Electronic and Functional Structure of Copper in Plant Cu/Zn Superoxide Dismutase with Combined Site-directed Mutagenesis and Electron Paramagnetic Resonance

Arabidopsis thaliana copper-zinc superoxide dismutase 1 (AtSOD1) is a typical metalloenzyme conferring cellular protection against the excessive accumulation of toxic reactive oxygen species, and is therefore considered as a critical protein. However, the structure and function of the vital amino acids around the active site of AtSOD1 remain poorly understood. Herein, the coordinated geometry of the catalytic center in AtSOD1 was reconstructed by electron paramagnetic resonance (EPR) technique, and it was found to be composed of copper and four histidine (H) residues using site-directed mutagenesis. Analysis of the mutants showed that H45 and H62 play essential roles in the catalytic reaction, and H119 plays an accessary role in facilitating substrate or proton transfer. The results indicated that the redox change of the Cu ion and the overall enzymatic activity of the protein were sustained by the H45-Cu-H62 core structure. In contrast, the residue H47 showed nearly no effect on the SOD catalytic activity. These data should contribute to a deeper understanding of the catalytic mechanism of the enzyme, and provide a new approach for the effective molecular modification of copper/zinc SODs to facilitate further research in this field.     

Crystal Structure and Superoxide Dismutase Activity of [Cu(ethylenediamine)<Subscript>2</Subscript>Cl][PF<Subscript>6</Subscript>]

Summary. The preparation, spectroscopic properties, and crystal structure of chlorobis(ethylenediamine)copper(II) hexafluorophosphate [Cu(en)₂Cl][PF₆], (en=ethylendiamine) are reported. The complex crystallizes in the monoclinic system, space group P2₁/c, with cell constants a=6.1488(9) Å, b=12.696(2) Å, c=17.7424(17) Å, =97.265(12)°, and Z=4. The copper(II) ion is coordinated to two bidentate en molecules, to one chlorine ion, and to a more distant fluorine atom of the PF₆ group, leaving the copper ion in a distorted octahedral coordination geometry. The superoxide dismutase mimetic activity of the complex was investigated using the indirect xanthine-xanthine oxidase- nitroblue tetrazolium method and compared to that of the native enzyme.     

On the Possibility of Uphill Intramolecular Electron Transfer in Multicopper Oxidases: Electrochemical and Quantum Chemical Study of Bilirubin Oxidase

The catalytic cycle of multicopper oxidases (MCOs) involves intramolecular electron transfer (IET) from the Cu‐T1 copper ion, which is the primary site of the one‐electron oxidations of the substrate, to the trinuclear copper cluster (TNC), which is the site of the four‐electron reduction of dioxygen to water. In this study we report a detailed characterization of the kinetic and electrochemical properties of bilirubin oxidase (BOx) – a member of the MCO family. The experimental results strongly indicate that under certain conditions, e.g. in alkaline solutions, the IET can be the rate‐limiting step in the BOx catalytic cycle. The data also suggest that one of the catalytically relevant intermediates (most likely characterized by an intermediate oxidation state of the TNC) formed during the catalytic cycle of BOx has a redox potential close to 0.4 V, indicating an uphill IET process from the T1 copper site (0.7 V) to the Cu‐T23. These suggestions are supported by calculations of the IET rate, based on the experimentally observed Gibbs free energy change and theoretical estimates of reorganization energy obtained by combined quantum and molecular mechanical (QM/MM) calculations.     

Kinetic and spectroscopic characterization of ACMSD from Pseudomonas fluorescens reveals a pentacoordinate mononuclear metallocofactor

The enzyme alpha-amino-beta-carboxy-muconic-epsilon-semialdehyde decarboxylase (ACMSD) plays an important role in the biodegradation of 2-nitrobenzoic acid in microorganisms and in tryptophan catabolism in humans. We report that the overexpressed ACMSD enzyme from Pseudomonas fluorescens requires a divalent metal, such as Co(II), Fe(II), Cd(II), or Mn(II), for catalytic activity and that neither a redox reagent nor an organic cofactor is required for the catalytic function. The metal ions can be taken up in either cell or cell-free preparations for generating the active form of ACMSD. The kinetic parameters and enzyme specific activity are shown to depend on the metal ion present in the enzyme, suggesting a catalytic role of the metal center. EPR spectrum of Co(II)-ACMSD provides a high-spin (S = 3/2 mononuclear metal ion in a non-heme, noncorrinoid environment with a mixed nitrogen/oxygen ligand field. We observe hyperfine interactions due to 59Co nucleus at temperatures below 5 K but not at higher temperatures. Ten hyperfine lines are present in the g(perpendicular) region, and three equivalent nitrogen hyperfine couplings are required to simulate the resonances in the EPR spectrum. The results for the metal binding site are also assessed using the copper-substituted enzyme, and the EPR spectral assignments for both cobalt and copper proteins give strong support for a distorted trigonal bipyramidal geometry of the metal center. Ultimately, these results suggest for the first time that ACMSD is a metal-dependent enzyme that catalyzes a novel nonoxidative decarboxylation.     

Characterisation of [Cu4S], the catalytic site in nitrous oxide reductase, by EPR spectroscopy

The enzyme nitrous oxide reductase (N(2)OR) has a unique tetranuclear copper centre [Cu(4)S], called Cu(Z), at the catalytic site for the two-electron reduction of N(2)O to N(2). The X- and Q-band EPR spectra have been recorded from two forms of the catalytic site of the enzyme N(2)OR from Paracoccus pantotrophus, namely, a form prepared anaerobically, Cu(Z), that undergoes a one-electron redox cycle and Cu(Z)*, prepared aerobically, which cannot be redox cycled. The spectra of both species are axial with that of Cu(Z) showing a rich hyperfine splitting in the g||-region at X-band. DFT calculations were performed to gain insight into the electronic configuration and ground-state properties of Cu(Z) and to calculate EPR parameters. The results for the oxidation state [Cu(+1)(3)Cu(+2)(1)S](3+) are in good agreement with values obtained from the fitting of experimental spectra, confirming the absolute oxidation state of Cu(Z). The unpaired spin density in this configuration is delocalised over four copper ions, thus, Cu(I) 20.1%, Cu(II) 9.5%, Cu(III) 4.8% and Cu(IV) 9.2%, the mu(4)-sulfide ion and oxygen ligand. The three copper ions carrying the highest spin density plus the sulfide ion lie approximately in the same plane while the fourth copper ion is perpendicular to this plane and carries only 4.8% spin density. It is suggested that the atoms in this plane represent the catalytic core of Cu(Z), allowing electron redistribution within the plane during interaction with the substrate, N(2)O.     

The coordination of the catalytic zinc ion in alcohol dehydrogenase studied by combined quantum-chemical and molecular mechanics calculations

Summary The coordination number of the catalytic zinc ion in alcohol dehydrogenase has been studied by integrated ab initio quantum-chemical and molecular mechanics geometry optimisations involving the whole enzyme. A four-coordinate active-site zinc ion is 100–200 kJ/mol more stable than a five-coordinate one, depending on the ligands. The only stable binding site for a fifth ligand at the zinc ion is opposite to the normal substrate site, in a small cavity buried behind the zinc ion. The zinc coordination sphere has to be strongly distorted to accommodate a ligand in this site, and the ligand makes awkward contacts with surrounding atoms. Thus, the results do not support proposals attributing an important role to five-coordinate zinc complexes in the catalytic mechanism of alcohol dehydrogenase. The present approach makes it possible also to quantify the strain induced by the enzyme onto the zinc ion and its ligands; it amounts to 42–87 kJ/mol for four-coordinate active-site zinc ion complexes and 131–172 kJ/mol for five-coordinate ones. The four-coordinate structure with a water molecule bound to the zinc ion is about 20 kJ/mol less strained than the corresponding structure with a hydroxide ion, indicating that the enzyme does not speed up the reaction by forcing the zinc coordination sphere into a structure similar to the reaction intermediates.     

Synthesis,Structure, and SOD‐like Activity of a Copper(II) Complex Containing a Bistriazole Group

The dinuclear complex [Cu₂(HL)₂(H₂O)₂](ClO₄)₂ ( 1 ) [H₂L = 5′‐(pyridin‐2‐yl)‐1‐H,2′‐H‐3, 3′‐bis(1, 2,4‐triazole)] was obtained and fully characterized. It exhibits a centrosymmetry configuration, in which each copper(II) ion is pentacoordinate with four nitrogen atoms of two triazole ligands and one oxygen atom from a water molecule. The net atomic charges distribution and atomic orbital contribution to frontier molecular orbitals were obtained using the Gaussian 98 program with Hartree‐Fock method at LANL2DZ level, indicating that the copper(II) ion has the potential to accept the electron of O₂ ^{· –}. The complex showed quasi‐reversible one‐electron Cu^II/Cu^I redox waves with redox potentials of –0.034 V. The SOD‐like activity (IC₅₀) of 1 was measured to be 0.18 ± 0.01 μM by xanthine/xanthine oxidase‐NBT assay at pH 7.8. The relatively high SOD activity suggests that the positive charge of protonated triazole can effectively steer O₂ ^{· –} to and from the active copper ion.     

Oxidations by copper metalloenzymes and some biomimetic approaches

This paper illustrates the various aspects of the reactivity of the Cu(II)–Cu(I) system in biological systems, with one example of an enzymatic reaction in which Cu(II) alone is oxidizing enough to carry out the reaction (superoxide dismutase), one example in which a Cu(II)-bound peroxo intermediate is the active species (tyrosinase) and the examples of galactose oxidase and copper amine oxidases in which Cu(II) is associated with a redox active organic cofactor. In some cases, we will show some illustrations of biomimetic approaches developed in our laboratories, aimed at a better understanding of reaction mechanisms and at an original design of new catalysts with potential applications in synthetic chemistry. Some comments are given concerning the respective features of copper and iron.     

Activation of peroxyl and molecular oxygen using bis -benzimidazole diamide copper (II) compounds

New tetradentatebis-benzimidazole ligands have been synthesized and utilized to prepare copper (II) complexes. Some of these copper (II) complexes have been characterized structurally. The copper (II) in these complexes is found to possess varying geometries. A distorted octahedral geometry is found with a highly unsymmetrical bidentate nitrate group. An unusual polymeric one-dimensional structure is observed where copper (II) is in a distorted square pyramidal geometry with a monodentate nitrate ion, having long Cu-O bond, while a distorted triagonal bipyramidal geometry is found with two carbonyl O atoms and a Cl atom in the equatorial plane, and two benzimidazole imine N atoms occupy the axial position. These compounds are found to activate the cumylperoxyl group, and this has been utilized in the facile oxidation of aromatic alcohols to aldehydes, where they act as catalysts with large turnovers. The yields of the respective products vary from 32 to 65%. The role of molecular oxygen has been studied and an attempt has been made to identify the “active copper species”. Activation of molecular oxygen has also been observed and has been used for oxidative dealkylation of a hindered phenol, producing di-butyl quinones with yields of 20–25% and 10–12 fold catalytic turnover. Dihydroxybenzenes and substituted catechols are also readily oxidized to the corresponding quinones, in oxygen-saturated solvents. Yields of 84% have been observed with 34-fold catalyst turnover, with di-t-butylcatechol. The activity of these copper (II) —bis-benzmidazolediamide compounds is reminiscent of the functioning of copper centres in galactose oxidase, tyrosinase and catechol oxidase.     

Two Coordination Compounds Bearing Bis(2-dimethylaminoethyl) Ether: Syntheses,Crystal Structures and Catalytic Application to the Henry Reaction

Two novel coordination compounds, namely [Cu₂(BDMAEE)(CH₃COO)₄]_n(1) and[Ni(BDMAEE)Cl₂](2)[BDMAEE=bis(2-dimethylaminoethyl) ether], have been synthesized and characterized by IR, elemental analysis, PXRD and X-ray single crystal diffraction. In compound 1, the central Cu(Ⅱ) ion is coordinated with four oxygen atoms and one nitrogen atom, forming a distorted square pyramidal geometry. The asymmetric units composed of one Cu(Ⅱ) ion, two acetates and a half of BDMAEE are connected to form an infinite 1D chain structure by the bridging acetate and the BDMAEE. In compound 2, the central Ni(Ⅱ) ion is coordinated with one oxygen atom, two chlorine anions and two nitrogen atoms, forming a distorted square pyramidal geometry. The compounds exhibited excellent catalytic properties in the Henry reaction of nitromethane with some aromatic aldehydes, and the optimized reaction conditions were obtained.     

Xanthine oxidase-assisted catalysis by dopamine β-hydroxylase: Mechanistic considerations on the role of superoxide anion

Dopamine β-monooxygenase catalyzes the transformation of dopamine into norepinephrine by inserting an O-atom on a benzylic C–H bond. The activation of O₂ occurs at a copper-containing active site in the presence of a reducer (ascorbate) that enables that copper ions be reduced to Cu(I) and reoxidized during catalysis. In the present paper, we establish that the xanthine/xanthine oxidase coupled system is a cofactor for this enzyme, and that hydroxylation of substrate tyramine is time-dependent. Using superoxide dismutase, we unambiguously prove that the species responsible for the hydroxylase activity is superoxide anion. The optimum pH for this activity is 6.8, a value about one pH unit higher than the physiological pH for the enzyme. Moreover, we propose a mechanism that takes into account all of our results, and describes putative interactions between the copper ions of the active site and superoxide anion.     

DFT investigation of the molybdenum cofactor in periplasmic nitrate reductases: structure of the Mo(V) EPR-active species

The periplasmic nitrate reductase NAP belongs to the DMSO reductase family that regroups molybdoenzymes housing a bis-molybdopterin cofactor as the active site. Several forms of the Mo(V) state, an intermediate redox state in the catalytic cycle of the enzyme, have been evidenced by EPR spectroscopy under various conditions, but their structure and catalytic relevance are not fully understood. On the basis of structural data available from the literature, we built several models that reproduce the first coordination sphere of the molybdenum cofactor and used DFT methods to make magneto-structural correlations on EPR-detected species. "High-g" states, which are the most abundant Mo(V) species, are characterized by a low-anisotropy g tensor and a high g(min) value. We assign this signature to a six-sulfur coordination sphere in a pseudotrigonal prismatic geometry with a partial disulfide bond. The "very high-g" species is well described with a sulfido ion as the sixth ligand. The "low-g" signal can be successfully associated to a Mo(V) sulfite-oxidase-type active site with only one pterin moiety coordinated to the molybdenum ion with an oxo or sulfido axial ligand. For all these species we investigate their catalytic activity using a thermodynamic point of view on the molybdenum coordination sphere. Beyond the periplasmic nitrate reductase case, this work provides useful magneto-structural correlations to characterize EPR-detected species in mononuclear molybdoenzymes.     

Molecular dynamics simulations of the enzyme Cu, Zn superoxide dismutase

The enzyme Cu, Zn superoxide dismutase (Cu,Zn-SOD) is a ubiquitous oxireductase, which is responsible for the cellular defense against oxidative stress caused by the high toxicity of the superoxide radical, and has been also linked to some cases of familiar amyotrophic lateral sclerosis. In the present study a set of molecular mechanics parameters for the active site of Cu,Zn-SOD has been derived. Afterward, an extensive molecular dynamics simulation has been carried out in an aqueous environment. The obtained results shed a further light on the structural flexibility of the backbone, where the active site is nested, and the solvation shell occupancy. The relatively small backbone deviation, shown by a root-mean-square deviation below 1.0 A, confirms the accuracy of the parameters. The solvent shell analysis has shown that the first solvation shell is located at about 5 A from the copper ion, generating an empty cavity with enough space to accommodate the superoxide radical. The low residence time means that a high permutation rate of water molecules in both solvation shells is consistent with the efficiency of this catalytic mechanism. Hybrid studies using ONIOM methodologies can now be done to evaluate the mechanistic implications of the explicit inclusion of the whole system.     

Evidence for inhibition of HIF-1α prolyl hydroxylase 3 activity by four biologically active tetraazamacrocycles

Hypoxia inducible factor 1 (HIF-1) is central to the hypoxic response in mammals. HIF-1α prolyl hydroxylase 3 (PHD3) degrades HIF through the hydroxylation of HIF-1α. Inhibition of PHD3 activity is crucial for up-regulating HIF-1α levels, thereby acting as HIF-dependent diseases therapy. Macrocyclic polyamines which display high stability on iron-chelating may well inhibit the enzyme activity. Thus inhibition and interaction on catalytic PHD3 by four biologically active tetraazamacrocycles (1-4), which have two types of parent rings to chelate iron(ii) dissimilarly, were studied. The apparent IC(50) values of 2.56, 1.91, 5.29 and 2.44 μM, respectively, showed good inhibition potency of the four compounds. K(I) values were 7.86, 3.69, 1.59 and 2.92 μM for 1-4, respectively. Different inhibition actions of the two groups of compounds were identified. Circular dichroism (CD) and fluorescence spectrometries proved that one type of compound has significant effects on protein conformation while another type does not. Computational methodology was constructed to employ the equilibrium geometry of enzyme active site with the presence of substrate competitive inhibitor. Iron(ii) coordination in the active site by inhibitors of this kind induces conformational change of the enzyme and blocks substrate binding.     

A Redox‐Active 2D Metal–Organic Framework for Efficient Lithium Storage with Extraordinary High Capacity

Metal–organic framework cathodes usually exhibit low capacity and poor electrochemical performance for Li‐ion storage owing to intrinsic low conductivity and inferior redox activity. Now a redox‐active 2D copper–benzoquinoid (Cu‐THQ) MOF has been synthesized by a simple solvothermal method. The abundant porosity and intrinsic redox character endow the 2D Cu‐THQ MOF with promising electrochemical activity. Superior performance is achieved as a Li‐ion battery cathode with a high reversible capacity (387 mA h g^?1), large specific energy density (775 Wh kg^?1), and good cycling stability. The reaction mechanism is unveiled by comprehensive spectroscopic techniques: a three‐electron redox reaction per coordination unit and one‐electron redox reaction per copper ion mechanism is demonstrated. This elucidatory understanding sheds new light on future rational design of high‐performance MOF‐based cathode materials for efficient energy storage and conversion.     

Crystal Structure and Superoxide Dismutase Activity of [Cu(Imidazole)2(Quinoline)Cl2]·0.5[Cu(Imidazole)4Cl2]

The preparation, spectroscopic properties and crystal structure of (bis-imidazole)quinoline-copper(II) dichloride [Cu(Im)₂(quin)Cl₂] (Im = imidazole, quin = quinoline) and tetraimidazole-copper(II)-dichloride [Cu(Im)₄Cl₂] are reported. Both cocrystallize on the triclinic system, space group P-1, with cell constants a = 8.095(5) Å, b = 12.141(5) Å, c = 13.847(5) Å, α = 108.816(5)°, β = 104.173(5)°, γ = 94.965(5)° and Z = 2. In the [Cu(Im)₂(quin)Cl₂] complex the copper(II) ion is coordinated to two imidazole molecules, to one quinoline and two chlorine ions, with the copper(II) ion in a distorted trigonal bipyramidal coordination geometry. In the [Cu(Im)₄Cl₂] complex, the copper(II) ion has a distorted octahedral coordination geometry. The superoxide dismutase mimetic activity of the complexes was investigated using the indirect xanthine-xanthine oxidase-nitroblue tetrazolium method and compared to that of the native enzyme.     

Spectroelectrochemical investigation of intramolecular and interfacial electron-transfer rates reveals differences between nitrite reductase at rest and during turnover

A combined fluorescence and electrochemical method is described that is used to simultaneously monitor the type-1 copper oxidation state and the nitrite turnover rate of a nitrite reductase (NiR) from Alcaligenes faecalis S-6. The catalytic activity of NiR is measured electrochemically by exploiting a direct electron transfer to fluorescently labeled enzyme molecules immobilized on modified gold electrodes, whereas the redox state of the type-1 copper site is determined from fluorescence intensity changes caused by Fo?rster resonance energy transfer (FRET) between a fluorophore attached to NiR and its type-1 copper site. The homotrimeric structure of the enzyme is reflected in heterogeneous interfacial electron-transfer kinetics with two monomers having a 25-fold slower kinetics than the third monomer. The intramolecular electron-transfer rate between the type-1 and type-2 copper site changes at high nitrite concentration (≥520 μM), resulting in an inhibition effect at low pH and a catalytic gain in enzyme activity at high pH. We propose that the intramolecular rate is significantly reduced in turnover conditions compared to the enzyme at rest, with an exception at low pH/nitrite conditions. This effect is attributed to slower reduction rate of type-2 copper center due to a rate-limiting protonation step of residues in the enzyme's active site, gating the intramolecular electron transfer.     

Understanding and tuning the catalytic bias of hydrogenase

When enzymes are optimized for biotechnological purposes, the goal often is to increase stability or catalytic efficiency. However, many enzymes reversibly convert their substrate and product, and if one is interested in catalysis in only one direction, it may be necessary to prevent the reverse reaction. In other cases, reversibility may be advantageous because only an enzyme that can operate in both directions can turnover at a high rate even under conditions of low thermodynamic driving force. Therefore, understanding the basic mechanisms of reversibility in complex enzymes should help the rational engineering of these proteins. Here, we focus on NiFe hydrogenase, an enzyme that catalyzes H(2) oxidation and production, and we elucidate the mechanism that governs the catalytic bias (the ratio of maximal rates in the two directions). Unexpectedly, we found that this bias is not mainly determined by redox properties of the active site, but rather by steps which occur on sites of the proteins that are remote from the active site. We evidence a novel strategy for tuning the catalytic bias of an oxidoreductase, which consists in modulating the rate of a step that is limiting only in one direction of the reaction, without modifying the properties of the active site.     

Pt-Cu / ZSM-5 for removal of nitrates from drinking water

Removal of nitrates from drinking water by catalytic hydrogenation over ZSM-5 supported Pt-Cu catalysts was studied. Bimetallics Pt-Cu were prepared by ion exchange of copper on a parent monometallic platinum catalyst. Monometallic platinum catalysts are inactive for nitrate reduction, while Pt-Cu bimetallic catalysts are active for nitrate removal. In the bimetallic catalyst, the role of copper is probably to reduce nitrate according to a redox reaction. The addition of copper to Pt catalysts decreases the production of ammonium ions     

Cyclic voltammetric simulation of electrochemically mediated enzyme reaction and elucidation of biosensor behaviors

A cyclic voltammetric simulation that can be applied to an electrochemically mediated enzyme reaction involving any substrate and mediator concentration was developed. Concentration polarization of the substrate in the vicinity of an electrode was considered as well as mediator concentration. Reversible electrochemical reaction with one electron followed by an enzyme reaction with two electrons was modeled. The differential equations for the mediator and substrate were solved using digital simulation techniques. The calculated cyclic voltammograms showed prepeaks when there was a low substrate concentration, high mediator concentration, and high enzyme activity. The prepeak was experimentally observed in the case of an enzyme electrode co-immobilized with a redox polymer. The enzyme electrode loaded at high redox polymer and high enzyme content showed a prepeak at low substrate concentration in the cyclic voltammogram.