Structural and electron paramagnetic resonance (EPR) studies of mononuclear molybdenum enzymes from sulfate-reducing bacteria

Unveiling novel pathways and key contributors in the nitrogen cycle: Validation of enrichment and taxonomic characterization of oxygenic denitrifying microorganisms in environmental samples

Microorganisms play a crucial role in both the nitrogen cycle and greenhouse gas emissions. A recent discovery has unveiled a new denitrification pathway called oxygenic denitrification, entailing the enzymatic reduction of nitrite to nitric oxide (NO) by a putative nitric oxide dismutase (nod) enzyme. In this study, the presence of the nod gene was detected and subsequently enriched in anaerobic-activated sludge, farmland soil, and paddy soil samples. After 150 days, the enriched samples exhibited significant denitrification, and concomitant oxygen production. The removal efficiency of nitrite ranged from 64.6 % to 79.0 %, while the oxygen production rate was between 15.4 μL/min and 18.6 μL/min when exposed to a sole nitrogen source of 80 mg/L sodium nitrite. Additionally, batch experiments and kinetic analyses revealed the intricate pathways and underlying mechanisms governing the oxygenic denitrification reaction by using CARBOXY-PTIO, 18O-labelled water, and acetylene to unravel the intricacies of the reaction. The quantitative polymerase chain reaction (qPCR) results indicated a significant surge in the abundance of nod genes, escalating from 7.59 to 10.12-fold. Moreover, analysis of 16S ribosomal DNA (rDNA) amplicons revealed Proteobacteria as the dominant phylum and Thauera as the main genus, with the presumed affiliation. In this study, a new nitrogen conversion pathway, oxygenic denitrification, was discovered in environmental samples. This process provides the possibility for the control of nitrous oxide in the treatment of nitrogenous wastewater.

Probing the interactions between amyloidogenic proteins and bio-membranes

Protein misfolding diseases (PMDs) in humans are characterized by the deposition of protein aggregates in tissues, including Alzheimer's disease, Parkinson's disease, type 2 diabetes, and amyotrophic lateral sclerosis. Misfolding and aggregation of amyloidogenic proteins play a central role in the onset and progression of PMDs, and these processes are regulated by multiple factors, especially the interaction between proteins and bio-membranes. Bio-membranes induce conformational changes in amyloidogenic proteins and affect their aggregation; on the other hand, the aggregates of amyloidogenic proteins may cause membrane damage or dysfunction leading to cytotoxicity. In this review, we summarize the factors that affect the binding of amyloidogenic proteins and membranes, the effects of bio-membranes on the aggregation of amyloidogenic proteins, mechanisms of membrane disruption by amyloidogenic aggregates, technical approaches for detecting these interactions, and finally therapeutic strategies targeting membrane damage caused by amyloidogenic proteins.

Formation of Mono Oxo Molybdenum(IV) PNP Pincer Complexes: Interplay between Water and Molecular Oxygen

The synthesis of cationic mono oxo MoIV PNP pincer complexes of the type [Mo(PNPMe-iPr)(O)X]+ (X = I, Br) from [Mo(PNPMe-iPr)(CO)X2] is described. These compounds are coordinatively unsaturated and feature a strong Mo≡O triple bond. The formation of these complexes proceeds via cationic 14e intermediates [Mo(PNPMe-iPr)(CO)X]+ and requires both molecular oxygen and water. ESI MS measurements with 18O labeled water (H2 18O) and molecular oxygen (18O2) indicates that water plays a crucial role in the formation of the Mo≡O bond. A plausible mechanism based on DFT calculations is provided. The X-ray structure of [Mo(PNPMe-iPr)(O)I]SbF6 is presented.

Dry reforming of methane over Co–Mo/Al2O3 catalyst under low microwave power irradiation

In this work, microwave (MW) irradiation was used to activate Co/Al₂O₃, Mo/Al₂O₃, and Co–Mo/Al₂O₃ catalysts for dry reforming of methane (DRM) reactions.

Transition from isolated to interacting copper(ii) pairs in extended lattices evaluated by single crystal EPR spectroscopy

Single crystal EPR experiments in copper-doped dimeric Zn(tda)(phen) allowed determination of Cu(ii) g- and A-matrices and ZFS parameters, which are used to evaluate the interdimeric exchange interaction in pure Cu(tda)(phen).

Isotropic exchange interaction between Mo and the proximal FeS center in the xanthine oxidase family member aldehyde oxidoreductase from Desulfovibrio gigas on native and polyalcohol inhibited samples: an EPR and QM/MM study

Aldehyde oxidoreductase from Desulfovibrio gigas (DgAOR) is a homodimeric molybdenum-containing protein that catalyzes the hydroxylation of aldehydes to carboxylic acids and contains a Mo-pyranopterin active site and two FeS centers called FeS 1 and FeS 2. The electron transfer reaction inside DgAOR is proposed to be performed through a chemical pathway linking Mo and the two FeS clusters involving the pyranopterin ligand. EPR studies performed on reduced as-prepared DgAOR showed that this pathway is able to transmit very weak exchange interactions between Mo(V) and reduced FeS 1. Similar EPR studies but performed on DgAOR samples inhibited with glycerol and ethylene glycol showed that the value of the exchange coupling constant J increases ~2 times upon alcohol inhibition. Structural studies in these DgAOR samples have demonstrated that the Mo-FeS 1 bridging pathway does not show significant differences, confirming that the changes in J observed upon inhibition cannot be ascribed to structural changes associated neither with pyranopterin and FeS 1 nor with changes in the electronic structure of FeS 1, as its EPR properties remain unchanged. Theoretical calculations indicate that the changes in J detected by EPR are related to changes in the electronic structure of Mo(V) determined by the replacement of the OHx labile ligand for an alcohol molecule. Since the relationship between electron transfer rate and isotropic exchange interaction, the present results suggest that the intraenzyme electron transfer process mediated by the pyranopterin moiety is governed by a Mo ligand-based regulatory mechanism.

Aromatic aldehydes at the active site of aldehyde oxidoreductase from Desulfovibrio gigas: reactivity and molecular details of the enzyme-substrate and enzyme-product interaction

Desulfovibrio gigas aldehyde oxidoreductase (DgAOR) is a mononuclear molybdenum-containing enzyme from the xanthine oxidase (XO) family, a group of enzymes capable of catalyzing the oxidative hydroxylation of aldehydes and heterocyclic compounds. The kinetic studies reported in this work showed that DgAOR catalyzes the oxidative hydroxylation of aromatic aldehydes, but not heterocyclic compounds. NMR spectroscopy studies using (13)C-labeled benzaldehyde confirmed that DgAOR catalyzes the conversion of aldehydes to the respective carboxylic acids. Steady-state kinetics in solution showed that high concentrations of the aromatic aldehydes produce substrate inhibition and in the case of 3-phenyl propionaldehyde a suicide substrate behavior. Hydroxyl-substituted aromatic aldehydes present none of these behaviors but the kinetic parameters are largely affected by the position of the OH group. High-resolution crystallographic structures obtained from single crystals of active-DgAOR soaked with benzaldehyde showed that the side chains of Phe425 and Tyr535 are important for the stabilization of the substrate in the active site. On the other hand, the X-ray data of DgAOR soaked with trans-cinnamaldehyde showed a cinnamic acid molecule in the substrate channel. The X-ray data of DgAOR soaked with 3-phenyl propionaldehyde showed clearly how high substrate concentrations inactivate the enzyme by binding covalently at the surface of the enzyme and blocking the substrate channel. The different reactivity of DgAOR versus aldehyde oxidase and XO towards aromatic aldehydes and N-heterocyclic compounds is explained on the basis of the present kinetic and structural data.

Kinetic and structural studies of aldehyde oxidoreductase from Desulfovibrio gigas reveal a dithiolene-based chemistry for enzyme activation and inhibition by H(2)O(2)

Mononuclear Mo-containing enzymes of the xanthine oxidase (XO) family catalyze the oxidative hydroxylation of aldehydes and heterocyclic compounds. The molybdenum active site shows a distorted square-pyramidal geometry in which two ligands, a hydroxyl/water molecule (the catalytic labile site) and a sulfido ligand, have been shown to be essential for catalysis. The XO family member aldehyde oxidoreductase from Desulfovibrio gigas (DgAOR) is an exception as presents in its catalytically competent form an equatorial oxo ligand instead of the sulfido ligand. Despite this structural difference, inactive samples of DgAOR can be activated upon incubation with dithionite plus sulfide, a procedure similar to that used for activation of desulfo-XO. The fact that DgAOR does not need a sulfido ligand for catalysis indicates that the process leading to the activation of inactive DgAOR samples is different to that of desulfo-XO. We now report a combined kinetic and X-ray crystallographic study to unveil the enzyme modification responsible for the inactivation and the chemistry that occurs at the Mo site when DgAOR is activated. In contrast to XO, which is activated by resulfuration of the Mo site, DgAOR activation/inactivation is governed by the oxidation state of the dithiolene moiety of the pyranopterin cofactor, which demonstrates the non-innocent behavior of the pyranopterin in enzyme activity. We also showed that DgAOR incubation with dithionite plus sulfide in the presence of dioxygen produces hydrogen peroxide not associated with the enzyme activation. The peroxide molecule coordinates to molybdenum in a η² fashion inhibiting the enzyme activity.

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.

The molybdenum oxotransferases and related enzymes

A perspective is provided of recent advances in our understanding of molybdenum-containing enzymes other than nitrogenase, a large and diverse group of enzymes that usually (but not always) catalyze oxygen atom transfer to or from a substrate, utilizing a Mo=O group as donor or acceptor. An emphasis is placed on the diversity of protein structure and reaction catalyzed by each of the three major families of these enzymes.

Effects of molybdate and tungstate on expression levels and biochemical characteristics of formate dehydrogenases produced by Desulfovibrio alaskensis NCIMB 13491

Formate dehydrogenases (FDHs) are enzymes that catalyze the formate oxidation to carbon dioxide and that contain either Mo or W in a mononuclear form in the active site. In the present work, the influence of Mo and W salts on the production of FDH by Desulfovibrio alaskensis NCIMB 13491 was studied. Two different FDHs, one containing W (W-FDH) and a second incorporating either Mo or W (Mo/W-FDH), were purified. Both enzymes were isolated from cells grown in a medium supplemented with 1 μM molybdate, whereas only the W-FDH was purified from cells cultured in medium supplemented with 10 μM tungstate. We demonstrated that the genes encoding the Mo/W-FDH are strongly downregulated by W and slightly upregulated by Mo. Metal effects on the expression level of the genes encoding the W-FDH were less significant. Furthermore, the expression levels of the genes encoding proteins involved in molybdate and tungstate transport are downregulated under the experimental conditions evaluated in this work. The molecular and biochemical properties of these enzymes and the selective incorporation of either Mo or W are discussed.

Evidence of disruption of conjugation involving delta bonds in intramolecular electronic coupling

A dimer of dimers containing two quadruply bonded [Mo(2)(DAniF)(3)](+) units (DAniF = N,N'-di(p-anisyl)formamidinate) linked by the S-donor linker, dimethyldithiooxamidate was synthesized, structurally characterized, and electronic communication was probed. The core of [Mo(2)(DAniF)(3)](2)(C(2)S(2)N(2)Me(2)), 1, formed by the Mo(2)NSC(2)SNMo(2) atoms shows two fused but non planar six-membered rings, which differs from that of the beta form of dimethyloxamidate analogue that has a heteronaphthalene-type structure (Cotton, F. A.; Liu, C. Y.; Murillo, C. A.; Villagran, D.; Wang, X. J. Am. Chem. Soc. 2004, 126, 14822). For these two analogous compounds electronic coupling between the two [Mo(2)] units, as determined by electrochemical measurements, diminishes considerably upon replacement of O-donor by S-donor atoms (DeltaE(1/2) = 531 mV and 440 mV, respectively). This suggests that the non planar conformation of the linker in 1 hampers a pathway leading to pi conjugation. Density functional theory (DFT) calculations show that the highest occupied molecular orbitals HOMO-HOMO-1 energy gap of 0.12 eV for 1 is much smaller than that of 0.61 eV for the O-donor analogue, which is consistent with the electrochemical data.

EPR studies of the Mo-enzyme aldehyde oxidoreductase from Desulfovibrio gigas: an application of the Bloch-Wangsness-Redfield theory to a system containing weakly-coupled paramagnetic redox centers with different relaxation rates

Electron transfer proteins and redox enzymes containing paramagnetic redox centers with different relaxation rates are widespread in nature. Despite both the long distances and chemical paths connecting these centers, they can present weak magnetic couplings produced by spin-spin interactions such as dipolar and isotropic exchange. We present here a theoretical model based on the Bloch-Wangsness-Redfield theory to analyze the dependence with temperature of EPR spectra of interacting pairs of spin 1/2 centers having different relaxation rates, as is the case of the molybdenum-containing enzyme aldehyde oxidoreductase from Desulfovibrio gigas. We analyze the changes of the EPR spectra of the slow relaxing center (Mo(V)) induced by the faster relaxing center (FeS center). At high temperatures, when the relaxation time T(1) of the fast relaxing center is very short, the magnetic coupling between centers is averaged to zero. Conversely, at low temperatures when T(1) is longer, no modulation of the coupling between metal centers can be detected.

Free energy landscapes for S-H bonds in Cp*2Mo2S4 complexes

An extensive family of thermochemical data is presented for a series of complexes derived from Cp*Mo(mu-S)(2)(mu-SMe)(mu-SH)MoCp* and Cp*Mo(mu-S)(2)(mu-SH)(2)MoCp*. These data include electrochemical potentials, pK(a) values, homolytic solution bond dissociation free energies (SBDFEs), and hydride donor abilities in acetonitrile. Thermochemical data ranged from +0.6 to -2.0 V vs FeCp(2)(+/o) for electrochemical potentials, 5 to 31 for pK(a) values, 43 to 68 kcal/mol for homolytic SBDFEs, and 44 to 84 kcal/mol for hydride donor abilities. The observed values for these thermodynamic parameters are comparable to those of many transition metal hydrides, which is consistent with the many parallels in the chemistry of these two classes of compounds. The extensive set of thermochemical data is presented in free energy landscapes as a useful approach to visualizing and understanding the relative stabilities of all of the species under varying conditions of pH and H(2) overpressure. In addition to the previously studied homogeneous reactivity and catalysis, Mo(2)S(4) complexes are also models for heterogeneous molybdenum sulfide catalysts, and therefore, the present results demonstrate the dramatic range of S-H bond strengths available in both homogeneous and heterogeneous reaction pathways.

Periplasmic nitrate reductase revisited: a sulfur atom completes the sixth coordination of the catalytic molybdenum

Nitrate reductase from Desulfovibrio desulfuricans ATCC 27774 (DdNapA) is a monomeric protein of 80 kDa harboring a bis(molybdopterin guanine dinucleotide) active site and a [4Fe-4S] cluster. Previous electron paramagnetic resonance (EPR) studies in both catalytic and inhibiting conditions showed that the molybdenum center has high coordination flexibility when reacted with reducing agents, substrates or inhibitors. As-prepared DdNapA samples, as well as those reacted with substrates and inhibitors, were crystallized and the corresponding structures were solved at resolutions ranging from 1.99 to 2.45 A. The good quality of the diffraction data allowed us to perform a detailed structural study of the active site and, on that basis, the sixth molybdenum ligand, originally proposed to be an OH/OH(2) ligand, was assigned as a sulfur atom after refinement and analysis of the B factors of all the structures. This unexpected result was confirmed by a single-wavelength anomalous diffraction experiment below the iron edge (lambda = 1.77 A) of the as-purified enzyme. Furthermore, for six of the seven datasets, the S-S distance between the sulfur ligand and the Sgamma atom of the molybdenum ligand Cys(A140) was substantially shorter than the van der Waals contact distance and varies between 2.2 and 2.85 A, indicating a partial disulfide bond. Preliminary EPR studies under catalytic conditions showed an EPR signal designated as a turnover signal (g values 1.999, 1.990, 1.982) showing hyperfine structure originating from a nucleus of unknown nature. Spectropotentiometric studies show that reduced methyl viologen, the electron donor used in the catalytic reaction, does not interact directly with the redox cofactors. The turnover signal can be obtained only in the presence of the reaction substrates. With use of the optimized conditions determined by spectropotentiometric titration, the turnover signal was developed with (15)N-labeled nitrate and in D(2)O-exchanged DdNapA samples. These studies indicate that this signal is not associated with a Mo(V)-nitrate adduct and that the hyperfine structure originates from two equivalent solvent-exchangeable protons. The new coordination sphere of molybdenum proposed on the basis of our studies led us to revise the currently accepted reaction mechanism for periplasmic nitrate reductases. Proposals for a new mechanism are discussed taking into account a molybdenum and ligand-based redox chemistry, rather than the currently accepted redox chemistry based solely on the molybdenum atom.

Modulating Electronic Coupling Using O- and S-donor Linkers

Structures of compounds having two dimolybdenum units Mo2(DAniF)3+ (DAniF = N,N'-di-p-anisylformamidinate) connected by unsubstituted oxamidate (1) and dithiooxamidate (2) linkers are isomorphous, and the cores of the molecules are planar because of two intramolecular hydrogen bonds within the linkers. Molecular mechanics calculations show a barrier of rotation along the C-C bond of approximately 10 kcal x mol(-1), which suggests that planar conformations are also expected in solution. Changing the two oxygen atoms in the linker of 1 to sulfur atoms results in a significant enhancement of the electronic coupling between the dimetal units (Delta(E1/2) = 204 mV for 1 and 407 mV for 2). The electronic spectrum of 2 shows an intense low energy (600 nm) metal-to-ligand charge transfer (MLCT) band, whereas that for 1 shows only a weak absorption band at 460 nm. DFT calculations on models 1' and 2', in which the anisyl groups were replaced by hydrogen atoms, show that the energy of the pi* orbital of the linker is much lower for 2'. This allows dpi-ddelta interactions from the electrons in the delta orbitals of the Mo2 unit to the sulfur atom that in turn facilitates an electron hopping pathway.

Correlating EPR and X-ray structural analysis of arsenite-inhibited forms of aldehyde oxidoreductase

Two arsenite-inhibited forms of each of the aldehyde oxidoreductases from Desulfovibrio gigas and Desulfovibrio desulfuricans have been studied by X-ray crystallography and electron paramagnetic resonance (EPR) spectroscopy. The molybdenum site of these enzymes shows a distorted square-pyramidal geometry in which two ligands, a hydroxyl/water molecule (the catalytic labile site) and a sulfido ligand, have been shown to be essential for catalysis. Arsenite addition to active as-prepared enzyme or to a reduced desulfo form yields two different species called A and B, respectively, which show different Mo(V) EPR signals. Both EPR signals show strong hyperfine and quadrupolar couplings with an arsenic nucleus, which suggests that arsenic interacts with molybdenum through an equatorial ligand. X-ray data of single crystals prepared from EPR-active samples show in both inhibited forms that the arsenic atom interacts with the molybdenum ion through an oxygen atom at the catalytic labile site and that the sulfido ligand is no longer present. EPR and X-ray data indicate that the main difference between both species is an equatorial ligand to molybdenum which was determined to be an oxo ligand in species A and a hydroxyl/water ligand in species B. The conclusion that the sulfido ligand is not essential to determine the EPR properties in both Mo-As complexes is achieved through EPR measurements on a substantial number of randomly oriented chemically reduced crystals immediately followed by X-ray studies on one of those crystals. EPR saturation studies show that the electron transfer pathway, which is essential for catalysis, is not modified upon inhibition.