A method for preparing analytically pure sodium dithionite. Dithionite quality and observed nitrogenase-specific activities

Resonance Raman Characterization of O2-Binding Heme Proteins

A vast array of critical in vivo processes and pathways are dependent on a multitude of O₂-binding heme proteins which contain a diverse range of functions. Resonance Raman (rR) spectroscopy is an ideal technique for structural investigation of these proteins, providing information about the geometry of the Fe-O-O fragment and its electrostatic interactions with the distal active site. Characterization of these oxy adducts is an endeavor that is complicated by their instability for many heme proteins in solution, an obstacle which can be overcome by applying the rR technique to cryogenically frozen samples. We describe here how to measure rR spectra of heme proteins with stable oxy forms, as well as the technical adaptations required to measure unstable samples at 77 K.

Azanone (HNO): generation, stabilization and detection

HNO (nitroxyl, azanone), joined the 'biologically relevant reactive nitrogen species' family in the 2000s. Azanone is impossible to store due to its high reactivity and inherent low stability. Consequently, its chemistry and effects are studied using donor compounds, which release this molecule in solution and in the gas phase upon stimulation. Researchers have also tried to stabilize this elusive species and its conjugate base by coordination to metal centers using several ligands, like metalloporphyrins and pincer ligands. Given HNO's high reactivity and short lifetime, several different strategies have been proposed for its detection in chemical and biological systems, such as colorimetric methods, EPR, HPLC, mass spectrometry, fluorescent probes, and electrochemical analysis. These approaches are described and critically compared. Finally, in the last ten years, several advances regarding the possibility of endogenous HNO generation were made; some of them are also revised in the present work.

Water-Soluble Nitroxyl Porphyrin Complexes FeIITPPSHNO and FeIITPPSNO- Obtained from Isolated FeIITPPSNO•

The first biomimetic water-soluble Fe^II-porphyrin nitroxyl complexes were obtained and characterized by UV-vis in protonated and deprotonated forms by reduction of previously isolated and characterized Fe^IITPPSNO^•. The pK_a involved in the Fe^II-HNO ⇄ Fe^II-NO^- + H⁺ equilibrium was estimated to be around 9.7. The Fe^IITPPSHNO complex spontaneously reoxidizes to the nitrosyl form following a first-order kinetic decay with a measured kinetic constant of k = 0.017 s^-1. Experiments show that the HNO adduct undergoes unimolecular homolytic cleavage of the H-NO bond. DFT calculations suggest a phlorin radical intermediate for this reaction. The deprotonated NO^- complex resulted to be more stable, with a half-life of about 10 min.

Methods for Expression, Purification, and Characterization of PqqE, a Radical SAM Enzyme in the PQQ Biosynthetic Pathway

PqqE is the first enzyme in the biosynthetic pathway of the redox cofactor pyrroloquinoline quinone (PQQ), catalyzing the formation of a carbon-carbon bond in the precursor peptide PqqA. PqqE is a radical S-adenosyl-l-methionine (SAM) (RS) enzyme, a family of enzymes that use the reductive cleavage of a [4Fe-4S] cluster-bound SAM molecule to generate a 5'-deoxyadenosyl radical. This radical is then used to initiate an array of reactions that otherwise would be unlikely to occur. PqqE is a founding member of a subset family of RS enzymes that, additionally to the SAM [4Fe-4S] cluster, have a SPASM domain containing additional, auxiliary Fe-S clusters. Most radical SAM enzymes are highly sensitive to oxygen, which destroys their Fe-S clusters. This can pose several limitations when working with these enzymes, since most of the work has to be done under anaerobic conditions. Here, we summarize the methods developed in our lab for the expression and purification of PqqE. We also highlight the several methods we have used for the characterization of the enzyme.

Removal of arsenite by reductive precipitation in dithionite solution activated by UV light

This study investigates the removal of arsenite (As(III)) from water using dithionite activated by UV light. This work evaluated the removal kinetics of As(III) under UV light irradiation as affected by dithionite dose and light intensity, and characterized the nature of the precipitated solids using XPS and SEM-EDS. Photolysis of dithionite was observed by measuring dithionite concentration using UV absorbance at 315nm. This study also investigated the effect of UV light path length on soluble As concentrations to understand resolubilization mechanisms. Total soluble As concentrations were observed to decrease with reaction time due to reduction of arsenite to form solids having a yellow-orange color. The removal mechanism was found to be reductive precipitation that formed solids of elemental arsenic or arsenic sulfide. However, these solids were observed to resolubilize at later times after dithionite had been consumed. Resolubilization of As was prevented and additional As removal was obtained by frequent dosing of dithionite throughout the experiment. As(III) removal is attributed to photolysis of dithionite by UV light and production of reactive radicals that reduce As(III) and convert it to solid forms.

Structural and mechanistic analysis of the arsenate respiratory reductase provides insight into environmental arsenic transformations

Arsenate respiration by bacteria was discovered over two decades ago and is catalyzed by diverse organisms using the well-conserved Arr enzyme complex. Until now, the mechanisms underpinning this metabolism have been relatively opaque. Here, we report the structure of an Arr complex (solved by X-ray crystallography to 1.6-Å resolution), which was enabled by an improved Arr expression method in the genetically tractable arsenate respirer Shewanella sp. ANA-3. We also obtained structures bound with the substrate arsenate (1.8 Å), the product arsenite (1.8 Å), and the natural inhibitor phosphate (1.7 Å). The structures reveal a conserved active-site motif that distinguishes Arr [(R/K)GRY] from the closely related arsenite respiratory oxidase (Arx) complex (XGRGWG). Arr activity assays using methyl viologen as the electron donor and arsenate as the electron acceptor display two-site ping-pong kinetics. A Mo(V) species was detected with EPR spectroscopy, which is typical for proteins with a pyranopterin guanine dinucleotide cofactor. Arr is an extraordinarily fast enzyme that approaches the diffusion limit (K_m = 44.6 ± 1.6 μM, k_cat = 9,810 ± 220 seconds^-1), and phosphate is a competitive inhibitor of arsenate reduction (K_i = 325 ± 12 μM). These observations, combined with knowledge of typical sedimentary arsenate and phosphate concentrations and known rates of arsenate desorption from minerals in the presence of phosphate, suggest that (i) arsenate desorption limits microbiologically induced arsenate reductive mobilization and (ii) phosphate enhances arsenic mobility by stimulating arsenate desorption rather than by inhibiting it at the enzymatic level.

An overview of advanced reduction processes for bromate removal from drinking water: Reducing agents, activation methods, applications and mechanisms

Bromate (BrO₃^-) is a possible human carcinogen regulated at a strict standard of 10μg/L in drinking water. Various techniques to eliminate BrO₃^- usually fall into three main categories: reducing bromide (Br^-) prior to formation of BrO₃^-, minimizing BrO₃^- formation during the ozonation process, and removing BrO₃^- from post-ozonation waters. However, the first two approaches exhibit low degradation efficiency and high treatment cost. The third workaround has obvious advantages, such as high reduction efficiency, more stable performance and easier combination with UV disinfection, and has therefore been widely implemented in water treatment. Recently, advanced reduction processes (ARPs), the photocatalysis of BrO₃^-, have attracted much attention due to improved performance. To increase the feasibility of photocatalytic systems, the focus of this work concerns new technological developments, followed by a summary of reducing agents, activation methods, operational parameters, and applications. The reaction mechanisms of two typical processes involving UV/sulfite homogeneous photocatalysis and UV/titanium dioxide heterogeneous photocatalysis are further summarized. The future research needs for ARPs to reach full-scale potential in drinking water treatment are suggested accordingly.

Role of the Proximal Cysteine Hydrogen Bonding Interaction in Cytochrome P450 2B4 Studied by Cryoreduction, Electron Paramagnetic Resonance, and Electron-Nuclear Double Resonance Spectroscopy

Crystallographic studies have shown that the F429H mutation of cytochrome P450 2B4 introduces an H-bond between His429 and the proximal thiolate ligand, Cys436, without altering the protein fold but sharply decreases the enzymatic activity and stabilizes the oxyferrous P450 2B4 complex. To characterize the influence of this hydrogen bond on the states of the catalytic cycle, we have used radiolytic cryoreduction combined with electron paramagnetic resonance (EPR) and (electron-nuclear double resonance (ENDOR) spectroscopy to study and compare their characteristics for wild-type (WT) P450 2B4 and the F429H mutant. (i) The addition of an H-bond to the axial Cys436 thiolate significantly changes the EPR signals of both low-spin and high-spin heme-iron(III) and the hyperfine couplings of the heme-pyrrole (14)N but has relatively little effect on the (1)H ENDOR spectra of the water ligand in the six-coordinate low-spin ferriheme state. These changes indicate that the H-bond introduced between His and the proximal cysteine decreases the extent of S → Fe electron donation and weakens the Fe(III)-S bond. (ii) The added H-bond changes the primary product of cryoreduction of the Fe(II) enzyme, which is trapped in the conformation of the parent Fe(II) state. In the wild-type enzyme, the added electron localizes on the porphyrin, generating an S = (3)/2 state with the anion radical exchange-coupled to the Fe(II). In the mutant, it localizes on the iron, generating an S = (1)/2 Fe(I) state. (iii) The additional H-bond has little effect on g values and (1)H-(14)N hyperfine couplings of the cryogenerated, ferric hydroperoxo intermediate but noticeably slows its decay during cryoannealing. (iv) In both the WT and the mutant enzyme, this decay shows a significant solvent kinetic isotope effect, indicating that the decay reflects a proton-assisted conversion to Compound I (Cpd I). (v) We confirm that Cpd I formed during the annealing of the cryogenerated hydroperoxy intermediate and that it is the active hydroxylating species in both WT P450 2B4 and the F429H mutant. (vi) Our data also indicate that the added H-bond of the mutation diminishes the reactivity of Cpd I.

Pyridine Hemochromagen Assay for Determining the Concentration of Heme in Purified Protein Solutions

Heme is a common cofactor in proteins, found in hemoglobin, myoglobin, cytochrome P450, DGCR8, and nitric oxide synthase, among others. This protocol describes a method for quantifying heme that works best in purified protein samples. This protocol might be used to, for example, determine whether a given heme-binding protein is fully occupied by heme, thus allowing correlation of heme content with activity. This requires the absolute heme concentration and an accurate protein concentration. Another use is to determine the extinction coefficients of a heme-bound protein. This assay is fast, easy, and reproducible if done correctly.

Novel lead structures and activation mechanisms for CO-releasing molecules (CORMs)

Carbon monoxide (CO) is an endogenous small signalling molecule in the human body, produced by the action of haem oxygenase on haem. Since it is very difficult to apply safely as a gas, solid storage and delivery forms for CO are now explored. Most of these CO-releasing molecules (CORMs) are based on the inactivation of the CO by coordinating it to a transition metal centre in a prodrug approach. After a brief look at the potential cellular target structures of CO, an overview of the design principles and activation mechanisms for CO release from a metal coordination sphere is given. Endogenous and exogenous triggers discussed include ligand exchange reactions with medium, enzymatically-induced CO release and photoactivated liberation of CO. Furthermore, the attachment of CORMs to hard and soft nanomaterials to confer additional target specificity to such systems is critically assessed. A survey of analytical methods for the study of the stoichiometry and kinetics of CO release, as well as the tracking of CO in living systems by using fluorescent probes, concludes this review. CORMs are very valuable tools for studying CO bioactivity and might lead to new drug candidates; however, in the design of future generations of CORMs, particular attention has to be paid to their drug-likeness and the tuning of the peripheral 'drug sphere' for specific biomedical applications. Further progress in this field will thus critically depend on a close interaction between synthetic chemists and researchers exploring the physiological effects and therapeutic applications of CO.

Spectroscopic characterization and mechanistic investigation of P-methyl transfer by a radical SAM enzyme from the marine bacterium Shewanella denitrificans OS217

Natural products containing carbon-phosphorus bonds elicit important bioactivity in many organisms. l-Phosphinothricin contains the only known naturally-occurring carbon-phosphorus-carbon bond linkage. In actinomycetes, the cobalamin-dependent radical S-adenosyl-l-methionine (SAM) methyltransferase PhpK catalyzes the formation of the second C-P bond to generate the complete C-P-C linkage in phosphinothricin. Here we use electron paramagnetic resonance and nuclear magnetic resonance spectroscopies to characterize and demonstrate the activity of a cobalamin-dependent radical SAM methyltransferase denoted SD_1168 from Shewanella denitrificans OS217, a marine bacterium that has not been reported to synthesize phosphinothricin. Recombinant, refolded, and reconstituted SD_1168 binds a four-iron, four-sulfur cluster that interacts with SAM and cobalamin. In the presence of SAM, a reductant, and methylcobalamin, SD_1168 surprisingly catalyzes the P-methylation of N-acetyl-demethylphosphinothricin and demethylphosphinothricin to produce N-acetyl-phosphinothricin and phosphinothricin, respectively. In addition, this enzyme is active in the absence of methylcobalamin if the strong reductant titanium (III) citrate and hydroxocobalamin are provided. When incubated with [methyl-(13)C] cobalamin and titanium citrate, both [methyl-(13)C] and unlabeled N-acetylphosphinothricin are produced. Our results suggest that SD_1168 catalyzes P-methylation using radical SAM-dependent chemistry with cobalamin as a coenzyme. In light of recent genomic information, the discovery of this P-methyltransferase suggests that S. denitrificans produces a phosphinate natural product.

Resonance Raman spectroscopy reveals that substrate structure selectively impacts the heme-bound diatomic ligands of CYP17

An important function of steroidogenic cytochromes P450 is the transformation of cholesterol to produce androgens, estrogens, and the corticosteroids. The activities of cytochrome P450c17 (CYP17) are essential in sex hormone biosynthesis, with severe developmental defects being a consequence of deficiency or mutations. The first reaction catalyzed by this multifunctional P450 is the 17α-hydroxylation of pregnenolone (PREG) to 17α-hydroxypregnenolone (17-OH PREG) and progesterone (PROG) to 17α-hydroxyprogesterone (17-OH PROG). The hydroxylated products then either are used for production of corticoids or undergo a second CYP17 catalyzed transformation, representing the first committed step of androgen formation. While the hydroxylation reactions are catalyzed by the well-known Compound I intermediate, the lyase reaction is believed to involve nucleophilic attack of the earlier peroxo- intermediate on the C20-carbonyl. Herein, resonance Raman (rR) spectroscopy reveals that substrate structure does not impact heme structure for this set of physiologically important substrates. On the other hand, rR spectra obtained here for the ferrous CO adducts with these four substrates show that substrates do interact differently with the Fe-C-O fragment, with large differences between the spectra obtained for the samples containing 17-OH PROG and 17-OH PREG, the latter providing evidence for the presence of two Fe-C-O conformers. Collectively, these results demonstrate that individual substrates can differentially impact the disposition of a heme-bound ligand, including dioxygen, altering the reactivity patterns in such a way as to promote preferred chemical conversions, thereby avoiding the profound functional consequences of unwanted side reactions.

An innovative cloning platform enables large-scale production and maturation of an oxygen-tolerant [NiFe]-hydrogenase from Cupriavidus necator in Escherichia coli

Expression of multiple heterologous genes in a dedicated host is a prerequisite for approaches in synthetic biology, spanning from the production of recombinant multiprotein complexes to the transfer of tailor-made metabolic pathways. Such attempts are often exacerbated, due in most cases to a lack of proper directional, robust and readily accessible genetic tools. Here, we introduce an innovative system for cloning and expression of multiple genes in Escherichia coli BL21 (DE3). Using the novel methodology, genes are equipped with individual promoters and terminators and subsequently assembled. The resulting multiple gene cassettes may either be placed in one vector or alternatively distributed among a set of compatible plasmids. We demonstrate the effectiveness of the developed tool by production and maturation of the NAD(+)reducing soluble [NiFe]-hydrogenase (SH) from Cupriavidus necator H16 (formerly Ralstonia eutropha H16) in E. coli BL21Star™ (DE3). The SH (encoded in hoxFUYHI) was successfully matured by co-expression of a dedicated set of auxiliary genes, comprising seven hyp genes (hypC1D1E1A2B2F2X) along with hoxW, which encodes a specific endopeptidase. Deletion of genes involved in SH maturation reduced maturation efficiency substantially. Further addition of hoxN1, encoding a high-affinity nickel permease from C. necator, considerably increased maturation efficiency in E. coli. Carefully balanced growth conditions enabled hydrogenase production at high cell-densities, scoring mg·(Liter culture)(-1) yields of purified functional SH. Specific activities of up to 7.2±1.15 U·mg(-1) were obtained in cell-free extracts, which is in the range of the highest activities ever determined in C. necator extracts. The recombinant enzyme was isolated in equal purity and stability as previously achieved with the native form, yielding ultrapure preparations with anaerobic specific activities of up to 230 U·mg(-1). Owing to the combinatorial power exhibited by the presented cloning platform, the system might represent an important step towards new routes in synthetic biology.

Nucleotide-assisted [Fe4S4] redox state interconversions of the Azotobacter vinelandii Fe protein and their relevance to nitrogenase catalysis

The [Fe4S4] cluster of the nitrogenase Fe protein from Azotobacter vinelandii can exist in three redox states: oxidized [Fe4S4](2+), dithionite reduced [Fe4S4](1+), and two forms of the all ferrous [Fe4S4](0), S = 4 and 0. Operation of the [Fe4S4](2+)/ [Fe4S4](1+) redox couple transfers one electron to the MoFe protein during catalysis with hydrolysis of two MgATPs. In contrast, the [Fe4S4](2+)/[Fe4S4](0) couple transfers two electrons per binding event, accompanied by hydrolysis of only two MgATPs. Both reactions occur at nearly identical rates even though the number of electrons transferred differs by a factor of 2. MgATP and MgADP facilitate interconversion of the three redox states: 2[Fe4S4](1+) + 4 MgATP = [Fe4S4](2+)(MgATP)2 + [Fe4S4](0)(MgATP)2, as demonstrated by the MgATP reaction. This reaction was investigated as a possible precursor reaction to provide two electrons in the form of [Fe4S4](0)(MgATP)2 for delivery to the MoFe protein to then conduct a two-electron substrate reduction. However, experiments showed that this disproportionation reaction, which readily occurs, was not viable during nitrogenase catalysis utilizing the [Fe4S4](1+) cluster state. The known cooperative behavior of the Fe protein in the [Fe4S4](1+) state taken together with a measured turnover potential of -460 mV with an n = 2 value, suggest a gating process on the MoFe protein involving a two electron step.

Advanced Reduction Processes: A New Class of Treatment Processes

A new class of treatment processes called advanced reduction processes (ARPs) is proposed. ARPs combine activation methods and reducing agents to form highly reactive reducing radicals that degrade oxidized contaminants. Batch screening experiments were conducted to identify effective ARPs by applying several combinations of activation methods (ultraviolet light, ultrasound, electron beam, and microwaves) and reducing agents (dithionite, sulfite, ferrous iron, and sulfide) to degradation of four target contaminants (perchlorate, nitrate, perfluorooctanoic acid, and 2,4 dichlorophenol) at three pH-levels (2.4, 7.0, and 11.2). These experiments identified the combination of sulfite activated by ultraviolet light produced by a low-pressure mercury vapor lamp (UV-L) as an effective ARP. More detailed kinetic experiments were conducted with nitrate and perchlorate as target compounds, and nitrate was found to degrade more rapidly than perchlorate. Effectiveness of the UV-L/sulfite treatment process improved with increasing pH for both perchlorate and nitrate. We present the theory behind ARPs, identify potential ARPs, demonstrate their effectiveness against a wide range of contaminants, and provide basic experimental evidence in support of the fundamental hypothesis for ARP, namely, that activation methods can be applied to reductants to form reducing radicals that degrade oxidized contaminants. This article provides an introduction to ARPs along with sufficient data to identify potentially effective ARPs and the target compounds these ARPs will be most effective in destroying. Further research will provide a detailed analysis of degradation kinetics and the mechanisms of contaminant destruction in an ARP.

Carbon dioxide reduction to methane and coupling with acetylene to form propylene catalyzed by remodeled nitrogenase

A doubly substituted form of the nitrogenase MoFe protein (α-70(Val)(→Ala), α-195(His→Gln)) has the capacity to catalyze the reduction of carbon dioxide (CO(2)) to yield methane (CH(4)). Under optimized conditions, 1 nmol of the substituted MoFe protein catalyzes the formation of 21 nmol of CH(4) within 20 min. The catalytic rate depends on the partial pressure of CO(2) (or concentration of HCO(3)(-)) and the electron flux through nitrogenase. The doubly substituted MoFe protein also has the capacity to catalyze the unprecedented formation of propylene (H(2)C = CH-CH(3)) through the reductive coupling of CO(2) and acetylene (HC≡CH). In light of these observations, we suggest that an emerging understanding of the mechanistic features of nitrogenase could be relevant to the design of synthetic catalysts for CO(2) sequestration and formation of olefins.

Reactivity of iron(II)-bound nitrosyl hydride (HNO, nitroxyl) in aqueous solution

The reactivity of coordinated nitroxyl (HNO) has been explored with the [Fe(II)(CN)(5)HNO](3-) complex in aqueous medium, pH 6. We discuss essential biorelevant issues as the thermal and photochemical decompositions, the reactivity toward HNO dissociation, the electrochemical behavior, and the reactions with oxidizing and reducing agents. The spontaneous decomposition in the absence of light yielded a two-electron oxidized species, the nitroprusside anion, [Fe(II)(CN)(5)NO](2-), and a negligible quantity of N(2)O, with k(obs)≈5×10(-7)s(-1), at 25.0°C. The value of k(obs) represents an upper limit for HNO release, comparable to values reported for other structurally related L ligands in the [Fe(II)(CN)(5)L](n-) series. These results reveal that the FeN bond is strong, suggesting a significant σ-π interaction, as already postulated for other HNO-complexes. The [Fe(II)(CN)(5)HNO](3-) ion showed a quasi-reversible oxidation wave at 0.32 V (vs normal hydrogen electrode), corresponding to the [Fe(II)(CN)(5)HNO](3-)/[Fe(II)(CN)(5)NO](3-),H(+) redox couple. Hexacyanoferrate(III), methylviologen and the nitroprusside ion have been selected as potential oxidants. Only the first reactant achieved a complete oxidation process, initiated by a proton-coupled electron transfer reaction at the HNO ligand, with nitroprusside as a final oxidation product. Dithionite acted as a reductant of [Fe(II)(CN)(5)HNO](3-), in a 4-electron process, giving NH(3). The high stability of bound HNO may resemble the properties in related Fe(II) centers of redox active enzymes. The very minor release of N(2)O shows that the redox conversions may evolve without disruption of the FeN bonds, under competitive conditions with the dissociation of HNO.

Temperature derivative spectroscopy to monitor the autoxidation decay of cytochromes P450

Temperature derivative spectroscopy (TDS), a type of relaxation spectroscopy, is a powerful tool to study protein dynamics (Berendzen, J.; Braunstein, D. Proc. Natl. Acad. Sci. U. S. A. 1990, 87, 1). We developed the version of temperature derivative spectroscopy to monitor kinetics of autoxidation of cytochromes P450 and applied it to study the properties of the oxy-ferrous complex of a human membrane bound P450, CYP19A1 (aromatase), and that of a bacterial soluble P450, CYP101 when bound with their most common substrates, androstenedione (AD) and camphor, respectively. TDS extends the panel of methods that can be used to monitor heme protein kinetics, providing a rapid measurement technique and enabling measurement of the autoxidation rate over a wide range of temperatures, yielding the activation energy as well as absolute reaction rate in a single experiment.

Defining CYP3A4 structural responses to substrate binding. Raman spectroscopic studies of a nanodisc-incorporated mammalian cytochrome P450

Resonance Raman (RR) spectroscopy is used to help define active site structural responses of nanodisc-incorporated CYP3A4 to the binding of three substrates: bromocriptine (BC), erythromycin (ERY), and testosterone (TST). We demonstrate that nanodisc-incorporated assemblies reveal much more well-defined active site RR spectroscopic responses as compared to those normally obtained with the conventional, detergent-stabilized, sampling strategies. While ERY and BC are known to bind to CYP3A4 with a 1:1 stoichiometry, only the BC induces a substantial conversion from low- to high-spin state, as clearly manifested in the RR spectra acquired herein. The third substrate, TST, displays significant homotropic interactions within CYP3A4, the active site binding up to 3 molecules of this substrate, with the functional properties varying in response to binding of individual substrate molecules. While such behavior seemingly suggests the possibility that each substrate binding event induces functionally important heme structural changes, up to this time spectroscopic evidence for such structural changes has not been available. The current RR spectroscopic studies show clearly that accommodation of different size substrates, and different loading of TST, do not significantly affect the structure of the substrate-bound ferric heme. However, it is here demonstrated that the nature and number of bound substrates do have an extraordinary influence on the conformation of bound exogenous ligands, such as CO or dioxygen and its reduced forms, implying an effective mechanism whereby substrate structure can impact reactivity of intermediates so as to influence function, as reflected in the diverse reactivity of this drug metabolizing cytochrome.

Stoichiometry of the redox neutral deamination and oxidative dehydrogenation reactions catalyzed by the radical SAM enzyme DesII

DesII from Streptomyces venezuelae is a radical SAM (S-adenosyl-l-methionine) enzyme that catalyzes the deamination of TDP-4-amino-4,6-dideoxy-d-glucose to form TDP-3-keto-4,6-dideoxy-d-glucose in the biosynthesis of TDP-d-desosamine. DesII also catalyzes the dehydrogenation of the nonphysiological substrate TDP-D-quinovose to TDP-3-keto-6-deoxy-d-glucose. These properties prompted an investigation of how DesII handles SAM in the redox neutral deamination versus the oxidative dehydrogenation reactions. This work was facilitated by the development of an enzymatic synthesis of TDP-4-amino-4,6-dideoxy-d-glucose that couples a transamination equilibrium to the thermodynamically favorable oxidation of formate. In this study, DesII is found to consume SAM versus TDP-sugar with stoichiometries of 0.96 +/- 0.05 and 1.01 +/- 0.05 in the deamination and dehydrogenation reactions, respectively, using Na(2)S(2)O(4) as the reductant. Importantly, no significant change in stoichiometry is observed when the flavodoxin/flavodoxin NADP(+) oxidoreductase/NADPH reducing system is used in place of Na(2)S(2)O(4). Moreover, there is no evidence of an uncoupled or abortive process in the deamination reaction, as indicated by the observation that dehydrogenation can take place in the absence of an external source of reductant whereas deamination cannot. Mechanistic and biochemical implications of these results are discussed.

Molecular basis for directional electron transfer

Biological macromolecules involved in electron transfer reactions display chains of closely packed redox cofactors when long distances must be bridged. This is a consequence of the need to maintain a rate of transfer compatible with metabolic activity in the framework of the exponential decay of electron tunneling with distance. In this work intermolecular electron transfer was studied in kinetic experiments performed with the small tetraheme cytochrome from Shewanella oneidensis MR-1 and from Shewanella frigidimarina NCIMB400 using non-physiological redox partners. This choice allowed the effect of specific recognition and docking to be eliminated from the measured rates. The results were analyzed with a kinetic model that uses the extensive thermodynamic characterization of these proteins reported in the literature to discriminate the kinetic contribution of each heme to the overall rate of electron transfer. This analysis shows that, in this redox chain that spans 23 A, the kinetic properties of the individual hemes establish a functional specificity for each redox center. This functional specificity combined with the thermodynamic properties of these soluble proteins ensures directional electron flow within the cytochrome even outside of the context of a functioning respiratory chain.

Modulation of the cytochrome P450 reductase redox potential by the phospholipid bilayer

Cytochrome P450 reductase (CPR) is a tethered membrane protein which transfers electrons from NADPH to microsomal P450s. We show that the lipid bilayer has a role in defining the redox potential of the CPR flavin domains. In order to quantitate the electrochemical behavior of this central redox protein, full-length CPR was incorporated into soluble nanometer scale discoidal membrane bilayers (nanodiscs), and potentials were measured using spectropotentiometry. The redox potentials of both FMN and FAD were found to shift to more positive values when in a membrane bilayer as compared to a solubilized version of the reductase. The potentials of the semiquinone/hydroquinone couple of both FMN and FAD are altered to a larger extent than the oxidized/semiquinone couple which is understood by a simple electrostatic model. When anionic lipids were used to change the membrane composition of the CPR-nanodisc, the redox potential of both flavins became more negative, favoring electron transfer from CPR to cytochrome P450.

The critical iron-oxygen intermediate in human aromatase

Aromatase (CYP19) is the target of several therapeutics used for breast cancer treatment and catalyzes the three-step conversion of androgens to estrogens, with an unusual C-C cleavage reaction in the third step. To better understand the CYP19 reaction, the oxy-ferrous complex of CYP19 with androstenedione substrate was cryotrapped, characterized by UV-vis spectroscopy, and cryoreduced to generate the next reaction cycle intermediate. EPR analysis revealed that the initial intermediate observed following cryoreduction is the unprotonated g(1)=2.254 peroxo-ferric intermediate, which is stable up to 180K. Upon gradual cryoannealing, the low-spin (g(1)=2.39) product complex is formed, with no evidence for accumulation of the g(1)=2.30 hydroperoxo-ferric intermediate. The relative stabilization of the peroxo-ferric heme and the lack of observed hydroperoxo-ferric heme distinguish CYP19 from other P450s, suggesting that the proton delivery pathway is more hindered in CYP19 than in most other P450s.

The One-electron Autoxidation of Human Cytochrome P450 3A4

Monomeric cytochrome P450 3A4 (CYP3A4), the most prevalent cytochrome P450 in human liver, can simultaneously bind one, two, or three molecules of substrates and effectors. The difference in the functional properties of such binding intermediates gives rise to homotropic and heterotropic cooperative kinetics of this enzyme. To understand the overall kinetic processes operating in CYP3A4, we documented the kinetics of autoxidation of the oxy-ferrous intermediate of CYP3A4 as a function of testosterone concentration. The rate of autoxidation in the presence of testosterone was significantly lower than that observed with no substrate present. Stability of the oxy-ferrous complex in CYP3A4 and the amplitude of the geminate CO rebinding increased significantly as a result of binding of just one testosterone molecule. In contrast, the slow phase in the kinetics of cyanide binding to the ferric CYP3A4 correlated with a shift of the heme iron spin state, which is only caused by the association of a second molecule of testosterone. Our results show that the first substrate binding event prevents the escape of diatomic ligands from the distal heme binding pocket, stabilizes the oxy-ferrous complex, and thus serves as an important modulator of the uncoupling channel in the cytochromes P450.

Thermodynamic and kinetic characterisation of individual haems in multicentre cytochromes c3

The characterisation of individual centres in multihaem proteins is difficult due to the similarities in the redox and spectroscopic properties of the centres. NMR has been used successfully to distinguish redox centres and allow the determination of the microscopic thermodynamic parameters in several multihaem cytochromes c(3) isolated from different sulphate-reducing bacteria. In this article we show that it is also possible to discriminate the kinetic properties of individual centres in multihaem proteins, if the complete microscopic thermodynamic characterisation is available and the system displays fast intramolecular equilibration in the time scale of the kinetic experiment. The deconvolution of the kinetic traces using a model of thermodynamic control provides a reference rate constant for each haem that does not depend on driving force and can be related to structural factors. The thermodynamic characterisation of three tetrahaem cytochromes and their kinetics of reduction by sodium dithionite are reported in this paper. Thermodynamic and kinetic data were fitted simultaneously to a model to obtain microscopic reduction potentials, haem-haem and haem-proton interacting potentials, and reference rate constants for the haems. The kinetic information obtained for these cytochromes and recently published data for other multihaem cytochromes is discussed with respect to the structural factors that determine the reference rates. The accessibility for the reducing agent seems to play an important role in controlling the kinetic rates, although is clearly not the only factor.

The ferrous-dioxygen intermediate in human cytochrome P450 3A4. Substrate dependence of formation and decay kinetics

The oxy-ferrous complex is the first of three branching intermediates in the catalytic cycle of cytochrome P450, in which the total efficiency of substrate turnover is curtailed by the side reaction of autoxidation. For human membrane-bound cytochromes P450, the oxy complex is believed to be the primary source of cytotoxic superoxide and peroxide, although information on the properties and stability of this intermediate is lacking. Here we document stopped-flow spectroscopic studies of the formation and decay of the oxy-ferrous complex in the most abundant human cytochrome P450 (CYP3A4) as a function of temperature in the substrate-free and substrate-bound form. CYP3A4 solubilized in purified monomeric form in nanoscale POPC bilayers is functionally and kinetically homogeneous. In substrate-free CYP3A4, the oxy complex is extremely unstable with a half-life of approximately 30 ms at 5 degrees C. Saturation with testosterone or bromocriptine stabilizes the oxy-ferrous intermediate. Comparison of the autoxidation rates with the available data on CYP3A4 turnover kinetics suggests that the oxy complex may be an important route for uncoupling.

Kinetics and Mechanism of the Iron Phthalocyanine Catalyzed Reduction of Nitrite by Dithionite and Sulfoxylate in Aqueous Solution

The reactions of sodium nitrite with sodium dithionite and sulfoxylate ion were studied in the presence of iron(III) tetrasulfophthalocyanine, Fe(III)(TSPc)3-, in aqueous alkaline solution. Kinetic parameters for the different reaction steps in the catalytic reduction by dithionite were determined. The final product of the reaction was found to be nitrous oxide. Contrary to this, the product of the catalytic reduction of nitrite by sulfoxylate was found to be ammonia. The striking difference in the reaction products is accounted for in terms of different structures of the intermediate complexes formed during the reduction by dithionite and sulfoxylate, in which nitrite is suggested to coordinate to the iron complex via nitrogen and oxygen, respectively. Sulfoxylate is shown to be a convenient reductant for the synthesis of the highly reduced iron phthalocyanine species Fe(I)(TSPc*)6- in aqueous solution. The kinetics of the reduction of Fe(I)(TSPc)5- to Fe(I)(TSPc*)6-, as well as the oxidation of the latter species by nitrite, was studied in detail.

Roles of KATP channels in delayed cardioprotection and intracellular Ca(2+) in the rat heart as revealed by kappa-opioid receptor stimulation with U50488H

The effect of preconditioning with U50488 H (UP), a selective kappa-opioid receptor (kappa-OR) agonist, on infarct size and intracellular Ca2+ ([Ca2+]i) in the heart subjected to ischaemic insults were studied and evaluated. U50488 H administered intravenously reduced the infarct size 18-48 h after administration in isolated hearts subjected to regional ischaemia/reperfusion (I/R). The effect was dose dependent. A peak effect was reached at 10 mg x kg-1 U50488 H and at 24 h after administration. The effect of 10 mg x kg-1 U50488 H at 24 h after administration was abolished by nor-binaltorphimine (nor-BNI), a selective kappa-OR antagonist, indicating the effect was kappa-OR mediated. The infarct reducing effect of U50488 H was attenuated when a selective blocker of mitochondrial (5-hydroxydecanoic acid, 5-HD) or sarcolemmal (HRM-1098) ATP-sensitive potassium channel (KATP) was coadministered with U50488 H 24 h before ischaemia or when 5-HD was administered just before ischaemia. U50488 H also attenuated the elevation in [Ca2+]i and reduction in electrically induced [Ca2+]i transient in cardiomyocytes subjected to ischaemic insults. The effects were reversed by blockade of KATP channel, which abolished the protective effect of preconditioning with U50488 H. The results indicated that mitochondrial KATP channel serves as both a trigger and a mediator, while sarcolemmal KATP channel as a trigger only, of delayed cardioprotection of kappa-OR stimulation. The effects of these channels may result from prevention/attenuation of [Ca2+]i overload induced by ischaemic insults.

Proton-assisted two-electron transfer in natural variants of tetraheme cytochromes from Desulfomicrobium Sp

The tetraheme cytochrome c3 isolated from Desulfomicrobium baculatum (DSM 1743)(Dsmb) was cloned, and the sequence analysis showed that this cytochrome differs in just three amino acid residues from the cytochrome c3 isolated from Desulfomicrobium norvegicum (Dsmn): (DsmnXXDsmb) Thr-37 --> Ser, Val-45 --> Ala, and Phe-88 --> Tyr. X-ray crystallography was used to determine the structure of cytochrome c3 from Dsmb, showing that it is very similar to the published structure of cytochrome c3 from Dsmn. A detailed thermodynamic and kinetic characterization of these two tetraheme cytochromes c3 was performed by using NMR and visible spectroscopy. The results obtained show that the network of cooperativities between the redox and protonic centers is consistent with a synergetic process to stimulate the hydrogen uptake activity of hydrogenase. This is achieved by increasing the affinity of the cytochrome for protons through binding electrons and, reciprocally, by favoring a concerted two-electron transfer assisted by the binding of proton(s). The data were analyzed within the framework of the differences in the primary and tertiary structures of the two proteins, showing that residue 88, close to heme I, is the main cause for the differences in the microscopic thermodynamic parameters obtained for these two cytochromes c3. This comparison reveals how replacement of a single amino acid can tune the functional properties of energy-transducing proteins, so that they can be optimized to suit the bioenergetic constraints of specific habitats.

Thermodynamic and kinetic characterization of trihaem cytochrome c3 from Desulfuromonas acetoxidans

Trihaem cytochrome c3 (also known as cytochrome c551.5 and cytochrome c7) is isolated from the periplasmic space of Desulfuromonas acetoxidans, a sulfur-reducing bacterium. Thermodynamic and kinetic data for the trihaem cytochrome c3 are presented and discussed in the context of the possible physiological implications of its functional properties with respect to the natural habitat of D. acetoxidans, namely as a symbiont with green sulfur bacteria working as a mini-sulfuretum. The thermodynamic properties were determined through the fit of redox titration data, followed by NMR and visible spectroscopy, to a model of four functional centres that describes the network of cooperativities between the three haems and one protolytic centre. The kinetics of trihaem cytochrome c3 reduction by sodium dithionite were studied using the stopped-flow technique and the data were fitted to a kinetic model that makes use of the thermodynamic properties to obtain the rate constants of the individual haems. This analysis indicates that the electrons enter the cytochrome mainly via haem I. The reduction potentials of the haems in this cytochrome show little variation with pH within the physiological range, and the kinetic studies show that the rates of reduction are also independent of pH in the range studied. Thus, although the trihaem cytochrome c3 is readily reduced by hydrogenases from Desulfovibrio sp. and its haem core is similar to that of the homologous tetrahaem cytochromes c3, its physico-chemical properties are quite different, which suggests that these multihaem cytochromes with similar structures perform different functions.

Effects of pharmacological preconditioning with U50488H on calcium homeostasis in rat ventricular myocytes subjected to metabolic inhibition and anoxia

1. The effects of pharmacological preconditioning with U50488H (U(50)), a selective kappa-opioid receptor agonist, on Ca(2+) homeostasis in rat ventricular myocytes subjected for 9 min to metabolic inhibition (MI) and anoxia (A), consequences of ischaemia, were studied and compared with those of preconditioning with brief periods of MI/A. 2. Precondition with 30 micro M of U(50) for three cycles of 1 min each cycle separated by 3 min of recovery (UP) significantly increased the percentage of non-blue cells following MI/A. The effect of UP is the same as that of preconditioning with an inhibitor of glycolysis and an oxygen scavenger for three 1-min cycles separated by three-minute recovery (MI/AP). The results indicate that like MI/AP, UP also confers cardioprotection. 3. MI/A increased intracellular Ca(2+) ([Ca(2+)](i)) and reduced the amplitude of caffeine-induced [Ca(2+)](i) transients, an indication of Ca(2+) content in the sarcoplasmic reticulum (SR). MI/A also reduced the electrically-induced [Ca(2+)](i) transient, that indicates Ca(2+)-release during excitation-contraction coupling, and Ca(2+) sparks in unstimulated myocytes, that indicates spontaneous Ca(2+)-release from SR. It also prolonged the decline of the electrically-induced [Ca(2+)](i) transient and slowed down the recovery of the electrically-induced [Ca(2+)](i) transient after administration of caffeine. In addition, MI/A prolonged the decline of caffeine induced [Ca(2+)](i) transient, an indication of Na(+)-Ca(2+) exchange activity, and UP prevented it. So UP, that confers cardioprotection, prevented the changes induced by MI/A. With the exception of Ca(2+)-spark, which was not studied, the effects of MI/AP are the same as those of UP. 4. It is concluded that pharmacological preconditioning with U(50), that confers immediate cardioprotection, prevents changes of Ca(2+) homeostasis altered by MI/A in the rat heart. This may be responsible, at least partly, for the cardioprotective action. 5. The study also provided evidence that MI/A causes mobilization of Ca(2+) from SR to cytoplasm causing Ca(2+)-overload which may be due to reduced Ca(2+)-uptake by SR. MI/A also reduces spontaneous and electrically induced Ca(2+) release from SR.

Duplication and extension of the Thorneley and Lowe kinetic model for Klebsiella pneumoniae nitrogenase catalysis using a MATHEMATICA software platform

The Thorneley and Lowe kinetic model for nitrogenase catalysis was developed in the early to mid 1980s, and has been of value in accounting for many aspects of nitrogenase catalysis. It has also been of value by providing a model for predicting new catalytic behavior. Since its original publication, new results have been obtained and have been successfully incorporated into the model. However, the computer program used for nitrogenase simulations has not been generally available. Using kinetic schemes and assumptions previously outlined by Thorneley and Lowe, we report attempts to duplicate the original T&L kinetic simulation for Klebsiella pneumoniae nitrogenase catalysis using an updated simulation based on the MATHEMATICA programming format, which makes it more user-friendly and more readily available. Comparisons of our simulations with the original T&L simulations are generally in agreement, but in some cases serious discrepancy is observed. Possible reasons for the differences are discussed. In addition to duplicating the original T&L model, we report effects of updating it by including information that has come to light subsequent to its original publication.

Steady-state kinetic studies of dithionite utilization, component protein interaction, and the formation of an oxidized iron protein intermediate during Azotobacter vinelandii nitrogenase catalysis

Steady-state kinetic analysis of the two-component protein system of Azotobacter vinelandii (Av) nitrogenase is reported. A precisely obeyed half-order reaction in dithionite was observed at concentrations up to 21 mM with no indication of saturation by this substrate. This behavior was monitored by optical, amperometric, and manometric kinetic techniques, and the results were mathematically fit to establish the half-order reaction in dithionite. Under conditions where the MgATP and dithionite concentrations remain unchanged, Av2 (the Fe protein component) interacts with Av1 (the MoFe protein component according to the rate law, suggesting a rapid 1:1 Av2-Av1 interaction: [formula: see text]. with [Av2] the free Fe protein concentration, K = 5.9 microM, and Vmax = 2314 nmol of H2 min-1 (mg of Av1)-1. Under dithionite-depleted conditions, Av2 undergoes an Av1-mediated, one-electron oxidation, consistent with its proposed role as a specific, single-electron reductant for Av1. During steady-state turnover as a function of Av2/Av1 ratio, optical spectroscopy demonstrated the presence of 25-30% oxidized Av2 as an enzyme intermediate. Computer-averaged EPR spectra showed that Av1 was > 95% EPR-silent and Av2 was up to 30% oxidized (Av2ox), consistent with the optical measurements. These optical and EPR results show that up to six Av2ox per Av1 can accumulate in the presence of dithionite during catalysis, suggesting that the conversion of Av2ox back into Av2red is a relatively slow process.