Spectroscopic studies of molybdenum and tungsten enzymes

Advancing Our Understanding of Pyranopterin-Dithiolene Contributions to Moco Enzyme Catalysis

The pyranopterin dithiolene ligand is remarkable in terms of its geometric and electronic structure and is uniquely found in mononuclear molybdenum and tungsten enzymes. The pyranopterin dithiolene is found coordinated to the metal ion, deeply buried within the protein, and non-covalently attached to the protein via an extensive hydrogen bonding network that is enzyme-specific. However, the function of pyranopterin dithiolene in enzymatic catalysis has been difficult to determine. This focused account aims to provide an overview of what has been learned from the study of pyranopterin dithiolene model complexes of molybdenum and how these results relate to the enzyme systems. This work begins with a summary of what is known about the pyranopterin dithiolene ligand in the enzymes. We then introduce the development of inorganic small molecule complexes that model aspects of a coordinated pyranopterin dithiolene and discuss the results of detailed physical studies of the models by electronic absorption, resonance Raman, X-ray absorption and NMR spectroscopies, cyclic voltammetry, X-ray crystallography, and chemical reactivity.

A bacterial tungsten-containing aldehyde oxidoreductase forms an enzymatic decorated protein nanowire

Aldehyde oxidoreductases (AORs) are tungsten enzymes catalyzing the oxidation of many different aldehydes to the corresponding carboxylic acids. In contrast to other known AORs, the enzyme from the denitrifying betaproteobacterium Aromatoleum aromaticum (AORAa) consists of three different subunits (AorABC) and uses nicotinamide adenine dinucleotide (NAD) as an electron acceptor. Here, we reveal that the enzyme forms filaments of repeating AorAB protomers that are capped by a single NAD-binding AorC subunit, based on solving its structure via cryo-electron microscopy. The polyferredoxin-like subunit AorA oligomerizes to an electron-conducting nanowire that is decorated with enzymatically active and W-cofactor (W-co) containing AorB subunits. Our structure further reveals the binding mode of the native substrate benzoate in the AorB active site. This, together with quantum mechanics:molecular mechanics (QM:MM)-based modeling for the coordination of the W-co, enables formulation of a hypothetical catalytic mechanism that paves the way to further engineering for applications in synthetic biology and biotechnology.

Nano-WSe2 Is Absorbable and Transformable by Rice Plants

As typical transition metal dichalcogenides (TMDC), tungsten selenide (WSe₂) nanosheets (nano-WSe₂) are widely used in various fields due to their layered structures and highly tunable electronic and magnetic properties, which results in the unwanted release of tungsten (W) and selenium (Se) into the environment. However, the environmental effects of nano-WSe₂ in plants are still unclear. Herein, we evaluated the impacts and fate of nano-WSe₂ and micro-WSe₂ in rice plants (Oryza sativa L.). It was found that both nano-WSe₂ and micro-WSe₂ did not affect the germination of rice seeds up to 5000 mg/L but nano-WSe₂ affected the growth of rice seedlings with shortened root lengths. The uptake and transportation of WSe₂ was found to be size-dependent. Moreover, W in WSe₂ was oxidized to tungstate while Se was transformed to selenocysteine, selenomethionine, Se^IV and Se^VI in the roots of rice when exposed to nano-WSe₂, suggesting the transformation of nano-WSe₂ in rice plants. The exposure to nano-WSe₂ brought lipid peroxidative damage to rice seedlings. However, Se in nano-WSe₂ did not contribute to the synthesis of glutathione peroxidase (GSH-Px) since the latter did not change when exposed to nano-WSe₂. This is the first report on the impacts and fate of nano-WSe₂ in rice plants, which has raised environmental safety concerns about the wide application of TMDCs, such as WSe₂ nanosheets.

Hg(II) Binding to Thymine Bases in DNA

The compounds of mercury can be highly toxic and can interfere with a range of biological processes, although many aspects of the mechanism of toxicity are still obscure or unknown. One especially intriguing property of Hg(II) is its ability to bind DNA directly, making interstrand cross-links between thymine nucleobases in AT-rich sequences. We have used a combination of small molecule X-ray diffraction, X-ray spectroscopies, and computational chemistry to study the interactions of Hg(II) with thymine. We find that the energetically preferred mode of thymine binding in DNA is to the N3 and predict only minor distortions of the DNA structure on binding one Hg(II) to two cross-adjacent thymine nucleotides. The preferred geometry is predicted to be twisted away from coplanar through a torsion angle of between 32 and 43°. Using 1-methylthymine as a model, the bis-thymine coordination of Hg(II) is found to give a highly characteristic X-ray spectroscopic signature that is quite distinct from other previously described biological modes of binding of Hg(II). This work enlarges and deepens our view of significant biological targets of Hg(II) and demonstrates tools that can provide a characteristic signature for the binding of Hg(II) to DNA in more complex matrices including intact cells and tissues, laying the foundation for future studies of mechanisms of mercury toxicity.

Examination of Protonation-Induced Dinitrogen Splitting by in Situ EXAFS Spectroscopy

The splitting of dinitrogen into nitride complexes emerged as a key reaction for nitrogen fixation strategies at ambient conditions. However, the impact of auxiliary ligands or accessible spin states on the thermodynamics and kinetics of N-N cleavage is yet to be examined in detail. We recently reported N-N bond splitting of a {Mo(μ²:η¹:η¹-N₂)Mo}-complex upon protonation of the diphosphinoamide auxiliary ligands. The reactivity was associated with a low-spin to high-spin transition that was induced by the protonation reaction in the coordination periphery, mainly based on computational results. Here, this proposal is evaluated by an XAS study of a series of linearly N₂ bridged Mo pincer complexes. Structural characterization of the transient protonation product by EXAFS spectroscopy confirms the proposed spin transition prior to N-N bond cleavage.

Electrochemical Separation of Molybdenum and Tungsten Using Aqueous-Organic Electrolytes

Molybdenum is one of the valuable metals for the industry; its special properties make it extremely urgent to study the process of separation of molybdenum from other impurities. The article considers the optimization of electrochemical separation of molybdenum from Mo-W system. The electrochemical dissolution of molybdenum and tungsten in solutions of LiCl and NH4NO3 in dimethylsulfoxide was studied using polarization curves and calculation of the efficiency of anodic dissolution of molybdenum in the presence of tungsten. The electrolyte with a composition of 0.5 M LiCl; 5.2 M dimethylsulfoxide; 32.2 M water was selected as an effective solution for the electrochemical separation of molybdenum in the potential range of 1.0‒2.2 V. Results obtained in this study can be used for the development of selective separation method in the molybdenum production.

Feasibility of Laboratory-Based EXAFS Spectroscopy with Cryogenic Detectors

Extended X-ray Absorption Fine Structure (EXAFS) spectroscopy is a powerful technique that gives element-specific information about the structure of molecules. The development of a laboratory EXAFS spectrometer capable of measuring transmission spectra would be a significant advance as the technique is currently only available at synchrotron radiation lightsources. Here, we explore the potential of cryogenic detectors as the energy resolving component of a laboratory transmission EXAFS instrument. We examine the energy resolution, count-rate, and detector stability needed for good EXAFS spectra and compare these to the properties of cryogenic detectors and conventional X-ray optics. We find that superconducting tunnel junction (STJ) detectors are well-suited for this application.

X-ray absorption spectroscopy of organic sulfoxides

Organic sulfoxides, a group of compounds containing the sulfinyl S Created by potrace 1.16, written by Peter Selinger 2001-2019 ]]> O group, are widespread in nature, important in health and disease, and used in a variety of applications in the pharmaceutical industry. We have examined the sulfur K-edge X-ray absorption near-edge spectra of a range of different sulfoxides and find that their spectra are remarkably similar. Spectra show an intense absorption peak that is comprised of two transitions; a S 1s → (S–O)σ* and a S 1s → [(S–O)π* + (S–C)σ*] transition. In most cases these are sufficiently close in energy that they are not properly resolved; however for dimethylsulfoxide the separation between these transitions increases in aqueous solution due to hydrogen bonding to the sulfinyl oxygen. We also examined tetrahydrothiophene sulfoxide using both the sulfur and oxygen K-edge. This compound has a mild degree of ring strain at the sulfur atom, which changes the energies of the two transitions so that the S 1s → [(S–O)π* + (S–C)σ*] is below the S 1s → (S–O)σ*. A comparison of the oxygen K-edge X-ray absorption near-edge spectra of tetrahydrothiophene sulfoxide with that of an unhindered sulfoxide shows little change, indicating that the electronic environment of oxygen is very similar.

This study develops an understanding of the X-ray absorption near-edge spectra of organic sulfoxides using the sulfur and oxygen K-edges.

Structural evidence for a reaction intermediate mimic in the active site of a sulfite dehydrogenase

We provide structural and spectroscopic evidence for a molybdenum–phosphate adduct mimicking a proposed reaction intermediate in the active site of a prokaryotic sulfite oxidizing enzyme.

Natural Compounds as Beneficial Antioxidant Agents in Neurodegenerative Disorders: A Focus on Alzheimer's Disease

The positive role of nutrition in chronic neurodegenerative diseases (NDs) suggests that dietary interventions represent helpful tools for preventing NDs. In particular, diets enriched with natural compounds have become an increasingly attractive, non-invasive, and inexpensive option to support a healthy brain and to potentially treat NDs. Bioactive compounds found in vegetables or microalgae possess special properties able to counteract oxidative stress, which is involved as a triggering factor in neurodegeneration. Here, we briefly review the relevant experimental data on curcuminoids, silymarin, chlorogenic acid, and compounds derived from the microalga Aphanizomenon flos aquae (AFA) which have been demonstrated to possess encouraging beneficial effects on neurodegeneration, in particular on Alzheimer's disease models.

Modeling Pyran Formation in the Molybdenum Cofactor: Protonation of Quinoxalyl-Dithiolene Promoting Pyran Cyclization

Mononuclear Mo and W enzymes require a unique ligand known as molybdopterin (MPT). This ligand binds the metal through a dithiolene chelate, and the dithiolene bridges a reduced pyranopterin group. Pyran scission and formation have been proposed as a reaction of the MPT ligand that may occur within the enzymes to adjust reactivity at the Mo atom. We address this issue by investigating oxo-Mo(IV) model complexes containing dithiolenes substituted by pterin or quinoxaline and a hydroxyalkyl poised to form a pyran ring. While the pterin-dithiolene model complex exhibits a low energy, reversible pyran cyclization, here we report that pyran cyclization does not spontaneously occur in the quinoxalyl-dithiolene model. However, protonating the quinoxalyl-dithiolene model induces pyran cyclization forming an unstable, pyrano-quinoxalyl-dithiolene complex which subsequently dehydrates and rearranges to a pyrrolo-quinoxlyl-dithiolene complex that was previously characterized. The protonated pyrano-quinoxalyl-dithiolene complex was characterized by absorption spectroscopy and cyclic voltammetry, and these results suggest pyran cyclization leads to a significant change in the Mo electronic structure exhibited as a strong intraligand charge transfer (ILCT) transition and 370 mV positive shift of the Mo(V/IV) reduction potential. The influence of protonation on quinoxaline reactivity supports the hypothesis that the local protein environment in the second coordination sphere of molybdenum cofactor (Moco) could control pyran cyclization. The results also demonstrate that the remarkable chemical reactivity of the pterin-dithiolene ligand is subtly distinct and not reproduced by the simpler quinoxaline analog that is often used to replace pterin in synthetic Moco models.

Effects of the Aphanizomenon flos-aquae Extract (Klamin®) on a Neurodegeneration Cellular Model

Cyanobacteria have been recognized as a source of bioactive molecules to be employed in nutraceuticals, pharmaceuticals, and functional foods. An extract of Aphanizomenon flos-aquae (AFA), commercialized as Klamin®, was subjected to chemical analysis to determine its compounds. The AFA extract Klamin® resulted to be nontoxic, also at high doses, when administered onto LAN5 neuronal cells. Its scavenging properties against ROS generation were evaluated by using DCFH-DA assay, and its mitochondrial protective role was determined by JC-1 and MitoSOX assays. Klamin® exerts a protective role against beta amyloid- (Aβ-) induced toxicity and against oxidative stress. Anti-inflammatory properties were demonstrated by NFβB nuclear localization and activation of IL-6 and IL-1β inflammatory cytokines through ELISA. Finally, by using thioflavin T (ThT) and fluorimetric measures, we found that Klamin® interferes with Aβ aggregation kinetics, supporting the formation of smaller and nontoxic structures compared to toxic Aβ aggregates alone. Altogether, these data indicate that the AFA extract may play a protective role against mechanisms leading to neurodegeneration.

X-ray spectroscopy and imaging of selenium in living systems

BACKGROUND

Selenium is an essential element with a rich and varied chemistry in living organisms. It plays a variety of important roles ranging from being essential in enzymes that are critical for redox homeostasis to acting as a deterrent for herbivory in hyperaccumulating plants. Despite its importance there are many open questions, especially related to its chemistry in situ within living organisms.

SCOPE OF REVIEW

This review discusses X-ray spectroscopy and imaging of selenium in biological samples, with an emphasis on the methods, and in particular the techniques of X-ray absorption spectroscopy (XAS) and X-ray fluorescence imaging (XFI). We discuss the experimental methods and capabilities of XAS and XFI, and review their advantages and their limitations. A perspective on future possibilities and next-generation of experiments is also provided.

MAJOR CONCLUSIONS

XAS and XFI provide powerful probes of selenium chemistry, together with unique in situ capabilities. The opportunities and capabilities of the next generation of advanced X-ray spectroscopy experiments are particularly exciting.

GENERAL SIGNIFICANCE

XAS and XFI provide versatile tools that are generally applicable to any element with a convenient X-ray absorption edge, suitable for investigating complex systems essentially without pre-treatment.

Trace metal metabolism in plants

Many trace metals are essential micronutrients, but also potent toxins. Due to natural and anthropogenic causes, vastly different trace metal concentrations occur in various habitats, ranging from deficient to toxic levels. Therefore, one focus of plant research is on the response to trace metals in terms of uptake, transport, sequestration, speciation, physiological use, deficiency, toxicity, and detoxification. In this review, we cover most of these aspects for the essential micronutrients copper, iron, manganese, molybdenum, nickel, and zinc to provide a broader overview than found in other recent reviews, to cross-link aspects of knowledge in this very active research field that are often seen in a separated way. For example, individual processes of metal usage, deficiency, or toxicity often were not mechanistically interconnected. Therefore, this review also aims to stimulate the communication of researchers following different approaches, such as gene expression analysis, biochemistry, or biophysics of metalloproteins. Furthermore, we highlight recent insights, emphasizing data obtained under physiologically and environmentally relevant conditions.

The active site structure and catalytic mechanism of arsenite oxidase

Arsenite oxidase is thought to be an ancient enzyme, originating before the divergence of the Archaea and the Bacteria. We have investigated the nature of the molybdenum active site of the arsenite oxidase from the Alphaproteobacterium Rhizobium sp. str. NT-26 using a combination of X-ray absorption spectroscopy and computational chemistry. Our analysis indicates an oxidized Mo(VI) active site with a structure that is far from equilibrium. We propose that this is an entatic state imposed by the protein on the active site through relative orientation of the two molybdopterin cofactors, in a variant of the Rây-Dutt twist of classical coordination chemistry, which we call the pterin twist hypothesis. We discuss the implications of this hypothesis for other putatively ancient molybdopterin-based enzymes.

Synthesis, characterization and oxygen atom transfer reactivity of a pair of Mo(iv)O- and Mo(vi)O2-enedithiolate complexes – a look at both ends of the catalytic transformation

A novel pair of mono-oxo and di-oxo bis-dithiolene molybdenum complexes were synthesized, characterized and catalytically investigated as models for a molybdenum dependent oxidoreductase.

Pyranopterin Coordination Controls Molybdenum Electrochemistry in Escherichia coli Nitrate Reductase

We test the hypothesis that pyranopterin (PPT) coordination plays a critical role in defining molybdenum active site redox chemistry and reactivity in the mononuclear molybdoenzymes. The molybdenum atom of Escherichia coli nitrate reductase A (NarGHI) is coordinated by two PPT-dithiolene chelates that are defined as proximal and distal based on their proximity to a [4Fe-4S] cluster known as FS0. We examined variants of two sets of residues involved in PPT coordination: (i) those interacting directly or indirectly with the pyran oxygen of the bicyclic distal PPT (NarG-Ser(719), NarG-His(1163), and NarG-His(1184)); and (ii) those involved in bridging the two PPTs and stabilizing the oxidation state of the proximal PPT (NarG-His(1092) and NarG-His(1098)). A S719A variant has essentially no effect on the overall Mo(VI/IV) reduction potential, whereas the H1163A and H1184A variants elicit large effects (ΔEm values of -88 and -36 mV, respectively). Ala variants of His(1092) and His(1098) also elicit large ΔEm values of -143 and -101 mV, respectively. An Arg variant of His(1092) elicits a small ΔEm of +18 mV on the Mo(VI/IV) reduction potential. There is a linear correlation between the molybdenum Em value and both enzyme activity and the ability to support anaerobic respiratory growth on nitrate. These data support a non-innocent role for the PPT moieties in controlling active site metal redox chemistry and catalysis.

Reductive activation of E. coli respiratory nitrate reductase

Over the past decades, a number of authors have reported the presence of inactive species in as-prepared samples of members of the Mo/W-bisPGD enzyme family. This greatly complicated the spectroscopic studies of these enzymes, since it is impossible to discriminate between active and inactive species on the basis of the spectroscopic signatures alone. Escherichia coli nitrate reductase A (NarGHI) is a member of the Mo/W-bisPGD family that allows anaerobic respiration using nitrate as terminal electron acceptor. Here, using protein film voltammetry on NarGH films, we show that the enzyme is purified in a functionally heterogeneous form that contains between 20 and 40% of inactive species that activate the first time they are reduced. This activation proceeds in two steps: a non-redox reversible reaction followed by an irreversible reduction. By carefully correlating electrochemical and EPR spectroscopic data, we show that neither the two major Mo(V) signals nor those of the two FeS clusters that are the closest to the Mo center are associated with the two inactive species. We also conclusively exclude the possibility that the major "low-pH" and "high-pH" Mo(V) EPR signatures correspond to species in acid-base equilibrium.

Behavior of anionic molybdenum(IV, VI) and tungsten(IV, VI) complexes containing bulky hydrophobic dithiolate ligands and intramolecular NH···S hydrogen bonds in nonpolar solvents

Molybdenum(IV, VI) and tungsten(IV, VI) complexes, (Et4N)2[M(IV)O{1,2-S2-3,6-(RCONH)2C6H2}2] and (Et4N)2[M(VI)O2{1,2-S2-3,6-(RCONH)2C6H2}2] (M = Mo, W; R = (4-(t)BuC6H4)3C), with bulky hydrophobic dithiolate ligands containing NH···S hydrogen bonds were synthesized. These complexes are soluble in nonpolar solvents like toluene, which allows the detection of unsymmetrical coordination structures and elusive intermolecular interactions in solution. The (1)H NMR spectra of the complexes in toluene-d8 revealed an unsymmetrical coordination structure, and proximity of the counterions to the anion moiety was suggested at low temperatures. The oxygen-atom-transfer reaction between the molybdenum(IV) complex and Me3NO in toluene was considerably accelerated in nonpolar solvents, and this increase was attributed to the favorable access of the substrate to the active center in the hydrophobic environment.

Structural and functional models in molybdenum and tungsten bioinorganic chemistry: description of selected model complexes, present scenario and possible future scopes

A brief description about some selected model complexes in molybdenum and tungsten bioinorganic chemistry is provided. The synthetic strategies involved and their limitations are discussed. Current status of molybdenum and tungsten bioinorganic modeling chemistry is presented briefly and synthetic problems associated therein are analyzed. Possible future directions which may expand the scope of modeling chemistry are suggested.

Incorporation of molybdenum in rubredoxin: models for mononuclear molybdenum enzymes

Molybdenum is found in the active site of enzymes usually coordinated by one or two pyranopterin molecules. Here, we mimic an enzyme with a mononuclear molybdenum-bis pyranopterin center by incorporating molybdenum in rubredoxin. In the molybdenum-substituted rubredoxin, the metal ion is coordinated by four sulfurs from conserved cysteine residues of the apo-rubredoxin and two other exogenous ligands, oxygen and thiol, forming a Mo((VI))-(S-Cys)4(O)(X) complex, where X represents -OH or -SR. The rubredoxin molybdenum center is stabilized in a Mo(VI) oxidation state, but can be reduced to Mo(IV) via Mo(V) by dithionite, being a suitable model for the spectroscopic properties of resting and reduced forms of molybdenum-bis pyranopterin-containing enzymes. Preliminary experiments indicate that the molybdenum site built in rubredoxin can promote oxo transfer reactions, as exemplified with the oxidation of arsenite to arsenate.

Shifting the metallocentric molybdoenzyme paradigm: the importance of pyranopterin coordination

In this review, we test the hypothesis that pyranopterin coordination plays a critical role in defining substrate reactivities in the four families of mononuclear molybdenum and tungsten enzymes (Mo/W-enzymes). Enzyme families containing a single pyranopterin dithiolene chelate have been demonstrated to have reactivity towards two (sulfite oxidase, SUOX-fold) and five (xanthine dehydrogenase, XDH-fold) types of substrate, whereas the major family of enzymes containing a bis-pyranopterin dithiolene chelate (dimethylsulfoxide reductase, DMSOR-fold) is reactive towards eight types of substrate. A second bis-pyranopterin enzyme (aldehyde oxidoreductase, AOR-fold) family catalyzes a single type of reaction. The diversity of reactions catalyzed by each family correlates with active site variability, and also with the number of pyranopterins and their coordination by the protein. In the case of the AOR-fold enzymes, inflexibility of pyranopterin coordination correlates with their limited substrate specificity (oxidation of aldehydes). In examples of the SUOX-fold and DMSOR-fold enzymes, we observe three types of histidine-containing charge-transfer relays that can: (1) connect the piperazine ring of the pyranopterin to the substrate-binding site (SUOX-fold enzymes); (2) provide inter-pyranopterin communication (DMSOR-fold enzymes); and (3) connect a pyran ring oxygen to deeply buried water molecules (the DMSOR-fold NarGHI-type nitrate reductases). Finally, sequence data mining reveals a number of bacterial species whose predicted proteomes contain large numbers (up to 64) of Mo/W-enzymes, with the DMSOR-fold enzymes being dominant. These analyses also reveal an inverse correlation between Mo/W-enzyme content and pathogenicity.

Molybdenum site structure of MOSC family proteins

Mo K-edge X-ray absorption spectroscopy has been used to probe as-isolated structures of the MOSC family proteins pmARC-1 and HMCS-CT. The Mo K-edge near-edge spectrum of HMCS-CT is shifted ~2.5 eV to lower energy compared to the pmARC-1 spectrum, which indicates that as-isolated HMCS-CT is in a more reduced state than pmARC-1. Extended X-ray absorption fine structure analysis indicates significant structural differences between pmARC-1 and HMCS-CT, with the former being a dioxo site and the latter possessing only a single terminal oxo ligand. The number of terminal oxo donors is consistent with pmARC-1 being in the Mo(VI) oxidation state and HMCS-CT in the Mo(IV) state. These structures are in accord with oxygen-atom-transfer reactivity for pmARC-1 and persulfide bond cleavage chemistry for HMCS-CT.

Nitrate and periplasmic nitrate reductases

The nitrate anion is a simple, abundant and relatively stable species, yet plays a significant role in global cycling of nitrogen, global climate change, and human health. Although it has been known for quite some time that nitrate is an important species environmentally, recent studies have identified potential medical applications. In this respect the nitrate anion remains an enigmatic species that promises to offer exciting science in years to come. Many bacteria readily reduce nitrate to nitrite via nitrate reductases. Classified into three distinct types--periplasmic nitrate reductase (Nap), respiratory nitrate reductase (Nar) and assimilatory nitrate reductase (Nas), they are defined by their cellular location, operon organization and active site structure. Of these, Nap proteins are the focus of this review. Despite similarities in the catalytic and spectroscopic properties Nap from different Proteobacteria are phylogenetically distinct. This review has two major sections: in the first section, nitrate in the nitrogen cycle and human health, taxonomy of nitrate reductases, assimilatory and dissimilatory nitrate reduction, cellular locations of nitrate reductases, structural and redox chemistry are discussed. The second section focuses on the features of periplasmic nitrate reductase where the catalytic subunit of the Nap and its kinetic properties, auxiliary Nap proteins, operon structure and phylogenetic relationships are discussed.

Infrared multiple photon dissociation spectroscopy of a gas-phase oxo-molybdenum complex with 1,2-dithiolene ligands

Electrospray ionization (ESI) in the negative ion mode was used to create anionic, gas-phase oxo-molybdenum complexes with dithiolene ligands. By varying ESI and ion transfer conditions, both doubly and singly charged forms of the complex, with identical formulas, could be observed. Collision-induced dissociation (CID) of the dianion generated exclusively the monoanion, while fragmentation of the monoanion involved decomposition of the dithiolene ligands. The intrinsic structure of the monoanion and the dianion were determined by using wavelength-selective infrared multiple-photon dissociation (IRMPD) spectroscopy and density functional theory calculations. The IRMPD spectrum for the dianion exhibits absorptions that can be assigned to (ligand) C=C, C–S, C—C≡N, and Mo=O stretches. Comparison of the IRMPD spectrum to spectra predicted for various possible conformations allows assignment of a pseudo square pyramidal structure with C_2v symmetry, equatorial coordination of MoO²⁺ by the S atoms of the dithiolene ligands, and a singlet spin state. A single absorption was observed for the oxidized complex. When the same scaling factor employed for the dianion is used for the oxidized version, theoretical spectra suggest that the absorption is the Mo=O stretch for a distorted square pyramidal structure and doublet spin state. A predicted change in conformation upon oxidation of the dianion is consistent with a proposed bonding scheme for the bent-metallocene dithiolene compounds [Lauher, J. W.; Hoffmann, R. J. Am. Chem. Soc.1976, 98, 1729−1742], where a large folding of the dithiolene moiety along the S···S vector is dependent on the occupancy of the in-plane metal d-orbital.

High-resolution molybdenum K-edge X-ray absorption spectroscopy analyzed with time-dependent density functional theory

X-ray absorption spectroscopy (XAS) is a widely used experimental technique capable of selectively probing the local structure around an absorbing atomic species in molecules and materials. When applied to heavy elements, however, the quantitative interpretation can be challenging due to the intrinsic spectral broadening arising from the decrease in the core-hole lifetime. In this work we have used high-energy resolution fluorescence detected XAS (HERFD-XAS) to investigate a series of molybdenum complexes. The sharper spectral features obtained by HERFD-XAS measurements enable a clear assignment of the features present in the pre-edge region. Time-dependent density functional theory (TDDFT) has been previously shown to predict K-pre-edge XAS spectra of first row transition metal compounds with a reasonable degree of accuracy. Here we extend this approach to molybdenum K-edge HERFD-XAS and present the necessary calibration. Modern pure and hybrid functionals are utilized and relativistic effects are accounted for using either the Zeroth Order Regular Approximation (ZORA) or the second order Douglas-Kroll-Hess (DKH2) scalar relativistic approximations. We have found that both the predicted energies and intensities are in excellent agreement with experiment, independent of the functional used. The model chosen to account for relativistic effects also has little impact on the calculated spectra. This study provides an important calibration set for future applications of molybdenum HERFD-XAS to complex catalytic systems.

Identification of a spin-coupled Mo(iii) in the nitrogenase iron–molybdenum cofactor

The molybdenum atom in FeMoco is imperative to the high activity of the enzyme and has been proposed to be Mo(iv). We demonstrate that only Mo(iii) fits Mo HERFD XAS data, the first example of Mo(iii) in biology. Theoretical calculations further reveal an unusual spin-coupled Mo(iii).

New insights into metal interactions with the prion protein: EXAFS analysis and structure calculations of copper binding to a single octarepeat from the prion protein

Copper coordination to the prion protein (PrP) has garnered considerable interest for almost 20 years, due in part to the possibility that this interaction may be part of the normal function of PrP. The most characterized form of copper binding to PrP has been Cu(2+) interaction with the conserved tandem repeats in the N-terminal domain of PrP, termed the octarepeats, with many studies focusing on single and multiple repeats of PHGGGWGQ. Extended X-ray absorption fine structure (EXAFS) spectroscopy has been used in several previous instances to characterize the solution structure of Cu(2+) binding into the peptide backbone in the HGGG portion of the octarepeats. All previous EXAFS studies, however, have benefitted from crystallographic structure information for [Cu(II) (Ac-HGGGW-NH2)(-2H)] but have not conclusively demonstrated that the complex EXAFS spectrum represents the same coordination environment for Cu(2+) bound to the peptide backbone. Density functional structure calculations as well as full multiple scattering EXAFS curve fitting analysis are brought to bear on the predominant coordination mode for Cu(2+) with the Ac-PHGGGWGQ-NH2 peptide at physiological pH, under high Cu(2+) occupancy conditions. In addition to the structure calculations, which provide a thermodynamic link to structural information, methods are also presented for extensive deconvolution of the EXAFS spectrum. We demonstrate how the EXAFS data can be analyzed to extract the maximum structural information and arrive at a structural model that is significantly improved over previous EXAFS characterizations. The EXAFS spectrum for the chemically reduced form of copper binding to the Ac-PHGGGWGQ-NH2 peptide is presented, which is best modeled as a linear two-coordinate species with a single His imidazole ligand and a water molecule. The extent of in situ photoreduction of the copper center during standard data collection is also presented, and EXAFS curve fitting of the photoreduced species reveals an intermediate structure that is similar to the Cu(2+) form with reduced coordination number.

Detrimental effect of the 6 His C-terminal tag on YedY enzymatic activity and influence of the TAT signal sequence on YedY synthesis

Background

YedY, a molybdoenzyme belonging to the sulfite oxidase family, is found in most Gram-negative bacteria. It contains a twin-arginine signal sequence that is cleaved after its translocation into the periplasm. Despite a weak reductase activity with substrates such as dimethyl sulfoxide or trimethylamine N-oxide, its natural substrate and its role in the cell remain unknown. Although sequence conservation of the YedY family displays a strictly conserved hydrophobic C-terminal residue, all known studies on Escherichia coli YedY have been performed with an enzyme containing a 6 histidine-tag at the C-terminus which could hamper enzyme activity.

Results

In this study, we demonstrate that the tag fused to the C-terminus of Rhodobacter sphaeroides YedY is detrimental to the enzyme’s reductase activity and results in an eight-fold decrease in catalytic efficiency. Nonetheless this C-terminal tag does not influence the properties of the molybdenum active site, as assayed by EPR spectroscopy. When a cleavable His-tag was fused to the N-terminus of the mature enzyme in the absence of the signal sequence, YedY was expressed and folded with its cofactor. However, when the signal sequence was added upstream of the N-ter tag, the amount of enzyme produced was approximately ten-fold higher.

Conclusion

Our study thus underscores the risk of using a C-terminus tagged enzyme while studying YedY, and presents an alternative strategy to express signal sequence-containing enzymes with an N-terminal tag. It brings new insights into molybdoenzyme maturation in R. sphaeroides showing that for some enzymes, maturation can occur in the absence of the signal sequence but that its presence is required for high expression of active enzyme.

The electronic nature of terminal oxo ligands in transition-metal complexes: ambiphilic reactivity of oxorhenium species

The synthesis of the Lewis acid-base adducts of B(C6F5)3 and BF3 with [DAAmRe(O)(X)] DAAm = N,N-bis(2-arylaminoethyl)methylamine; aryl = C6F5 (X = Me, 1, COCH3, 2, Cl, 3) as well as their diamidopyridine (DAP) (DAP=(2,6-bis((mesitylamino)methyl)pyridine) analogues, [DAPRe(O)(X)] (X = Me, 4, Cl, 5, I, 6, and COCH3,7), are described. In these complexes the terminal oxo ligands act as nucleophiles. In addition we also show that stoichiometric reactions between 3 and triarylphosphine (PAr3) result in the formation of triarylphosphine oxide (OPAr3). The electronic dependence of this reaction was studied by comparing the rates of oxygen atom transfer for various para-substituted triaryl phosphines in the presence of CO. From these experiments a reaction constant ρ = -0.29 was obtained from the Hammett plot. This suggests that the oxygen atom transfer reaction is consistent with nucleophilic attack of phosphorus on an electrophilic metal oxo. To the best of our knowledge, these are the first examples of mono-oxo d(2) metal complexes in which the oxo ligand exhibits ambiphilic reactivity.

Oxo-Mo(IV)(dithiolene)thiolato complexes: analogue of reduced sulfite oxidase

A series of [Mo(IV)O(mnt)(SR)(N-N)](-) (mnt = maleonitriledithiolate; R = Ph, nap, p-Cl-Ph, p-CO2H-Ph, and p-NO2-Ph; N-N = 2,2'-bipyridine (bipy) and 1,10-phenanthroline (phen)) complexes analogous to the reduced active site of enzymes of the sulfite oxidase family has been synthesized and their participation in electron transfer reactions studied. Equatorial thiolate and dithiolene ligations have been used to closely simulate the three sulfur coordinations present in the native molybdenum active site. These synthetic analogues have been shown to participate in electron transfer via a pentavalent EPR-active Mo(V) intermediate with minimal structural change as observed electrochemically by reversible oxidative responses. The role of the redox-active dithiolene ligand as an electron transfer gate between external oxidants and the molybdenum center could be envisaged in one of the analogue systems where the initial transient EPR signal with <g> = 2.008 is replaced by the appearance of a typical Mo(V)-centered EPR (<g> = 1.976) signal. The appearance of such a ligand-based transient radical at the initial stage has been supported by the ligand-centered frontier orbital from DFT calculation. A stepwise rationale has been provided by computational study to show that the coupled effects of the diimine bite angle and the thiolato dihedral angle determine the metal- or ligand-based frontier orbital occupancy. DFT calculation has further supported the similarity between the reduced, semireduced, and oxidized resting state of the molybdenum center in Moco of SO with the synthesized complexes and their corresponding one-electron and fully oxidized species.

The prokaryotic Mo/W-bisPGD enzymes family: a catalytic workhorse in bioenergetic

Over the past two decades, prominent importance of molybdenum-containing enzymes in prokaryotes has been put forward by studies originating from different fields. Proteomic or bioinformatic studies underpinned that the list of molybdenum-containing enzymes is far from being complete with to date, more than fifty different enzymes involved in the biogeochemical nitrogen, carbon and sulfur cycles. In particular, the vast majority of prokaryotic molybdenum-containing enzymes belong to the so-called dimethylsulfoxide reductase family. Despite its extraordinary diversity, this family is characterized by the presence of a Mo/W-bis(pyranopterin guanosine dinucleotide) cofactor at the active site. This review highlights what has been learned about the properties of the catalytic site, the modular variation of the structural organization of these enzymes, and their interplay with the isoprenoid quinones. In the last part, this review provides an integrated view of how these enzymes contribute to the bioenergetics of prokaryotes. This article is part of a Special Issue entitled: Metals in Bioenergetics and Biomimetics Systems.

X-ray-induced photo-chemistry and X-ray absorption spectroscopy of biological samples

As synchrotron light sources and optics deliver greater photon flux on samples, X-ray-induced photo-chemistry is increasingly encountered in X-ray absorption spectroscopy (XAS) experiments. The resulting problems are particularly pronounced for biological XAS experiments. This is because biological samples are very often quite dilute and therefore require signal averaging to achieve adequate signal-to-noise ratios, with correspondingly greater exposures to the X-ray beam. This paper reviews the origins of photo-reduction and photo-oxidation, the impact that they can have on active site structure, and the methods that can be used to provide relief from X-ray-induced photo-chemical artifacts.

X-ray absorption spectroscopy at a protein crystallography facility: the Canadian Light Source beamline 08B1-1

It is now possible to perform X-ray absorption spectroscopy (XAS) on metalloprotein crystals at the Canadian Macromolecular Crystallography Facility bend magnet (CMCF-BM) beamline (08B1-1) at the Canadian Light Source. The recent addition of a four-element fluorescence detector allows users to acquire data suitable for X-ray absorption near-edge structure and extended X-ray absorption fine-structure based studies by monitoring fluorescence. CMCF beamline users who wish to supplement their diffraction data with XAS can do so with virtually no additional sample preparation. XAS data collection is integrated with the established Mx Data Collector software package used to collect diffraction data. Mainstream XAS data-processing software packages are available for the users; assistance with data processing and interpretation by staff is also available upon request.