Crystal structure of nitrile hydratase reveals a novel iron centre in a novel fold

Nitric oxide transfer between nominal Fe and Co biomimetics of the nitrile hydratase active site

Related to the inactive form of nitrile hydratase, NHase, that contains Fe(NO) within tripeptide N2S2 binding environment, the NO transfer reactivity of (bis-mercaptoethane diazacycloheptane)Fe(NO) and (bis-mercaptoethane diazadimethylethane)Fe(NO) is compared to Co(NO) analogs. Acceptors of NO include cobalt octaethylporphyrin and the [(N2S2)M] dimeric precursors in the synthesis of the Fe(NO) and Co(NO) biomimetics. Qualitative rates are augmented by a definitive kinetic study finding that rates of NO transfer from (N2S2)M(NO) to [(N2S2)M']2 are dependent on M and M' as well as the hydrocarbon N to N and N to S linkers. We conclude that while Fe(NO) and Co(NO) units are similar in chemical stability, minor first coordination sphere differences may favor the former, Fe(NO), consistent with the discovery of Fe(NO), but not Co(NO), in the as-isolated NHase active site.

Significant Enhancement Catalytic Activity of Nitrile Hydratase by Balancing the Subunits Expression

Escherichia coli (E. coli) is the most commonly used bacterial recombinant protein production system due to its easy genetic modification properties. In our previous study, a recombinant plasmid expressing the Fe-type nitrile hydratase derived from Rhodococcus erythropolis CCM2595 (ReNHase) was successfully constructed and the recombinant ReNHase exerted an excellent catalytic effect on dinitrile compounds. Nevertheless, the ReNHases were confronted with imbalanced subunit expression during heterologous expression, which restricted the enzymes assemble functionally. In this study, the secondary structure of mRNA in the ribosome binding sequence region of the β-subunit was optimized to elevate the translation efficiency of the β-subunit gene and balance the expression of α- and β-subunits in ReNHase. The optimized ReNHase showed a 12-fold increase in specific enzyme activity over wild-type ReNHase. To further enhance the soluble expression of ReNHase, the ReNHase was labeled using three different fusion tags, resulting in three new recombinant ReNHases. In these recombinant ReNHases, some of the fusion tags promoted the soluble expression of ReNHase, but also affected the balance of α-/β-subunit expression and the secondary structure of the ReNHase, and reduced the enzyme activity. In conclusion, our results provide an optimized strategy for the heterologous expression of multi-subunit proteins.

From [2Mn2S] Diamond Cores to Butterfly Rhombs: Transformations That Highlight Alternating Peptide Binding Sites

Thiocarboxamide chelates are known to assemble [2Mn2S] diamond core complexes via μ-S bridges that connect two MnI(CO)3 fragments. These can exist as syn- and anti-isomers and interconvert via 16-electron, monomeric intermediates. Herein, we demonstrate that reduction of such Mn2 derivatives leads to a loss of one thiocarboxamide ligand and a switch of ligand binding mode from an O- to N-donor of the amide group, yielding a dianionic butterfly rhomb with a short Mn0-Mn0 distance, 2.52 Å. Structural and chemical analyses suggest that reduction of the Mn(I) centers is dependent on the protonation state of the amide-H, as total deprotonation followed by reduction does not result in the reduction of the Mn2 core. Partial deprotonation followed by reduction suggests a pathway that involves monomeric Mn(CO)3(S-O) and Mn(CO)3(S-N) intermediates. Ligand modifications to tertiary amides that remove the possibility of amide-H reduction led to complexes that preserve the [2Mn2S] diamond core during chemical reduction. Further comparison with the tethered system, linking the Mn(CO)3(S-O) sites together, suggests that dimer dissociation is necessary for the overall reductive transformation. These results highlight organomanganese carbonyl chemistry to establish illustrations of peptide fragment binding modes in the uptake of low-valent metal carbonyls related to binuclear active sites of biocatalysts.

Molecular Modification Strategies of Nitrilase for Its Potential Application in Agriculture

Some feed source plants will produce secondary metabolites such as cyanogenic glycosides during metabolism, which will produce some poisonous nitrile compounds after hydrolysis and remain in plant tissues. The consumption of feed-source plants without proper treatment affect the health of the animals' bodies. Nitrilases can convert nitriles and have been used in industry as green biocatalysts. However, due to their bottleneck problems, their application in agriculture is still facing challenges. Acid-resistant nitrilase preparations, high-temperature resistance, antiprotease activity, strong activity, and strict reaction specificity urgently need to be developed. In this paper, the application potential of nitrilase in agriculture, especially in feed processing industry was explored, the source properties and catalytic mechanism of nitrilase were reviewed, and modification strategies for nitrilase application in agriculture were proposed to provide references for future research and application of nitrilase in agricultural and especially in the biological feed scene.

Structure-oriented engineering of nitrile hydratase: Reshaping of substrate access tunnel and binding pocket for efficient synthesis of cinnamamide

Cinnamamide and its derivatives are the most common and important building blocks widely present in natural products. Currently, nitrile hydratase (NHase, EC 4.2.1.84) has been widely used in large-scale industrial production of nicotinamide and acrylamide, while its catalytic activity is extremely low or inactive for bulky nitrile substrates such as cinnamonitrile. Therefore, beneficial variant βF37P/L48P/F51N were obtained from PtNHase of Pseudonocardia thermophila JCM3095 by reshaping of substrate access tunnel and binding pocket, which exhibited 14.88-fold improved catalytic efficiency compared to the wild-type PtNHase. Structure analysis, molecular dynamics simulations and dynamical cross-correlation matrix (DCCM) analysis revealed that the introduced mutations enlarged the substrate access tunnel and binding pocket, enhanced overall anti-correlated movements of enzymes, which would promote product release during the dynamic process of catalysis. In a hydration process, the complete conversion of 5 mM cinnamonitrile was achieved by βF37P/L48P/F51N in a 50 mL reaction, with cinnamamide yield of almost 100 % and productivity of 0.736 g L-1 h-1. The study demonstrates the co-evolution of substrate access tunnel and binding pocket is an effective strategy, and provides a valuable reference for future research. Furthermore, NHases have huge potential for catalyzing bulky nitriles to form corresponding amides in large-scale industrial production.

N-terminal loops at the tetramer interface of nitrile hydratase act as "hooks" determining resistance to high amide concentrations

Nitrile hydratase (NHase) has been extensively utilized in industrial acrylamide production. However, the vulnerability to high concentrations of acrylamide limits its further application. Herein, we redesigned the N-terminal loop at the tetramer interface of a thermophilic NHase from Pseudonocardia thermophila JCM3095 (PtNHase), and its catalytic activity, resistance to high acrylamide concentrations, and thermostability were improved. Amino acid residues located in the N-terminal loop of the tetramer interface that are responsible for enhancing the resistance to high acrylamide concentrations were identified via static structural analysis and molecular dynamics simulations. A variant library was used to fine-tune the tetramer interface. Variant αL6T exhibited 3.5-fold greater resistance to 50% (v/v) acrylamide, whereas its activity was 1.2-fold higher than that of the wild-type (WT) enzyme, revealing no activity-stability trade-off. Compared to the use of Escherichia coli harboring the WT enzyme, the use of E. coli harboring αL6T increased the acrylamide concentration from 398.1 g/L to 500 g/L. Crystal structure-guided analysis of αL6T and molecular dynamics simulations revealed that increased enzyme surface hydration and the introduction of positive cross-correlation into the N-terminal loop of the tetramer interface caused the two loop regions to hook to each other, thus improving the resistance to high acrylamide concentrations.

Design of a Flexible, Zn-Selective Protein Scaffold that Displays Anti-Irving-Williams Behavior

Selective metal binding is a key requirement not only for the functions of natural metalloproteins but also for the potential applications of artificial metalloproteins in heterogeneous environments such as cells and environmental samples. The selection of transition-metal ions through protein design can, in principle, be achieved through the appropriate choice and the precise positioning of amino acids that comprise the primary metal coordination sphere. However, this task is made difficult by the intrinsic flexibility of proteins and the fact that protein design approaches generally lack the sub-Å precision required for the steric selection of metal ions. We recently introduced a flexible/probabilistic protein design strategy (MASCoT) that allows metal ions to search for optimal coordination geometry within a flexible, yet covalently constrained dimer interface. In an earlier proof-of-principle study, we used MASCoT to generate an artificial metalloprotein dimer, (AB)₂, which selectively bound Co^II and Ni^II over Cu^II (as well as other first-row transition-metal ions) through the imposition of a rigid octahedral coordination geometry, thus countering the Irving-Williams trend. In this study, we set out to redesign (AB)₂ to examine the applicability of MASCoT to the selective binding of other metal ions. We report here the design and characterization of a new flexible protein dimer, B₂, which displays Zn^II selectivity over all other tested metal ions including Cu^II both in vitro and in cellulo. Selective, anti-Irving-Williams Zn^II binding by B₂ is achieved through the formation of a unique trinuclear Zn coordination motif in which His and Glu residues are rigidly placed in a tetrahedral geometry. These results highlight the utility of protein flexibility in the design and discovery of selective binding motifs.

"Toolbox" construction of an extremophilic nitrile hydratase from Streptomyces thermoautotrophicus for the promising industrial production of various amides

Nitrile hydratase (NHase; EC 4.2.1.84) is widely used to synthesize the corresponding amides from nitriles, which is the most successful green biocatalyst. However, the limited acceptability of substrates and instability under harsh reaction conditions have hindered its widespread industrial application. Here, a gene encoding an extremophilic NHase from Streptomyces thermoautotrophicus (S.t NHase) was successfully overexpressed in Escherichia coli. The enzyme exhibited excellent thermostability, retaining >50 % of residual activity after heat treatment at 65 °C for 252 min. To further improve the catalytic performance of S.t NHase, semi-rational engineering of its substrate access tunnel was performed. A mutant βL48D showed a specific activity of 566.18 ± 18.86 U/mg towards 3-cyanopyridine, which was 7.7 times higher than its parent enzyme (73.80 ± 5.76 U/mg). Molecular dynamics simulation showed that the introduction of aspartic acid into βLeu48 resulted in a larger and more frequent opening of the substrate access tunnel entrance. On this basis, a "toolbox" containing various mutants on the substrate access tunnel was further established, whose catalytic activity towards various nitrile substrates was extensively improved, showing great potential for efficient synthesis of multiple high-value amides.

SPARC: Structural properties associated with residue constraints

SPARC facilitates the generation of plausible hypotheses regarding underlying biochemical mechanisms by structurally characterizing protein sequence constraints. Such constraints appear as residues co-conserved in functionally related subgroups, as subtle pairwise correlations (i.e., direct couplings), and as correlations among these sequence features or with structural features. SPARC performs three types of analyses. First, based on pairwise sequence correlations, it estimates the biological relevance of alternative conformations and of homomeric contacts, as illustrated here for death domains. Second, it estimates the statistical significance of the correspondence between directly coupled residue pairs and interactions at heterodimeric interfaces. Third, given molecular dynamics simulated structures, it characterizes interactions among constrained residues or between such residues and ligands that: (a) are stably maintained during the simulation; (b) undergo correlated formation and/or disruption of interactions with other constrained residues; or (c) switch between alternative interactions. We illustrate this for two homohexameric complexes: the bacterial enhancer binding protein (bEBP) NtrC1, which activates transcription by remodeling RNA polymerase (RNAP) containing σ⁵⁴, and for DnaB helicase, which opens DNA at the bacterial replication fork. Based on the NtrC1 analysis, we hypothesize possible mechanisms for inhibiting ATP hydrolysis until ADP is released from an adjacent subunit and for coupling ATP hydrolysis to restructuring of σ⁵⁴ binding loops. Based on the DnaB analysis, we hypothesize that DnaB 'grabs' ssDNA by flipping every fourth base and inserting it into cavities between subunits and that flipping of a DnaB-specific glutamine residue triggers ATP hydrolysis.

Gordonia hydrophobica Nitrile Hydratase for Amide Preparation from Nitriles

The active pharmaceutical ingredient levetiracetam has anticonvulsant properties and is used to treat epilepsies. Herein, we describe the enantioselective preparation of the levetiracetam precursor 2-(pyrrolidine-1-yl)butanamide by enzymatic dynamic kinetic resolution with a nitrile hydratase enzyme. A rare representative of the family of iron-dependent nitrile hydratases from Gordonia hydrophobica (GhNHase) was evaluated for its potential to form 2-(pyrrolidine-1-yl)butanamide in enantioenriched form from the three small, simple molecules, namely, propanal, pyrrolidine and cyanide. The yield and the enantiomeric excess (ee) of the product are determined most significantly by the substrate concentrations, the reaction pH and the biocatalyst amount. GhNHase is also active for the hydration of other nitriles, in particular for the formation of N-heterocyclic amides such as nicotinamide, and may therefore be a tool for the preparation of various APIs.

Increasing reactivity by incorporating π-acceptor ligands into coordinatively unsaturated thiolate-ligated iron(II) complexes

Reported herein is the structural, spectroscopic, redox, and reactivity properties of a series of iron complexes containing both a π-donating thiolate, and π-accepting N-heterocycles in the coordination sphere, in which we systematically vary the substituents on the N-heterocycle, the size of the N-heterocycle, and the linker between the imine nitrogen and tertiary amine nitrogen. In contrast to our primary amine/thiolate-ligated Fe(II) complex, [Fe^II(S^Me2N₄(tren))]⁺ (1), the Fe(II) complexes reported herein are intensely colored, allowing us to visually monitor reactivity. Ferrous complexes with R = H substituents in the 6-position of the pyridines, [Fe^II(S^Me2N₄(6-H-DPPN)]⁺ (6) and [Fe^II(S^Me2N₄(6-H-DPEN))(MeOH)]⁺ (8-MeOH) are shown to readily bind neutral ligands, and all of the Fe(II) complexes are shown to bind anionic ligands regardless of steric congestion. This reactivity is in contrast to 1 and is attributed to an increased metal ion Lewis acidity assessed via aniodic redox potentials, E_p,a, caused by the π-acid ligands. Thermodynamic parameters (ΔH, ΔS) for neutral ligand binding were obtained from T-dependent equilibrium constants. All but the most sterically congested complex, [Fe^II(S^Me2N₄(6-Me-DPPN)]⁺ (5), react with O₂. In contrast to our Mn(II)-analogues, dioxygen intermediates are not observed. Rates of formation of the final mono oxo-bridged products were assessed via kinetics and shown to be inversely dependent on redox potentials, E_p,a, consistent with a mechanism involving electron transfer.

Effect and mechanism analysis of different linkers on efficient catalysis of subunit-fused nitrile hydratase

Protein fusion using a linker plays an important role for protein evolution. However, designing suitable linkers for protein evolution is yet challenging and under-explored. To further clarify the regular pattern of suitable type of linker for fusion proteins, one nitrile hydratase (NHase) was used as a target protein and subunit fusion strategy was carried out to improve its efficient catalysis. Subunit-fused variants with three different types of linkers were constructed and characterized. All variants exhibited higher stability than that of the wild type. The longer the linker was, the higher stability NHase showed, however, too long linker affected NHase activity and expression. Among the three types of linkers, the α-helical linker seemed more suitable for NHase than flexible or rigid linkers. Though it is not clear how the linkers affecting the activity, structure analysis indicated that the stability improvement is dependent on the additional salt bridge, H-bond, and the subunit interface area increasing due to the linker insertion, among which the additional salt bridge and interface area were more important factors. The results described here may be useful for redesigning other enzymes through subunit fusion.

In vivo and in vitro reconstitution of unique key steps in cystobactamid antibiotic biosynthesis

Cystobactamids are myxobacteria-derived topoisomerase inhibitors with potent anti-Gram-negative activity. They are formed by a non-ribosomal peptide synthetase (NRPS) and consist of tailored para-aminobenzoic acids, connected by a unique α-methoxy-L-isoasparagine or a β-methoxy-L-asparagine linker moiety. We describe the heterologous expression of the cystobactamid biosynthetic gene cluster (BGC) in Myxococcus xanthus. Targeted gene deletions produce several unnatural cystobactamids. Using in vitro experiments, we reconstitute the key biosynthetic steps of linker formation and shuttling via CysB to the NRPS. The biosynthetic logic involves a previously uncharacterized bifunctional domain found in the stand-alone NRPS module CysH, albicidin biosynthesis and numerous BGCs of unknown natural products. This domain performs either an aminomutase (AM) or an amide dehydratase (DH) type of reaction, depending on the activity of CysJ which hydroxylates CysH-bound L-asparagine. Furthermore, CysQ O-methylates hydroxyl-L-(iso)asparagine only in the presence of the AMDH domain. Taken together, these findings provide direct evidence for unique steps in cystobactamid biosynthesis.

Recent Advances and Promises in Nitrile Hydratase: From Mechanism to Industrial Applications

Nitrile hydratase (NHase, EC 4.2.1.84) is one type of metalloenzyme participating in the biotransformation of nitriles into amides. Given its catalytic specificity in amide production and eco-friendliness, NHase has overwhelmed its chemical counterpart during the past few decades. However, unclear catalytic mechanism, low thermostablity, and narrow substrate specificity limit the further application of NHase. During the past few years, numerous studies on the theoretical and industrial aspects of NHase have advanced the development of this green catalyst. This review critically focuses on NHase research from recent years, including the natural distribution, gene types, posttranslational modifications, expression, proposed catalytic mechanism, biochemical properties, and potential applications of NHase. The developments of NHase described here are not only useful for further application of NHase, but also beneficial for the development of the fields of biocatalysis and biotransformation.

Metal-Templated, Tight Loop Conformation of a Cys-X-Cys Biomimetic Assembles a Dimanganese Complex

With the goal of generating anionic analogues to MN₂ S₂ ⋅Mn(CO)₃ Br we introduced metallodithiolate ligands, MN₂ S₂ ^2- prepared from the Cys-X-Cys biomimetic, ema^4- ligand (ema=N,N'-ethylenebis(mercaptoacetamide); M=Ni^II , [V^IV ≡O]²⁺ and Fe^III ) to Mn(CO)₅ Br. An unexpected, remarkably stable dimanganese product, (H₂ N₂ (CH₂ C=O(μ-S))₂ )[Mn(CO)₃ ]₂ resulted from loss of M originally residing in the N₂ S₂ ^4- pocket, replaced by protonation at the amido nitrogens, generating H₂ ema^2- . Accordingly, the ema ligand has switched its coordination mode from an N₂ S₂ ^4- cavity holding a single metal, to a binucleating H₂ ema^2- with bridging sulfurs and carboxamide oxygens within Mn-μ-S-CH₂ -C-O, 5-membered rings. In situ metal-templating by zinc ions gives quantitative yields of the Mn₂ product. By computational studies we compared the conformations of "linear" ema^4- to ema^4- frozen in the "tight-loop" around single metals, and to the "looser" fold possible for H₂ ema^2- that is the optimal arrangement for binucleation. XRD molecular structures show extensive H-bonding at the amido-nitrogen protons in the solid state.

Enzyme immobilized in BioMOFs: Facile synthesis and improved catalytic performance

Biological metal-organic frameworks (BioMOFs), an emerging sub-class of MOFs, are prepared from metals and biological ligands (bioligands). Benefit from the low toxicity and good biocompatibility of bioligands, BioMOFs can be used in biomedicine and biocatalysis. In this work, a novel approach was developed for fabricating BioMOFs materials (Co-Cys BioMOFs) from cobalt salt and cystine, meanwhile nitrile hydratase (NHase) was in-situ encapsulated during the synthesis process. The obtained NHase-BioMOFs biocomposits named NHase@Co-Cys was characterized by SEM, TEM, XPS, etc. The preparation parameters and stabilities of NHase@Co-Cys were investigated. The maximum encapsulation yield and specific activity of NHase@Co-Cys were 92.71% and 139.04 U/g_{immobilized NHase}, respectively. The thermal stability of NHase@Co-Cys was improved by approximately 5-fold at 55 °C. The activity of NHase after immobilization was retained nearly 60% after incubating at pH 4.0 and 10.0 for 7 h. The NHase@Co-Cys showed similar catalytic capacity compared with free NHase in producing nicotinamide. After 7 h of reaction catalyzed by free NHase (14.51 U) and NHase@Co-Cys (12.76 U), the yield of nicotinamide was 90.94% and 86.36%, respectively. The activity of NHase@Co-Cys remained 83.85% of the original activity after recycling for 10 times. These results suggested that the NHase@Co-Cys is an effective approach to enhance the enzymatic properties and demonstrated a broad application prospect in industrial production.

Light-induced release of nitric oxide from the nitric oxide-bound CDGSH-type [2Fe-2S] clusters in mitochondrial protein Miner2

Human mitochondrial matrix protein Miner2 hosts two [2Fe-2S] clusters via two CDGSH (Cys-Asp-Gly-Ser-His) motifs. Unlike other iron-sulfur clusters in proteins, the reduced CDGSH-type [2Fe-2S] clusters in Miner2 are able to bind nitric oxide (NO) and form stable NO-bound [2Fe-2S] clusters without disruption of the clusters. Here we report that the NO-bound Miner2 [2Fe-2S] clusters can quickly release NO upon the visible light excitation. The UV-visible and Electron Paramagnetic Resonance (EPR) measurements show that the NO-bound Miner2 [2Fe-2S] clusters are converted to the reduced Miner2 [2Fe-2S] clusters upon the light excitation under anaerobic conditions, suggesting that NO binding in the reduced Miner2 [2Fe-2S] clusters is reversible. Additional studies reveal that binding of NO effectively inhibits the redox transition of the Miner2 [2Fe-2S] clusters, indicating that NO may modulate the physiological activity of Miner2 in mitochondria by directly binding to the CDGSH-type [2Fe-2S] clusters in the protein.

Protein Substrates for Reaction Discovery: Site-Selective Modification with Boronic Acid Reagents

Chemical modification of natural proteins must navigate difficult selectivity questions in a complex polyfunctional aqueous environment, within a narrow window of acceptable conditions. Limits on solvent mixtures, pH, and temperature create challenges for most synthetic methods. While a protein's complex polyfunctional environment undoubtedly creates challenges for traditional reactions, we wondered if it also might create opportunities for pursuing new bioconjugation reactivity directly on protein substrates. This Account describes our efforts to date to discover and develop new and useful reactivity for protein modification by starting from an open-ended screen of potential transition-metal catalysts for boronic acid reactivity with a model protein substrate. By starting from a broad screen, we were hoping to take advantage of the very many potential reactive sites on even a small model protein. And perhaps more importantly, whole proteins as reaction screening substrates might exhibit uniquely reactive local environments, the results of a dense combination of functional groups that would be nearly impossible to mimic in a small-molecule context. This effort has resulted in the discovery of four new protein modification reactions with boronic acid reagents, including a remarkable modification of specific backbone N-H bonds. This histidine-directed Chan-Lam coupling, based on specific proximity of an imidazole and two amide groups, is one important example of powerful reactivity that depends on a combination of functional groups that proteins make possible. Other bioconjugation reactions uncovered include a three-component tyrosine metalation with rhodium(III), a nickel-catalyzed cysteine arylation, and an unusual ascorbate-mediated oxidative process for N-terminal modification. The remarkably broad scope of reactivity types encountered in this work is a testament to the breadth of boronic acid reactivity. It is also a demonstration of the diverse reactivities that are possible by the combined alteration of boronic acid structure and metal promoter. The discovery of specific backbone modification chemistry has been a broadly empowering reactivity. Pyroglutamate, a naturally occurring posttranslational modification, exhibits remarkably high reactivity in histidine-directed backbone modification, which allows us to treat pyroglutamate as a reactive bioorthogonal handle that is readily incorporated into proteins of interest by natural machinery. In another research direction, the development of a vinylogous photocleavage system has allowed us to view backbone modification as a photocaging modification which is released by exposure to light.

Co(III) Complexes with N2S3-Type Ligands as Structural/Functional Models for the Isocyanide Hydrolysis Reaction Catalyzed by Nitrile Hydratase

It has been before reported that, in addition to hydration of nitriles, the Fe-type nitrile hydratase (NHase) also catalyzes the hydrolysis of tert-butylisocyanide ( tBuNC). In order to investigate the unique isocyanide hydrolysis by NHase, we prepared three related Co(III) model complexes, PPh₄[Co(L)] (1), PPh₄[Co(L-O₃)] (2), and PPh₄[Co(L-O₄)] (3), where L is bis( N-(2-mercapto-2-methylpropionyl)aminopropyl)sulfide. The suffixes L-O₃ and L-O₄ indicate ligands with a sulfenate and a sulfinate and with two sulfinates, respectively, instead of the two thiolates of L. The X-ray analyses of 1 and 3 reveal trigonal bipyramidal and square pyramidal structures, respectively. Complex 2, however, has five-coordinate trigonal-bipyramidal geometry with η²-type S-O coordination by a sulfenyl group. Addition of tBuNC to 1, 2, and 3 induces an absorption spectral change as a result of formation of an octahedral Co(III) complex. This interpretation is also supported by the crystal structures of PPh₄[Co(L-O₄)( tBuNC)] (4) and (PPh₄)₂[Co(L-O₄)(CN)] (5). A water molecule interacts with 3 but cannot be activated as reported previously, as demonstrated by the lack of absorption spectral change in the pH range of 5.5-10.2. Interestingly, the coordinated tBuNC is hydrolyzed by 2 and 3 at pH 10.2 to produce tBuNH₂ and CO molecule, but 1 does not react. These findings provide strong evidence that hydrolysis of tBuNC by NHase proceeds not by activation of the coordinated water molecule but by coordination of the substrate. The mechanism of the hydrolysis reaction of tBuNC is explained with support provided by DFT calculations; a positively polarized C atom of tBuNC on the Co(III) center is nucleophilically attacked by a hydroxide anion activated through an interaction of the sulfenyl/sulfinyl oxygen with the nucleophile.

Multiple States of Nitrile Hydratase from Rhodococcus equi TG328-2: Structural and Mechanistic Insights from Electron Paramagnetic Resonance and Density Functional Theory Studies

Iron-type nitrile hydratases (NHases) contain an Fe(III) ion coordinated in a characteristic "claw setting" by an axial cysteine thiolate, two equatorial peptide nitrogens, the sulfur atoms of equatorial cysteine-sulfenic and cysteine-sulfinic acids, and an axial water/hydroxyl moiety. The cysteine-sulfenic acid is susceptible to oxidation, and the enzyme is traditionally prepared using butyric acid as an oxidative protectant. The as-prepared enzyme exhibits a complex electron paramagnetic resonance (EPR) spectrum due to multiple low-spin (S = 1/2) Fe(III) species. Four distinct signals can be assigned to the resting active state, the active state bound to butyric acid, an oxidized Fe(III)-bis(sulfinic acid) form, and an oxidized complex with butyric acid. A combination of comparison with earlier work, development of methods to elicit individual signals, and design and application of a novel density functional theory method for reproducing g tensors to unprecedentedly high precision was used to assign the signals. These species account for the previously reported EPR spectra from Fe-NHases, including spectra observed upon addition of substrates. Completely new EPR signals were observed upon addition of inhibitory boronic acids, and the distinctive g1 features of these signals were replicated in the steady state with the slow substrate acetonitrile. This latter signal constitutes the first EPR signal from a catalytic intermediate of NHase and is assigned to a key intermediate in the proposed catalytic cycle. Earlier, apparently contradictory, electron nuclear double resonance reports are reconsidered in the context of this work.

High-valent copper in biomimetic and biological oxidations

A long-standing debate in the Cu-O₂ field has revolved around the relevance of the Cu(III) oxidation state in biological redox processes. The proposal of Cu(III) in biology is generally challenged as no spectroscopic or structural evidence exists currently for its presence. The reaction of synthetic Cu(I) complexes with O₂ at low temperature in aprotic solvents provides the opportunity to investigate and define the chemical landscape of Cu-O₂ species at a small-molecule level of detail; eight different types are characterized structurally, three of which contain at least one Cu(III) center. Simple imidazole or histamine ligands are competent in these oxygenation reactions to form Cu(III) complexes. The combination of synthetic structural and reactivity data suggests (1) that Cu(I) should be considered as either a one or two electron reductant reacting with O₂, (2) that Cu(III) reduction potentials of these formed complexes are modest and well within the limits of a protein matrix and (3) that primary amine and imidazole ligands are surprisingly good at stabilizing Cu(III) centers. These Cu(III) complexes are efficient oxidants for hydroxylating phenolate substrates with reaction hallmarks similar to that performed in biological systems. The remarkable ligation similarity of the synthetic and biological systems makes it difficult to continue to exclude Cu(III) from biological discussions.

An investigation of nitrile transforming enzymes in the chemo-enzymatic synthesis of the taxol sidechain

Paclitaxel (taxol) is an antimicrotubule agent widely used in the treatment of cancer. Taxol is prepared in a semisynthetic route by coupling the N-benzoyl-(2R,3S)-3-phenylisoserine sidechain to the baccatin III core structure. Precursors of the taxol sidechain have previously been prepared in chemoenzymatic approaches using acylases, lipases, and reductases, mostly featuring the enantioselective, enzymatic step early in the reaction pathway. Here, nitrile hydrolysing enzymes, namely nitrile hydratases and nitrilases, are investigated for the enzymatic hydrolysis of two different sidechain precursors. Both sidechain precursors, an openchain α-hydroxy-β-amino nitrile and a cyanodihydrooxazole, are suitable for coupling to baccatin III directly after the enzymatic step. An extensive set of nitrilases and nitrile hydratases was screened towards their activity and selectivity in the hydrolysis of two taxol sidechain precursors and their epimers. A number of nitrilases and nitrile hydratases converted both sidechain precursors and their epimers.

A switch in a substrate tunnel for directing regioselectivity of nitrile hydratases towards α,ω-dinitriles

The β37 residue of nitrile hydratase (NHase) from Pseudomonas putida and NHase from Comamonas testosteroni played a critical role in directing enzyme regioselectivity.

Reactivity of a Fe(III)-Bound Methoxide Supported with a Tris(thiolato)phosphine Ligand: Activation of C-Cl Bond in CH2Cl2 by Nucleophilic Attack of a Fe(III)-OCH3 Moiety

Two mononuclear nonheme Fe(III) complexes, [PPh4][Fe(III)(PS3″)(OCH3)] (1) and [PPh4][Fe(III)(PS3″)(Cl)] (2), supported by a tris(benzenethiolato)phosphine derivative PS3″ (PS3″ = P(C6H3-3-Me3Si-2-S)3(3-)) have been synthesized and characterized. The structures resolved from X-ray crystallography show that Fe(III) centers in both complexes adopt distorted trigonal-bipyramidal geometry with a methoxide or a chloride binding in the axial position. The magnetic data for both are consistent with intermediate-spin Fe(III) centers with a C3 symmetry (S = 3/2 ground state). The bound methoxide in 1 is labile and can be replaced by a CH3CN molecule. The forming Fe(III)-CH3CN species can be further reduced by cobaltcene quantitatively to a stable Fe(II)-CH3CN complex, [Fe(PS3″)(CH3CN)](-). One-electron oxidation of 2 by ferrocenium gave a Fe(IV) analogue, [Fe(IV)(PS3″)(Cl)]. Importantly, the Fe(III)-OCH3 moiety in complex 1 acts as a strong nucleophile that activates the C-Cl bond in CH2Cl2, leading to the formation of complex 2 quantitatively. Complex 1 also reacts with other electrophiles, benzyl chloride and benzyl bromide, to generate Fe(III)-X species (X = Cl or Br). The reactions were investigated and monitored by UV-vis-NIR, NMR, and ESI-MS spectroscopies.

Spectroscopic and Computational Studies of Nitrile Hydratase: Insights into Geometric and Electronic Structure and the Mechanism of Amide Synthesis

Nitrile hydratases (NHases) are mononuclear nonheme enzymes that catalyze the hydration of nitriles to amides. NHase is unusual in that it utilizes a low-spin (LS) Fe^III center and a unique ligand set comprised of two deprotonated backbone amides, cysteine-based sulfenic acid (RSO(H)) and sulfinic acid (RSO₂^-), and an unmodified cysteine trans to an exogenous ligand site. Electron paramagnetic resonance (EPR), magnetic circular dichroism (MCD) and low-temperature absorption (LT-Abs) spectroscopies are used to determine the geometric and electronic structures of butyrate-bound (NHaseBA) and active (NHaseAq) NHase. These data calibrate DFT models, which are then extended to explore the mechanism of nitrile hydration by NHase. In particular, the nitrile is activated by coordination to the LS Fe^III and the sulfenate group is found to be deprotonated and a significantly better nucleophile than water that can attack the coordinated nitrile to form a cyclic species. Attack at the sulfenate S atom of the cyclic species is favorable and leads to a lower kinetic barrier than attack by water on coordinated, uncyclized nitrile, while attack at the C of the cyclic species is unfavorable. The roles of the unique ligand set and low-spin nature of the NHase active site in function are also explored. It is found that the oxidized thiolate ligands are crucial to maintaining the LS state, which is important in the binding and activation of nitrile susbtrates. The dominant role of the backbone amidate ligands appears to be as a chelate in keeping the sulfenate properly oriented for nucleophilic attack on the coordinated substrate.

Synthetic advances inspired by the bioactive dinitrosyl iron unit

Resulting from biochemical iron-NO interactions, dinitrosyl iron complexes (DNICs) are small organometallic-like molecules, considered to serve as vehicles for NO transport and storage in vivo. Formed by the interaction of NO with cellular iron sulfur clusters or with the cellular labile iron pool, DNICs have been documented to be the largest NO-derived adduct in cells, even surpassing the well-known nitrosothiols (RSNOs). Continuing efforts in biological chemistry are aimed at understanding the movement of DNICs in and out of cells, and their important role in NO-induced iron efflux leading to apoptosis in cells. Intrigued by the integrity of the unique dinitrosyl iron unit (DNIU) and the possibility of roles for it in human physiology or medicinal applications, the understanding of fundamental properties such as ligand effects on its ability to switch between two redox levels has been pursued through biomimetic complexes. Using metallodithiolates and N-heterocyclic carbenes (NHCs) as ligands to Fe(NO)2, the synthesis of a library of novel DNICs, in both the oxidized, {Fe(NO)2}(9), and reduced, {Fe(NO)2}(10), forms (Enemark-Feltham notation), offers opportunity to examine structural, reactivity, and spectroscopic features. The raison d'etre for the MN2S2·Fe(NO)2 synthesis development is for the potential to exploit the ease of accessing two redox levels on two different metal sites, a property presumably required for achieving two electron redox processes in base metals. Hence such molecules may be viewed as synthetic analogues of [NiFe]- or [FeFe]-hydrogenase active sites in nature, both of which use bridging thiolates for connection of the two centers. A particular success was the development of an Fe(NO)N2S2·Fe(NO)2(+/0) redox pair for proton reduction electrocatalysis. Monomeric, reduced NHC-DNICs of the L2Fe(NO)2 type are synthesized via the Fe(CO)2(NO)2 precursor, and oxidized thiolate-containing forms are derived from the dimeric (μ-RS)2[Fe(NO)2]2. Monomeric NHC-DNICs are four coordinate, pseudotetrahedral compounds with planar Fe(NO)2 units in which the slightly bent Fe-NO groups are directed symmetrically inward at both redox levels. They serve as stable analogues of biological histidine binding sites. In agreement with IR data, Mössbauer spectroscopic parameters, and DFT computations, the prototypic NHC-DNICs indicate extensive delocalization of the electron density of iron via π-backbonding. Such π-delocalization presents an unusual reaction path for the one electron process of RS(-)/RSSR interconversion. Comparisons with imidazole-DNICs find NHCs to be the "better" ligands to Fe(NO)2 and prompted investigations in (a) possible relationships between such imidazole- and NHC-containing DNICs, (b) systems that might mimic the reactivity of DNICs with the endogenous gaseotransmitter CO, and (c) mechanistic details of such processes. In a broader context, these studies aim to further describe the behavior of the {Fe(NO)2} unit as a single molecular entity when subjected to various ligand environments and reaction conditions.

Recent Advances in Multinuclear Metal Nitrosyl Complexes

The coordination chemistry of metal nitrosyls has expanded rapidly in the past decades due to major advances of nitric oxide and its metal compounds in biology. This review article highlights advances made in the area of multinuclear metal nitrosyl complexes, including Roussin's salts and their ester derivatives from 2003 to present. The review article focuses on isolated multinuclear metal nitrosyl complexes and is organized into different sections by the number of metal centers and bridging ligands.