CD and MCD studies of the non-heme ferrous active site in (4-hydroxyphenyl)pyruvate dioxygenase: correlation between oxygen activation in the extradiol and alpha-KG-dependent dioxygenases

(4-Hydroxyphenyl)pyruvate dioxygenase (HPPD) is an unusual alpha-keto acid-dependent non-heme iron dioxygenase as it incorporates both atoms of dioxygen into a single substrate, paralleling the extradiol dioxygenases. CD/MCD studies of the catalytically active ferrous site and its interaction with substrate reveal a geometic and electronic structure and mechanistic approach to oxygen activation which bridges those of the alpha-KG-dependent and the extradiol dioxygenases.     

S K-edge X-ray absorption spectroscopic investigation of the Ni-containing superoxide dismutase active site: new structural insight into the mechanism

Superoxide dismutases protect cells from the toxic effects of reactive oxygen species derived from superoxide. Nickel-containing superoxide dismutases (NiSOD), found in Streptomyces species and in cyanobacteria, are distinct from Mn-, Fe-, or Cu/Zn-containing SODs in amino acid sequence and metal ligand environment. Sulfur K-edge X-ray absorption spectroscopic investigations were carried out for a series of mono- and binuclear Ni model compounds with varying sulfur ligation, and for oxidized and reduced NiSOD to elucidate the types of Ni-S interactions found in the two oxidation states. The S K-edge XAS spectra clearly indicate the presence of Ni(III)-bound terminal thiolate in the oxidized enzyme and the absence of such coordination to Ni(II) in the peroxide-reduced enzyme. This striking change in the S ligation for Ni with redox suggests that, upon peroxide reduction, an electron is transferred to the Ni(III) site and the terminal thiolate becomes protonated, providing an efficient mechanism for proton-coupled electron transfer.     

Extradiol oxidative cleavage of catechols by ferrous and ferric complexes of 1,4,7-triazacyclononane: insight into the mechanism of the extradiol catechol dioxygenases.

The major oxygenation product of catechol by dioxygen in the presence of FeCl(2) or FeCl(3), 1,4,7-triazacyclononane (TACN), and pyridine in methanol is the extradiol cleavage product 2-hydroxymuconic semi-aldehyde methyl ester (Lin, G.; Reid, G.; Bugg, T. D. H. J. Chem. Soc. Chem. Commun. 2000, 1119--1120). Under these conditions, extradiol cleavage of a range of 3- and 4-substituted catechols with electron-donating substituents is observed. The reaction shows a preference in selectivity and rate for iron(II) rather than iron(III) for the extradiol cleavage, which parallels the selectivity of the extradiol dioxygenase family. The reaction also shows a high selectivity for the macrocyclic ligand, TACN, over a range of other nitrogen- and oxygen-containing macrocycles. Reaction of anaerobically prepared iron-TACN complexes with dioxygen gave the same product as monitored by UV/vis spectroscopy. KO(2) is able to oxidize catechols with both electron-donating and electron-withdrawing substituents, implying a different mechanism for extradiol cleavage. Saturation kinetics were observed for catechols, which fit the Michaelis--Menten equation to give k(cat)(app) = 4.8 x 10(-3) s(-1) for 3-(2',3'-dihydroxyphenyl)propionic acid. The reaction was also found to proceed using monosodium catecholate in the absence of pyridine, but with different product ratios, giving insight into the acid/base chemistry of extradiol cleavage. In particular, extradiol cleavage in the presence of iron(II) shows a requirement for a proton donor, implying a role for an acidic group in the extradiol dioxygenase active site.     

Geometric and electronic structure studies of the binuclear nonheme ferrous active site of toluene-4-monooxygenase: parallels with methane monooxygenase and insight into the role of the effector proteins in O2 activation

Multicomponent monooxygenases, which carry out a variety of highly specific hydroxylation reactions, are of great interest as potential biocatalysts in a number of applications. These proteins share many similarities in structure and show a marked increase in O2 reactivity upon addition of an effector component. In this study, circular dichroism (CD), magnetic circular dichroism (MCD), and variable-temperature, variable-field (VTVH) MCD have been used to gain spectroscopic insight into the Fe(II)Fe(II) active site in the hydroxylase component of Toluene-4 monoxygenase (T4moH) and the complex of T4moH bound by its effector protein, T4moD. These results have been correlated to spectroscopic data and density functional theory (DFT) calculations on MmoH and its interaction with MmoB. Together, these data provide further insight into the geometric and electronic structure of these biferrous active sites and, in particular, the perturbation associated with component B/D binding. It is found that binding of the effector protein changes the geometry of one iron center and orientation of its redox active orbital to accommodate the binding of O2 in a bridged structure for efficient 2-electron transfer that can form a peroxo intermediate.     

An insight into the protonation property of a diiron azadithiolate complex pertinent to the active site of Fe-only hydrogenases

Protonation of [{(mu-SCH2)2N(C6H4-p-NO2)}{Fe(CO)2(PMe3)}2] in the presence of 4 equiv. of HOTf afforded two species, a micro-hydride diiron complex, the molecular structure of which was crystallographically characterized, and a micro-S-protonated species, which was readily deprotonated in the presence of pyridine.     

X-ray and NMR crystallography in an enzyme active site: the indoline quinonoid intermediate in tryptophan synthase

Chemical-level details such as protonation and hybridization state are critical for understanding enzyme mechanism and function. Even at high resolution, these details are difficult to determine by X-ray crystallography alone. The chemical shift in NMR spectroscopy, however, is an extremely sensitive probe of the chemical environment, making solid-state NMR spectroscopy and X-ray crystallography a powerful combination for defining chemically detailed three-dimensional structures. Here we adopted this combined approach to determine the chemically rich crystal structure of the indoline quinonoid intermediate in the pyridoxal-5'-phosphate-dependent enzyme tryptophan synthase under conditions of active catalysis. Models of the active site were developed using a synergistic approach in which the structure of this reactive substrate analogue was optimized using ab initio computational chemistry in the presence of side-chain residues fixed at their crystallographically determined coordinates. Various models of charge and protonation state for the substrate and nearby catalytic residues could be uniquely distinguished by their calculated effects on the chemical shifts measured at specifically (13)C- and (15)N-labeled positions on the substrate. Our model suggests the importance of an equilibrium between tautomeric forms of the substrate, with the protonation state of the major isomer directing the next catalytic step.     

Hydrolytically active tetranuclear nickel complexes with structural resemblance to the active site of urease

Reaction of the new asymmetric ligand 2-(N-isopropyl-N-((1-methylimidazolyl)methyl)aminomethyl)-6-(N-carboxylmethyl-N-((1-methylimidazolyl)methyl) aminomethyl)-4-methylphenol (ICIMP) with nickel perchlorate and diphenylacetic acid leads to the formation of tetranuclear nickel complexes, whose crystal structures reveal that they consist of dimers of dimers in which each Ni(2) unit has a coordination environment that is similar to the active site of urease. One complex has been shown to coordinate urea and catalyze the hydrolysis of an organophosphate monoester.     

Insights into the reaction mechanism of soluble epoxide hydrolase from theoretical active site mutants

Density functional theory calculations of active site mutants are used to gain insights into the reaction mechanism of the soluble epoxide hydrolases (sEHs). The quantum chemical model is based on the X-ray crystal structure of the human soluble epoxide hydrolase. The role of two conserved active site tyrosines is explored through in silico single and double mutations to phenylalanine. Full potential energy curves for hydrolysis of (1S,2S)-beta-methylstyrene oxide are presented. The results indicate that the two active site tyrosines act in concert to lower the activation barrier for the alkylation step. For the wild-type and three different tyrosine mutant models, the regioselectivity of epoxide opening is compared for the substrates (1S,2S)-beta-methylstyrene oxide and (S)-styrene oxide. An additional part of our study focuses on the importance of the catalytic histidine for the alkylation half-reaction. Different models are presented to explore the protonation state of the catalytic histidine in the alkylation step and to evaluate the possibility of an interaction between the nucleophilic aspartate and the catalytic histidine.     

Characterization of a putative sensory [FeFe]-hydrogenase provides new insight into the role of the active site architecture

[FeFe]-hydrogenases are known for their high rates of hydrogen turnover, and are intensively studied in the context of biotechnological applications. Evolution has generated a plethora of different subclasses with widely different characteristics. The M2e subclass is phylogenetically distinct from previously characterized members of this enzyme family and its biological role is unknown. It features significant differences in domain- and active site architecture, and is most closely related to the putative sensory [FeFe]-hydrogenases. Here we report the first comprehensive biochemical and spectroscopical characterization of an M2e enzyme, derived from Thermoanaerobacter mathranii. As compared to other [FeFe]-hydrogenases characterized to-date, this enzyme displays an increased H₂ affinity, higher activation enthalpies for H⁺/H₂ interconversion, and unusual reactivity towards known hydrogenase inhibitors. These properties are related to differences in active site architecture between the M2e [FeFe]-hydrogenase and “prototypical” [FeFe]-hydrogenases. Thus, this study provides new insight into the role of this subclass in hydrogen metabolism and the influence of the active site pocket on the chemistry of the H-cluster.

Characterization of a group D putative sensory [FeFe]-hydrogenase reveals how the active site can be tuned to decrease CO inhibition and increase stability of a reduced H-cluster while retaining the ability to catalyze H⁺/H₂ interconversion.     

Verapamil: new insight into the molecular mechanism of drug oxidation in the human heart

Verapamil is a commonly prescribed cardiovascular drug, but surprisingly its metabolism in the target tissue of pharmacotherapy is basically unknown. We therefore investigated its biotransformation in human heart tissue and correlate the production of metabolites with the gene expression of major drug metabolising enzymes. Using electrospray LC–MS–MS and LC–MS³ experiments, a total of nine metabolites were observed in incubation experiments with verapamil and microsomes isolated from the human heart tissue, and this included a carbinolamine-, N-formyl-, ahemiacetale-, and formate-intermediate of N-demethyl- and O-demethylverapamil. We also observed a hydroxylation product at the benzylic position of atom C-7 (M9). Metabolites M5–M9 are novel and were not observed in previous studies with liver or other human tissues. A fine example of the considerable metabolic competence of human heart is the formation of M1–M4, e.g. dealkylverapamil, norverapamil and isomers of O-demethylverapamil, which were believed to be exclusively produced by the liver.     

A computational study on the amine-oxidation mechanism of monoamine oxidase: insight into the polar nucleophilic mechanism

The proposed polar nucleophilic mechanism of MAO was investigated using quantum chemical calculations employing the semi-empirical PM3 method. In order to mimic the reaction at the enzyme's active site, the reactions between the flavin and the p-substituted benzylamine substrate analogs were modeled. Activation energies and rate constants of all the reactions were calculated and compared with the published experimental data. The results showed that electron-withdrawing groups at the para position of benzylamine increase the reaction rate. A good correlation between the log of the calculated rate constants and the electronic parameter (sigma) of the substituent was obtained. These results agree with the previous kinetic experiments on the effect of p-substituents on the reduction of MAO-A by benzylamine analogs. In addition, the calculated rate constants showed a correlation with the rate of reduction of the flavin in MAO-A. In order to verify the results obtained from the PM3 method single-point B3LYP/6-31G*//PM3 calculations were performed. These results demonstrated a strong reduction in the activation energy for the reaction of benzylamine derivatives having electron-withdrawing substituents, which is in agreement with the PM3 calculations and the previous experimental QSAR study. PM3 and B3LYP/6-31G* energy surfaces were obtained for the overall reaction of benzylamine with flavin. Results suggest that PM3 is a reasonable method for studying this kind of reaction. These theoretical findings support the proposed polar nucleophilic mechanism for MAO-A.     

A theoretical insight into the reaction mechanism of photochemical transposition from pyrazole to imidazole

The mechanisms of the photochemical isomerization reactions were investigated by using a model system of 1,3,5-trimethylpyrazole ( 1) with the CASSCF (eight-electron/six-orbital active space) and MP2-CAS methods and the 6-311G(d) basis set. Three reaction pathways were examined in the present work. They are denoted as the ring-contraction-ring-expansion path (path I), the internal-cyclization-isomerization path (path II), and the conical-intersection path (path III). Our model investigations suggest that the preferred reaction route for the pyrazoles is as follows: reactant --> Franck-Condon region --> conical intersection --> photoproduct. In particular, the conical-intersection mechanism (path III) found in this work gives a better explanation than the previously proposed two other mechanisms (paths I and II). The theoretical findings also indicate that path III-1 should be favored over path III-2 from a kinetic point of view. This suggests that the quantum yield of 1,2,4-trimethylimidazole ( 2) should be greater than that of 1,2,5-trimethylimidazole ( 3), which supports the available experimental observations. Additionally, we propose a simple p-pi orbital topology model, which can be used as a diagnostic tool to predict the location of the conical intersections, as well as the geometries of the phototransposition products of various heterocycles.     

Epoxidation and 1,2-dihydroxylation of alkenes by a nonheme iron model system - DFT supports the mechanism proposed by experiment

The FeII complexes of two isomeric pentadentate bispidine ligands in the presence of H2O2 are catalytically active for the epoxidation and 1,2-dihydroxylation of cyclooctene (bispidine = 3,7-diazabicyclo[3.3.1]nonane; the two isomeric pentadentate bispidine ligands discussed here have two tertiary amine and three pyridine donors). The published spectroscopic and mechanistic data, which include an extensive set of 18O labeling experiments, suggest that the FeIV=O complex is the catalytically active species, which produces epoxide as well as cis- and trans-1,2-dihydroxylated products. Several observations from the published experimental study are addressed with hybrid density functional methods and, in general, the calculations support the proposed, for nonheme iron model systems novel mechanism, where the formation of a radical intermediate emerges from the reaction of the FeIV=O oxidant and cyclooctene. The calculations suggest that the S = 1 ground state of the FeIV=O complex reacts with cyclooctene in a stepwise reaction, leading to the formation of a carbon-based radical intermediate. This radical is captured by O2 from air to produce the majority of the epoxide products in an aerobic atmosphere. Under anaerobic conditions, the produced epoxide product is due to the cyclization of the radical intermediate. Several possible spin states (ST = 3, 2, 1, 0) of the radical intermediate are close in energy. As a result of the substantial energy barrier, calculated for the ST = 3 spin ground state, a spin-crossover during the cyclization step is assumed, and a possible two-state scenario is found, where the S = 2 state of the FeIV=O complex participates in the catalytic mechanism. The 1,2-dihydroxylation proceeds, as suggested by experiment, via an unprecedented pathway, where the radical intermediate is captured by a hydroxyl radical, the source of which is FeIII-OOH, and this reaction is barrierless. The calculations suggest that dihydroxylation can also occur by a direct oxidation pathway from FeIII-OOH. The strikingly different reactivities observed with the two isomeric bispidine FeII complexes are rationalized on the basis of structural and electronic differences.     

Structures of E. coli peptide deformylase bound to formate: insight into the preference for Fe2+ over Zn2+ as the active site metal

E. coli peptide deformylase (PDF) catalyzes the deformylation of nascent polypeptides generated during protein synthesis. While PDF was originally thought to be a zinc enzyme, subsequent studies revealed that the active site metal is iron. In an attempt to understand this unusual metal preference, high-resolution structures of Fe-, Co-, and Zn-PDF were determined in complex with its deformylation product, formate. In all three structures, the formate ion binds the metal and forms hydrogen-bonding interactions with the backbone nitrogen of Leu91, the amide side chain of Gln50, and the carboxylate side chain of Glu133. One key difference, however, is how the formate binds the metal. In Fe-PDF and Co-PDF, formate binds in a bidentate fashion, while in Zn-PDF, it binds in a monodentate fashion. Importantly, these structural results provide the first clues into the origins of PDF's metal-dependent activity differences. On the basis of these structures, we propose that the basis for the higher activity of Fe-PDF stems from the better ability of iron to bind and activate the tetrahedral transition state required for cleavage of the N-terminal formyl group.     

Deeper insight into the mechanism of the reaction of photogenerated metallaketenes and imines

The reaction mechanism between Fischer carbene complexes and imines to produce beta-lactams has been studied by a combination of computational (DFT) and experimental methodologies. After the photogeneration of metalla-cyclopropanone species, the reaction initiates by 1,3-migration of the metal fragment from the former carbene carbon atom to the oxygen in the S o hypersurface. In spite of the endothermic nature of this rearrangement, it is biased by the more favorable HOMO(imine)-LUMO+1 interaction in the oxygen-coordinated ketene. This species reacts with the imine to yield metalla-zwitterions, which form the final products through a four electron conrotatory ring closure. The presence of the metal moiety during the whole reaction coordinate is demonstrated by the use of a chiral chromium(0) alkoxycarbene complex, which produces low but significant ee in the reaction with imines. The cis-trans stereoselection derives from the nucleophilic addition of the nitrogen atom of the imine to the oxygen-coordinated ketene, since there are no significant differences between the classical and the metallated processes in the electrocyclation step leading to the final 2-azetidinones.     

Definitive evidence for monoanionic binding of 2,3-dihydroxybiphenyl to 2,3-dihydroxybiphenyl 1,2-dioxygenase from UV resonance Raman spectroscopy, UV/Vis absorption spectroscopy, and crystallography

Ultraviolet resonance Raman spectroscopy (UVRRS), electronic absorption spectroscopy, and X-ray crystallography were used to probe the nature of the binding of 2,3-dihydroxybiphenyl (DHB) to the extradiol ring-cleavage enzyme, 2,3-dihydroxybiphenyl 1,2-dioxygenase (DHBD; EC 1.13.11.39). The lowest lying transitions in the electronic absorption spectrum of DHBD-bound DHB occurred at 299 nm, compared to 305 nm for the monoanionic DHB species in buffer. In contrast, the corresponding transitions in neutral and dianionic DHB occurred at 283 and 348 nm, respectively, indicating that DHBD-bound DHB is monoanionic. These binding-induced spectral changes, and the use of custom-designed optical fiber probes, facilitated UVRR experiments. The strongest feature of the UVRR spectrum of DHB was a Y8a-like mode around 1600 cm(-1), whose position depended strongly on the protonation state of the DHB. In the spectrum of the DHBD-bound species, this feature occurred at 1603 cm(-1), as observed in the spectrum of monoanionic DHB. Raman band shifts were observed in deuterated solvent, ruling out dianionic binding of the substrate. Thus, the electronic absorption and UVRRS data demonstrate that DHBD binds its catecholic substrate as a monoanion, definitively establishing this feature of the proposed mechanism of extradiol dioxygenases. This conclusion is supported by a crystal structure of the DHBD:DHB complex at 2.0 A resolution, which suggests that the substrate's 2-hydroxyl substituent, and not the 3-hydroxyl group, deprotonates upon binding. The structural data also show that the aromatic rings of the enzyme-bound DHB are essentially orthogonal to each other. Thus, the 6 nm blue shift of the transition for bound DHB relative to the monoanion in solution could indicate a conformational change upon binding. Catalytic roles of active site residues are proposed based on the structural data and previously proposed mechanistic schemes.     

First synthesis of 2'-deoxyfluoropuromycin analogues: experimental insight into the mechanism of the Staudinger reaction

The N(6),N(6)-dedimethyl-2'-deoxyfluoro analogue of puromycin (= 3'-deoxy-N(6),N(6)-dimethyl-3'-[O-methyltyrosylamido]adenosine), its 2',3'-regioisomer and a 3'-cytidyl-5'-(2'-deoxyfluoro)puromycyl dinucleotide analogue were synthesized following an approach involving i) the diastereospecific nitrite-assisted formation of a lyxo nucleosidic 2',3'-epoxide from an adenosine-2',3'-ditriflate derivative in a biphasic solvent mixture; ii) the regio- and stereoselective epoxide ring opening with sodium azide under mildly acidic aqueous conditions, iii) the stereospecific introduction of the fluor atom using DAST and iv) the reaction between the nucleosidyl or dinucleotidyl azide and an active ester of the N-protected amino acid using highly efficient solution conditions for the Staudinger-Vilarrasa coupling, to obtain the corresponding carboxamide directly from the in situ formed iminophosphorane. This coupling reaction furnished sterically quite demanding amides in 94 % isolated yields under very mild conditions and should therefore be of a more general value. Under certain reaction conditions we isolated (amino)acyltriazene derivatives from which dinitrogen was not eliminated. These secondary products are trapped and stabilized witnesses of the first intermediate of the Staudinger reaction, the phosphatriazenes (phosphazides, triazaphosphadienes) which usually eliminate dinitrogen in situ and rapidly rearrange into iminophosphoranes, unless they are derived from conjugated or sterically bulky azides and phosphines. The acyltriazenes could either be thermally decomposed or converted to the corresponding N-alkyl carboxamides through proton-assisted elimination of dinitrogen. All compounds were carefully characterized through MS spectrometry, (1)H, (19)F, (31)P and (13)C NMR spectroscopy.