Synthesis and structural characterization of cross-linked histidine-phenol Cu(ii) complexes as cytochrome c oxidase active site models

Tridentate cross-linked histidine-phenol Cu(ii) ether and ester complexes, chemical analogs of the active site of several heme-copper oxidases, have been synthesized and crystallized.     

Formation and spectroscopic characterization of the dioxygen adduct of a heme-Cu complex possessing a cross-linked tyrosine-histidine mimic: modeling the active site of cytochrome c oxidase

A binucleating porphyrin with covalently appended copper chelates having a cross-linked imidazole-phenol group as the novel active site model of cytochrome c oxidase has been prepared, and the dioxygen adduct of its iron(II)-copper(I) complex was spectroscopically characterized.     

Functional biomimetic models for the active site in the respiratory enzyme cytochrome c oxidase

A functional analog of the active site in the respiratory enzyme, cytochrome c oxidase (CcO) reproduces every feature in CcO's active site: a myoglobin-like heme (heme a3), a distal tridentate imidazole copper complex (Cu(B)), a phenol (Tyr244), and a proximal imidazole. When covalently attached to a liquid-crystalline SAM film on an Au electrode, this functional model continuously catalyzes the selective four-electron reduction of dioxygen at physiological potential and pH, under rate-limiting electron flux (as occurs in CcO).     

Synthesis and spectroscopic characterization of a porphyrin–dibenzimidazole dinucleating ligand and its cobalt–copper heterodinuclear complex as a cytochrome C oxidase active site model

A new dinucleating ligand consisting of a tetraphenylporphyrin derivative covalently linked with di(2-benzimidazolylmethyl)imine and its homodinuclear Co–Co and heterodinuclear Co–Cu complexes were synthesized and spectroscopically characterized. The heterobimetallic Co–Cu complex, a cytochrome c oxidase active site model, can be obtained by a simple metathesis reaction of the homodinuclear complex with the metal salt in high yield.     

Model studies of the Cu(B) site of cytochrome c oxidase utilizing a Zn(II) complex containing an imidazole-phenol cross-linked ligand

Cytochrome c oxidase, the enzyme complex responsible for the four-electron reduction of O2 to H2O, contains an unusual histidine-tyrosine cross-link in its bimetallic heme a3-CuB active site. We have synthesised an unhindered, tripodal chelating ligand, BPAIP, containing the unusual ortho-imidazole-phenol linkage, which mimics the coordination environment of the CuB center. The ligand was used to investigate the physicochemical (pKa, oxidation potential) and coordination properties of the imidazole-phenol linkage when bound to a dication. Zn(II) coordination lowers the pKa of the phenol by 0.6 log units, and increases the potential of the phenolate/phenoxyl radical couple by approximately 50 mV. These results are consistent with inductive withdrawal of electron density from the phenolic ring. Spectroscopic data and theoretical calculations (DFT) were used to establish that the cationic complex [Zn(BPAIP)Br]+ has an axially distorted trigonal bipyramidal structure, with three coordinating nitrogen ligands (two pyridine and one imidazole) occupying the equatorial plane and the bromide and the tertiary amine nitrogen of the tripod in the axial positions. Interestingly, the Zn-Namine bonding interaction is weak or absent in [Zn(BPAIP)Br]+ and the complex gains stability in basic solutions, as indicated by 1H NMR spectroscopy. These observations are supported by theoretical calculations (DFT), which suggest that the electron-donating capacity of the equatorial imidazole ligand can be varied by modulation of the protonation and/or redox state of the cross-linked phenol. Deprotonation of the phenol makes the equatorial imidazole a stronger sigma-donor, resulting in an increased Zn-Nimd interaction and thereby leading to distortion of the axial ligand axis toward a more tetrahedral geometry.     

Synthesis, Characterization of Heterodinuclear Co-Cu Complex and Its Electrocatalytic Activity towards 02 Reduction： Implications for Cytochrome c Oxidase Active Site Modeling

A new dinudeating ligand consisting of a tetraphanylporphyrin derivative covalently linked with tris(2-benzimidazylmethyl)-amine and its homodinudear Co-Co and heterodinnelear Co-Cu complexes were synthesized and spectroscopically character-ized. The heterobimetallie cobalt-copper complex bearing three benzimidazole ligands for copper, as cytochrome c oxidase ac-tive site model, was applied to the surface of glassy carbon elec-trode to show electrocatalytie activity for O2 reduction in aque-ous solution at an addity level dose to physiological pH value.The kinetic parameters of this electrocatalytic process were ob-tained.     

Modified active site coordination in a clinical mutant of sulfite oxidase

The molybdenum site of the Arginine 160 --> Glutamine clinical mutant of the physiologically vital enzyme sulfite oxidase has been investigated by a combination of X-ray absorption spectroscopy and density functional theory calculations. We conclude that the mutant enzyme has a six-coordinate pseudo-octahedral active site with coordination of Glutamine Oepsilon to molybdenum. This contrasts with the wild-type enzyme which is five-coordinate with approximately square-based pyramidal geometry. This difference in the structure of the molybdenum site explains many of the properties of the mutant enzyme which have previously been reported.     

Solvation of the active site of cytochrome P450-cam

Summary Energetically favorable water binding sites in the substrate pocket of cytochrome P450-cam have been predicted by a molecular mechanics method. Binding sites corresponding to all the experimentally observed water sites in this region of the enzyme were located. The calculations also indicate the presence of two further water binding sites. One of these is located in a hydrophobic region of the protein where a water molecule would not bind tightly to the substrate-free enzyme. However, in the substrate-bound enzyme, a water molecule in this region could donate a hydrogen bond of optimum geometry to the carbonyl oxygen atom of the camphor substrate and could therefore contribute to the correct positioning of the comphor substrate for 5-exo-hydroxylation. These calculations also suggest that a steric analogue of camphor, containing an alkyl group which could prevent a water molecule from binding in this region, might inhibit cytochrome P450-cam by forming a more stable enzyme-ligand complex than camphor itself.     

The active site of arsenite oxidase from Alcaligenes faecalis

Arsenite oxidase, a member of the DMSO reductase family of molybdenum enzymes, has two molecules of guanosine dinucleotide molybdenum cofactor coordinating the molybdenum at the active site. X-ray absorption spectroscopy indicates that the Mo-S bonds shorten from 2.47 to 2.37 A upon reduction with the physiological substrate. It also indicates the presence of an oxo ligand at 1.70 A in both oxidized and reduced forms of the enzyme, together with a short, 1.83 A, Mo-O bond in the oxidized form that is lost upon reduction. Resonance Raman spectroscopy indicates that the two pterin dithiolene moieties have different aromaticities, with one, the Q-pterin, having a more discrete dithiolate structure while the other, the P-pterin, has considerable pi-delocalization. Our results indicate that the structure of arsenite oxidase is intermediate between that seen in other molybdenum enzymes, in which one ligand to the metal is provided by the polypeptide (serine, cysteine, or selenocysteine), and tungsten enzymes that lack a peptide ligand.     

Construction and characterization of a manganese-binding site in cytochrome c peroxidase: towards a novel manganese peroxidase

Background: Manganese-binding sites are found in several heme peroxidases, namely manganese peroxidase (MnP), chloroperoxidase, and the cationic isozyme of peanut peroxidase. The Mn-binding site in MnP is of particular interest. Oxidation of Mn(II) to Mn(III) is a key step in the biodegradation of lignin, a complex phenylpropanoid polymer, as well as of many aromatic pollutants. Cytochrome c peroxidase (CcP), which is structurally homologous to MnP despite a poor sequence homology, does not bind manganese. Thus, engineering a Mn-binding site into CcP will allow us to elucidate principles behind designing metal-binding sites in proteins, to understand the structure and function of this class of Mn-binding centers, and to prepare novel enzymes that can degrade both lignin and other xenobiotic compounds.Results: Based on a comparison of the crystal structures of CcP and MnP, a site-directed triple mutant (GIy41→ Glu, Val45 →- GIu, His181 → Asp) of residues near the putative Mn-binding site in CcP was prepared and purified to homogeneity. Titrating MnSO₄ into freshly prepared mutant CcP resulted in electronic absorption spectral changes similar to those observed in MnP. The calculated apparent dissociation constant and the stoichiometry of Mn-binding of CcP were also similar to MnP. Titration with MnSO₄ resulted in the disappearance of specific paramagnetically shifted nuclear magnetic resonance spectroscopy signals assigned to residues close to the putative Mn-binding site in the mutant CcP. None of the spectral features were observed in wild-type CcP. In addition, the triple mutant was capable of oxidizing Mn(II) at least five times more efficiently than the native CcP.Conclusions: A Mn-binding site has been created in CcP and based on our spectroscopic studies the designed Mn-binding site is similar to the Mn-binding site in MnP. The results provide a basis for understanding the structure and function of the Mn-binding site and its role in different heme peroxidases.     

Role of the Tyr-Cys cross-link to the active site properties of galactose oxidase

The catalytically relevant, oxidized state of the active site [Cu(II)-Y·-C] of galactose oxidase (GO) is composed of antiferromagnetically coupled Cu(II) and a post-translationally generated Tyr-Cys radical cofactor [Y·-C]. The thioether bond of the Tyr-Cys cross-link has been shown experimentally to affect the stability, the reduction potential, and the catalytic efficiency of the GO active site. However, the origin of these structural and energetic effects on the GO active site has not yet been investigated in detail. Here we present copper and sulfur K-edge X-ray absorption data and a systematic computational approach for evaluating the role of the Tyr-Cys cross-link in GO. The sulfur contribution of the Tyr-Cys cross-link to the redox active orbital is estimated from sulfur K-edge X-ray absorption spectra of oxidized GO to be about 24 ± 3%, compared to the values from computational models of apo-GO (15%) and holo-GO (22%). The results for the apo-GO computational models are in good agreement with the previously reported value for apo-GO (20 ± 3% from EPR). Surprisingly, the Tyr-Cys cross-link has only a minimal effect on the inner sphere, coordination geometry of the Cu site in the holo-protein. Its effect on the electronic structure is more striking as it facilitates the delocalization of the redox active orbital onto the thioether sulfur derived from Cys, thereby reducing the spin coupling between the [Y·-C] radical and the Cu(II) center (752 cm(-1)) relative to the unsubstituted [Y·] radical and the Cu(II) center (2210 cm(-1)). Energetically, the Tyr-Cys cross-link lowers the reduction potential by about 75 mV (calculated) allowing a more facile oxidation of the holo active site versus the site without the cross-link. Overall, the Tyr-Cys cross-link confers unique ground state properties on the GO active site that tunes its function in a remarkably nuanced fashion.     

Nature of the catalytically labile oxygen at the active site of xanthine oxidase

In this paper we report the results of molybdenum K-edge X-ray absorption studies performed on the oxidized active site of xanthine oxidase at pH 6 and 10. These results indicate that the active site possesses one terminal oxygen ligand (Mo=O), two thiolate ligands (Mo-S), one terminal sulfido ligand (Mo=S), and one Mo-OH moiety. EXAFS analysis demonstrates that the Mo-OH bond shortens from 1.97 A at pH 6 to 1.75 A at pH 10, which is consistent with the generation of a Mo-O- moiety. This study provides convincing structural evidence that the catalytic oxygen donor at the oxidized active site of xanthine oxidase is Mo-OH rather than the Mo-OH2 ligation previously suggested by X-ray crystallography. These results support a mechanism initiated by base-assisted nucleophilic attack of the substrate by Mo-OH.     

Inactivation of nitroalkane oxidase upon mutation of the active site base and rescue with a deprotonated substrate

Mutation of Asp402 in nitroalkane oxidase to Asn or Ala inactivates the enzyme with neutral nitroethane as substrate, but the activity can be rescued with the nitroethane anion. The V/K values of the D402N and D402A enzymes with the nitroethane anion are independent of pH, whereas the V/K values of the wild-type and D402E enzymes are pH dependent with both the protonated and the deprotonated forms of nitroethane. Moreover, although the V/K value of the D402E enzyme with neutral nitroethane is 20-fold less than that of the wild-type enzyme, there is only a 2-fold difference in the V/K values with the nitroethane anion. These results are fully consistent with a primary role for Asp402 as the active site base in nitroalkane oxidase which abstracts the substrate alpha-proton.     

Indirect evidence of direct electron communication between the active site of galactose oxidase and a graphite electrode

Bi-enzymatic biosensor based on galactose oxidase (GalOD) and horseradish peroxidase (HRP) using ferrocene as an efficient mediator was constructed. When a dependence of a working potential on the sensor performance was examined, an unusual behaviour was observed. With increasing of an applied working potential a lower concentration of substrate to attain full linear range was needed. A fully linear dependence from the first substrate addition was observed at and above the working potential of 150 mV. This activation of the biosensor response by an applied working potential very well corresponds with a formal potential of GalOD (156 mV). When a membrane prevented GalOD access to the electrode surface was applied, no activation effect of a working potential on the sensor performance was observed. Thus, it can be assumed that direct electron communication between GalOD and the electrode occurred.     

Complete N-1 regiocontrol in the formation of N-arylimidazoles. Synthesis of the active site His-Tyr side chain coupled dipeptide of cytochrome c oxidase

Under catalysis by copper(II) acetate, complete regiocontrol (N-1 versus N-3) was obtained in the arylation of substituted imidazoles with aryllead(IV) reagents. The mildness of the reaction conditions (rt, no added base) allows for the first synthesis of the histidine-tyrosine side chain coupled dipeptide found in the active site of cytochrome c oxidase.     

Pyrene.pyrene complexes at the active site of cytochrome P450 3A4: evidence for a multiple substrate binding site

Cytochrome P450 monooxygenases (CYPs) metabolize nearly all drugs and toxins. Recently, it has become clear that CYPs exhibit both homotropic and heterotropic allosteric kinetics for many substrates. However, the mechanism of cooperative kinetics has not been established for any specific human CYP/substrate combination. Suggested mechanisms include binding of multiple substrates within distinct, static, subsites of a single large active site or binding of multiple substrates within a single fluid active site. CYP3A4 hydroxylates pyrene with positive cooperativity. Therefore, experiments were designed to exploit the fluorescence properties of pyrene, which diagnostically distinguish between pyrene.pyrene complexes versus spatially separated pyrene substrates. Pyrene complexes (excimers) yield an emission spectrum clearly distinct from pyrene monomers. In lipid-free aqueous/glycerol solutions of CYP3A4, addition of pyrene affords a concentration-dependent low-spin to high-spin conversion of the CYP3A4 heme prosthetic group, indicating occupancy of the active site by pyrene. Under the same conditions, in the presence of CYP3A4 but not other heme proteins, the excimer/monomer ratio (E/M) of pyrene was decreased in emission spectra, compared to pyrene alone. However, excitation spectra indicate a CYP3A4-dependent increase in the wavelength shift for the excimer excitation spectrum versus the monomer excitation spectrum, as well as changes in the excimer excitation peak shape and vibronic structure. These changes are reversed by the CYP3A4 substrate testosterone. Together, the results demonstrate that pyrene.pyrene ground-state complexes occupy the CYP3A4 active site, and they provide the first spectroscopic evidence for substrate complexes within a single fluid active site. Functional implications include the possibility that turnover rate, regioselectivity, and stereoselectivity of the reaction are determined by the substrate.substrate complex rather than individual substrates.     

Model of the iron hydrogenase active site covalently linked to a ruthenium photosensitizer: synthesis and photophysical properties

A model of the iron hydrogenase active site with the structure [(mu-ADT)Fe2(CO)6] (ADT = azadithiolate (S-CH2-NR-CH2-S), (2: R = 4-bromophenyl, 3: R = 4-iodophenyl)) has been assembled and covalently linked to a [Ru(terpy)2]2+ photosensitizer. This trinuclear complex 1 represents one synthetic step toward the realization of our concept of light-driven proton reduction. A rigid phenylacetylene tether has been incorporated as the linking unit in 1 in order to prolong the lifetime of the otherwise short-lived [Ru(terpy)2]2+ excited state. The success of this strategy is demonstrated by comparison of the photophysical properties of 1 and of two related ruthenium complexes bearing acetylenic terpyridine ligands, with those of [Ru(terpy)2]2+. IR and electrochemical studies reveal that the nitrogen heteroatom of the ADT bridge has a marked influence on the electronic properties of the [Fe2(CO)6] core. Using the Rehm-Weller equation, the driving force for an electron transfer from the photoexcited *[Ru(terpy)2]2+ to the diiron site in 1 was calculated to be uphill by 0.59 eV. During the construction of the trinuclear complex 1, n-propylamine has been identified as a decarbonylation agent on the [(mu-ADT)Fe2(CO)6] portion of the supermolecule. Following this procedure, the first azadithiolate-bridged dinuclear iron complex coordinated by a phosphine ligand [(mu-ADT)Fe2(CO)5PPh3] (4, R = 4-bromophenyl) was synthesized.