibiotic nosiheptide. In this work we investigated NosL catalysis by using a series of Trp analogues as the molecular probes. Using a benzofuran substrate 2‐amino‐3‐(benzofuran‐3‐yl)propanoic acid (ABPA), we clearly demonstrated that the 5′‐deoxyadenosyl (dAdo) radical‐mediated hydrogen abstraction in NosL catalysis is not from the indole nitrogen but likely from the amino group of L ‐Trp. Unexpectedly, the major product of ABPA is a decarboxylated compound, indicating that NosL was transformed to a novel decarboxylase by an unnatural substrate. Furthermore, we showed that, for the first time to our knowledge, the dAdo radical‐mediated hydrogen abstraction can occur from an alcohol hydroxy group. Our study demonstrates the intriguing promiscuity of NosL catalysis and highlights the potential of engineering radical SAM enzymes for novel activities.     

Enzymatic Cascade Reactions in Biosynthesis

Enzyme‐mediated cascade reactions are widespread in biosynthesis. To facilitate comparison with the mechanistic categorizations of cascade reactions by synthetic chemists and delineate the common underlying chemistry, we discuss four types of enzymatic cascade reactions: those involving nucleophilic, electrophilic, pericyclic, and radical reactions. Two subtypes of enzymes that generate radical cascades exist at opposite ends of the oxygen abundance spectrum. Iron‐based enzymes use O₂ to generate high valent iron‐oxo species to homolyze unactivated C?H bonds in substrates to initiate skeletal rearrangements. At anaerobic end, enzymes reversibly cleave S‐adenosylmethionine (SAM) to generate the 5′‐deoxyadenosyl radical as a powerful oxidant to initiate C?H bond homolysis in bound substrates. The latter enzymes are termed radical SAM enzymes. We categorize the former as “thwarted oxygenases”.     

Mechanisms of formation of free radicals in biological catalysis

A large number of selective metabolic reactions involve intermediate free radicals. To do so, enzymatic systems rely upon a great variety of efficient radical sources, such as adenosylcobalamin, S-adenosylmethionine and oxygen for reaction initiation. In most cases, activation depends on a metallocofactor. The review article focuses on some of these chemical mechanisms for biological radical generation.     

EPR Spectroscopic Studies of Lipoxygenases

Polyunsaturated fatty acids are sources of diverse natural, and chemically designed products. The enzyme lipoxygenase selectively oxidizes fatty acid acyl chains using controlled free radical chemistry; the products are regio‐ and stereo‐chemically unique hydroperoxides. A conserved structural fold of ≈600 amino acids harbors a long and narrow substrate channel and a well‐shielded catalytic iron. Oxygen, a co‐substrate, is blocked from the active site until a hydrogen atom is abstracted from substrate bis‐allylic carbon, in a non‐heme iron redox cycle. EPR spectroscopy of ferric intermediates in lipoxygenase catalysis reveals changes in the metal coordination and leads to a proposal on the nature of the reactive intermediate. Remarkably, free radicals are so well controlled in lipoxygenase chemistry that spin label technology can be applied as well. The current level of understanding of steps in lipoxygenase catalysis, from the EPR perspective, will be reviewed.     

DFT studies on key intermediates in thiamin catalysis

The diphosphate ester (ThDP) of thiamin (vitamin B₁) is an important cofactor of enzymes within the carbohydrate metabolism. From experiments of site‐specific variants and nuclear magnetic resonance (NMR) studies, it is known that the protonation of the N1′ atom is a significant step in the coenzyme activation by the enzymatic environment. Therefore, we have performed density functional theory (DFT) calculations on the B3LYP/6‐31G* level of N1′H and N1′CH₃ thiamin as model systems to study the protonation and methylation effect on the structure and the electronic properties of the 4′‐amino group. The relaxed rotational barriers related to the C4′‐4′N bond are correlated with findings of ¹H NMR studies and proton/deuterium exchange experiments. Moreover, the effect of N1′ protonation was studied in more detail on the hydroxyethyl‐thiamin carbanion (HETh^?), a key intermediate during catalysis of some ThDP‐dependent enzymes. The relaxed rotational barriers related to the C2? C2α bond and the reaction coordinates of the proton transfer 4′N? H→C2α of HETh^? and N1′H‐HETh^? show that they are significantly determined by the protonation at N1′ of HETh^?. The influence of the apoenzyme environment on the active coenzyme conformation is modeled in a very simple way. The characteristic torsion angles Φ_T and Φ_P are considered to be restricted in terms of their values in the corresponding enzyme as well as free optimization parameters. Frequency calculations were performed to characterize the minima and transition state structures, respectively. The applicability of the DFT method was checked by comparing calculations on the MP2‐HF‐SCF/6‐31G* level. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2004     

Intramolecular hydrogen bond in the hydroxycyclohexadienyl peroxy radicals

The hydroxycyclohexadienyl peroxy radicals (HO? C₆H₆? O₂) produced from the reaction of OH‐benzene adduct with O₂ were studied with density functional theory (DFT) calculations to determine their characteristics. The optimized geometries, vibrational frequencies, and total energies of 2‐hydroxycyclohexadienyl peroxy radical II_s and 4‐hydroxycyclohexadienyl peroxy radical III_s were calculated at the following theoretical levels, B3LYP/6‐31G(d), B3LYP/6‐311G(d,p), and B3LYP/6‐311+G(d,p). Both were shown to contain a red‐shifted intramolecular hydrogen bond (O? H … O? H bond). According to atoms‐in‐molecules (AIM) analysis, the intramolecular hydrogen bond in the 2‐hydroxycyclohexadienyl peroxy radical II_s is stronger than that one in 4‐hydroxycyclohexadienyl peroxy radical III_s, and the former is the most stable conformation among its isomers. Generally speaking, hydrogen bonding in these radicals plays an important role to make them more stable. Based on natural bond orbital (NBO) analysis, the stabilization energy between orbitals is the main factor to produce red‐shifted intramolecular hydrogen bond within these peroxy radicals. The hyperconjugative interactions can promote the transfer of some electron density to the O? H antibonding orbital, while the increased electron density in the O? H antibonding orbital leads to the elongation of the O? H bond and the red shift of the O? H stretching frequency. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

A Cofactor‐Substrate‐Based Supramolecular Fluorescent Probe for the Ultrafast Detection of Nitroreductase under Hypoxic Conditions

Identifying the location and expression levels of enzymes under hypoxic conditions in cancer cells is vital in early‐stage cancer diagnosis and monitoring. By encapsulating a fluorescent substrate, L‐NO₂ , within the NADH mimic‐containing metal–organic capsule Zn‐ MPB , we developed a cofactor‐substrate‐based supramolecular luminescent probe for ultrafast detection of hypoxia‐related enzymes in solution in vitro and in vivo. The host–guest structure fuses the coenzyme and substrate into one supramolecular probe to avoid control by NADH, switching the catalytic process of nitroreductase from a double‐substrate mechanism to a single‐substrate one. This probe promotes enzyme efficiency by altering the substrate catalytic process and enhances the electron transfer efficiency through an intra‐molecular pathway with increased activity. The enzyme content and fluorescence intensity showed a linear relationship and equilibrium was obtained in seconds, showing potential for early tumor diagnosis, biomimetic catalysis, and prodrug activation.     

Accelerating Enzymatic Catalysis Using Vortex Fluidics

Enzymes catalyze chemical transformations with outstanding stereo‐ and regio‐specificities, but many enzymes are limited by their long reaction times. A general method to accelerate enzymes using pressure waves contained within thin films is described. Each enzyme responds best to specific frequencies of pressure waves, and an acceleration landscape for each protein is reported. A vortex fluidic device introduces pressure waves that drive increased rate constants (k_cat) and enzymatic efficiency (k_cat/K_m). Four enzymes displayed an average seven‐fold acceleration, with deoxyribose‐5‐phosphate aldolase (DERA) achieving an average 15‐fold enhancement using this approach. In solving a common problem in enzyme catalysis, a powerful, generalizable tool for enzyme acceleration has been uncovered. This research provides new insights into previously uncontrolled factors affecting enzyme function.     

On the Reaction of Glycerol Dehydratase with But‐3‐ene‐1,2‐diol

Intriguing inactivation : Calculations suggest that the ability of relatively high‐energy radical intermediates to inactivate glycerol dehydratase (GDH) may reflect a general and hitherto unidentified inactivation mechanism in the reaction of coenzyme B₁₂‐dependent enzymes and 3‐unsaturated 1,2‐diols (see scheme; AdoCbl: adenosylcobalamin or coenzyme B₁₂).

     

Enzyme Catalysis Induced Polymer Growth in Nanochannels: A New Approach to Regulate Ion Transport and to Study Enzyme Kinetics in Nanospace

Method that could regulate the ion transport in nanochannel in an efficient and rapid manner is still a challenge. Here, we introduced enzyme‐catalysis‐induced polymer growth in nanochannels to develop a new method to regulate the ion transport and evaluate the enzyme catalysis kinetics in nano‐space. As a model enzyme, Horseradish peroxidase (HRP) was immobilized in the nanochannels through a volume‐controlled‐drying method. In the presence of H₂O₂, HRP catalyzed o‐phenylenediamine (o‐PD) to trigger its polymer growth, in turn blocked the ion transport and led to the decrease of the ion current. Taking advantages of the high efficiency of enzyme catalysis and the nano‐confinement of nanochannels, the system readily achieved blocking ratios of ion current even reaching 99.6 % of the initial. Based on above concept, we developed a new method to evaluate the enzyme catalysis kinetics in nano‐confined space. By comparing with those in free state in solution and absorbed on planar surface, HRP confined in nanochannels presented similar apparent Michaelis constant (K_m) values for the substrate H₂O₂ but much higher K_m values for the substrate o‐PD, due to the steric hindrance and diffusion suppression. The enzyme‐catalysis‐induced polymerization in nanochannels might lead to new concept for the nano‐blocking/switching and provide a new platform for single molecule analysis and detection.