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Rapid and Reversible Reactions of [NiFe]-Hydrogenases with Sulfide
Abstract
Rapid and reversible binding of sulfide to [NiFe]-hydrogenases (particularly the enzyme from Desulfovibrio vulgaris) under weakly acidic conditions (pH 6) has been studied by protein film voltammetry, which tracks the formation of different species as a function of potential. Sulfide (most likely entering as H2S) rapidly attacks the active site during H2 oxidation. The inactive adduct is formed (and is stable) only at potentials substantially more positive than the comparable species formed with oxygen species and is easily reactivated upon reduction. The sulfide adduct also reacts further with O2 to produce a new species that undergoes reductive activation very slowly. The results clarify complex and controversial chemistry reported in the literature and provide insight into how these enzymes would cope with sulfide production in sulfate-reducing bacteria.
... The three-dimensional orientation of amino acids may be important for S-persulfidation of these proteins as well [40], although there appears to be no evidence in the literature of hydrogenases being covalently modified in this way. This being said, it is known that hydrogenases are inhibited by H 2 S [51], perhaps by attack on the metal center, as suggested for NO [38]. ...
... Nevertheless, these studies indicate that NO can indeed influence hydrogenase activity. Furthermore, such hydrogenases have also been identified as being inhibited by H 2 S [51]. As plants are known to produce both NO [66] and H 2 S [67], there is potential for an interaction between gaseous signalling species, this would effectively modulate H 2 metabolism and any subsequent downstream effects. ...
Molecular hydrogen (H2) has been suggested to be a beneficial treatment for a range of species, from humans to plants. Hydrogenases catalyze the reversible oxidation of H2, and are found in many organisms, including plants. One of the cellular effects of H2 is the selective removal of reactive oxygen species (ROS) and reactive nitrogen species (RNS), specifically hydroxyl radicals and peroxynitrite. Therefore, the function of hydrogenases and the action of H2 needs to be reviewed in the context of the signalling roles of a range of redox active compounds. Enzymes can be controlled by the covalent modification of thiol groups, and although motifs targeted by nitric oxide (NO) can be predicted in hydrogenases sequences it is likely that the metal prosthetic groups are the target of inhibition. Here, a selection of hydrogenases, and the possibility of their control by molecules involved in redox signalling are investigated using a bioinformatics approach. Methods of treating plants with H2 along with the role of H2 in plants is also briefly reviewed. It is clear that studies report significant effects of H2 on plants, improving growth and stress responses, and therefore future work needs to focus on the molecular mechanisms involved.
... At 20°C and 100 kPa, about 9.0 mg of oxygen can be dissolved in one liter of water, while only 1.63 mg of hydrogen can be dissolved in one liter of water at same conditions. Although a dispersion of semiconductor-water could form hydrogen and oxygen simultaneously theoretically under above band-gap irradiation, [56][57][58][59][60] frequently used cocatalyst Pt would catalyze hydrogen and oxygen recombination back reaction under normal conditions [60][61][62]. If one wants achieve hydrogen evolution, the oxygen and hydrogen recombination back reaction must be inhibited by suitable method, for examples by removing dissolved oxygen from catalyst dispersion [42,63,64]. ...
... The corresponding bond angle of FeASAFe was 118.6°, which was also close to theoretical angle of 111.2°of active center Fe 2 S 2 cluster in [FeFe]-hydrogenases (Fig. 2a). Those data were further supported by the results of Raman experiment ( Figure S3) [56][57][58]. The peak center at 43.27°could be assigned to (2 0 0) facet of NiO, which confirmed the results of TEM [59]. ...
... These enzymes also use channels to guide the diffusion of the gaseous substrate H 2 to and from the deeply buried active site [8][9][10]. Hydrogenases are inhibited by several small molecules including O 2 , CO, acetylene and NO [9,[11][12][13][14][15]. While inhibition of hydrogenases by O 2 or CO has been widely studied, much less is known about the mechanism of NO inhibition. ...
Hydrogenases reversibly catalyze the oxidation of molecular hydrogen and are inhibited by several small molecules including O2, CO and NO. In the present work, we investigate the mechanism of inhibition by NO of the oxygen-sensitive NiFe hydrogenase from Desulfovibrio fructosovorans by coupling site-directed mutagenesis, Protein Film Voltammetry (PFV) and EPR spectroscopy. We show that micromolar NO strongly inhibits NiFe hydrogenase and that the mechanism of inhibition is complex, with NO targeting several metallic sites in the protein. NO reacts readily at the NiFe active site according to a two-step mechanism. The first and faster step is the reversible binding of NO to the active site followed by a slower and irreversible transformation at the active site. NO also induces irreversible damage of the iron–sulfur centers chain. We give direct evidence of preferential nitrosylation of the medial [3Fe-4S] to form dinitrosyl-iron complexes.
... opacus und A. vinosum einen [4Fe4S]-Cluster Zaborosch et al. 1995;Long et al. 2007 (Gu et al. 1996;Müller et al. 1997;Löscher et al. 2005 (Klibanov und Puglisi 1980;Ratzka et al. 2012). Des Weiteren wurde bereits der Einsatz von Hydrogenasen als Wasserstoffsensor (Abbildung 32F) und in biologischen Brennstoffzellen gezeigt Vincent et al. 2006 ...
Die NAD+-reduzierende Hydrogenase aus Ralstonia eutropha (SH) katalysiert die reversible H2-Oxidation in Verbindung mit der Reduktion von NAD+ in Gegenwart von Sauerstoff. Die bemerkenswerte O2-Toleranz des Enzyms wurde zuvor auf eine für [NiFe]-Hydrogenasen ungewöhnliche Struktur des Wasserstoff-spaltenden Zentrums zurückgeführt. Diese Hypothese wurde in dieser Arbeit mittels in situ-Spektroskopie an SH-haltigen Zellen widerlegt. Um die folgende Untersuchung der aus sechs Untereinheiten und mindestens acht Kofaktoren bestehenden SH zu erleichtern, wurde das Enzym mittels genetischer Methoden in seine beiden Module aufgeteilt. Das die H2-Oxidation katalysierende Hydrogenase-Modul beinhaltete ein FMN-Molekül, welches für die reduktive Reaktivierung des oxidativ modifizierten Zentrums benötigt wird. Das Diaphorase-Modul besaß ebenfalls ein FMN, und die Reduktion von NAD+ wurde von der Anwesenheit von O2 nicht beeinträchtigt. Neben Wasserstoff reagierte das [NiFe]-Zentrum der SH auch mit Sauerstoff. Dabei wurde sowohl Wasserstoffperoxid- als auch Wasser im Hydrogenase-Modul freigesetzt. Die Sauerstofftoleranz der SH basiert auf einer kontinuierlichen Reaktivierung des durch Sauerstoff oxidierten [NiFe]-Zentrums. Aufgrund der außergewöhnlichen Sauerstofftoleranz stellt die SH ein vielversprechendes System für die wasserstoffgetriebene Regeneration von NADH in gekoppelten enzymatischen Reaktionen dar. In dieser Arbeit wurde ein SH-Derivat durch rationale Mutagenese konstruiert, das in der Lage war, ebenso den Kofaktor NADP+ wasserstoffabhängig zu reduzieren. Durch Ganzzellansätze kann die zeitaufwändige und kostenintensive Proteinreinigung vermieden werden. Um die wasserstoffabhängige in-vivo-Kofaktorregeneration zu ermöglichen, wurde die SH in Pseudomonas putida heterolog produziert. Die in dieser Arbeit erzielten Ergebnisse sind sowohl für das molekulare Verständnis der H2-abhängigen Katalyse als auch für die biotechnologische Anwendung der O2-toleranten SH relevant.
... Practically, this means that the hydrogenase is an effective electrocatalyst for H 2 oxidation even in the presence of sulfides providing it does not experience potentials above about 0 V (Figure 7). 37 It is interesting to compare the mild and reversible 'poisoning' of hydrogenases by small molecules such as sulfides and CO with the serious effects of these molecules on Pt for which inhibition is difficult to reverse. ...
A number of redox enzymes function as excellent electrocatalysts when attached to electrodes or conductor/semi-conductor surfaces. A particular focus of this review is on hydrogenases, enzymes which use a di-iron or nickel-iron center to interconvert 2H(+) and H-2 at extremely high turnover frequencies, although the concepts we highlight apply to a wider range of redox enzymes. Taking hydrogenases as our main case study, we examine how a detailed electrochemical understanding of the electrocatalytic behaviour of an enzyme can inform the development of devices in which the enzyme exchanges electrons directly with a range of inorganic materials, including graphite electrodes and particles, semi-conductor electrodes and quantum dots. We review recent developments in composite enzyme-inorganic catalysts, some of the biological and materials challenges in building devices based on enzymes, and the future opportunities for devices based on biological catalysts, including fuel cells, light-driven fuel production and coupled catalysis for chemical synthesis.
... Reactivation of Ni-A is a very slow process 14 . Exposure to O 2 at more reducing conditions will lead mainly to the Ni-B state 25,26 . At lower potentials, an O 2 -sensitive hydrogenase can sustain H 2 production in the presence of small amounts of O 2 (ref. ...
Hydrogenases are nature's efficient catalysts for both the generation of energy via oxidation of molecular hydrogen and the production of hydrogen via the reduction of protons. However, their O2 sensitivity and deactivation at high potential limit their applications in practical devices, such as fuel cells. Here, we show that the integration of an O2-sensitive hydrogenase into a specifically designed viologen-based redox polymer protects the enzyme from O2 damage and high-potential deactivation. Electron transfer between the polymer-bound viologen moieties controls the potential applied to the active site of the hydrogenase and thus insulates the enzyme from excessive oxidative stress. Under catalytic turnover, electrons provided from the hydrogen oxidation reaction induce viologen-catalysed O2 reduction at the polymer surface, thus providing self-activated protection from O2. The advantages of this tandem protection are demonstrated using a single-compartment biofuel cell based on an O2-sensitive hydrogenase and H2/O2 mixed feed under anode-limiting conditions.
... Electrochemically, however, [NiFe] hydrogenases were also shown to react with sulfide. 85 Fig. 3) which was first synthesised and characterised by Zhu et al. 71 Rauchfuss and coworkers reported the protonated form of the complex [4H] + as the first example of a Ni-Fe hydride relevant to the [NiFeS 2 (µ-H)] core in the active site. 86,87 This has also been related to the Ni-R state of the hydrogenase. ...
Hydrogen is being considered as a versatile alternative fuel with the ever increasing energy demand and oil prices. Hydrogenases (H2ases) found in bacteria, archaea and eukaryotes are very efficient catalysts for biological hydrogen production. An important and unique hydrogenase enzyme is the [NiFe] H2ase, with an unusual heterobimetallic site. Since the determination of its crystal structure, a variety of complexes have been synthesised and studied. Bioinspired and biomimetic complexes have been investigated as potential catalysts. So far, of all the reported complexes only a few of them have been found to be catalytically active. Moreover, most of the reports are on the reverse reaction, e.g. proton reduction rather than dihydrogen oxidation. This perspective article therefore reviews the structural and functional aspects of the very recently reported model complexes that mimic the [NiFe] hydrogenase active site either in structure or function or both.
... Hydrogenases solve these limitations because they use earth abundant metals in their active site (Fe and Ni), whose activity is comparable to Pt 372 and their inhibition by H 2 S and CO is mostly reversible; some hydrogenases are even immune to them. 318,324,385,529,530 The use of hydrogenases in fuel cells and electrolytic cells have been recently reviewed in detail. 371,531 As it is not the main focus of this review we will only summarize the most recent and important advances demonstrating how these enzymes or enzyme-based catalysts could be used in future devices. ...
Hydrogenases are a diverse group of metalloenzymes that catalyze one of the simplest molecular reactions, the conversion of dihydrogen into protons and electrons and the reverse reaction, the generation of dihydrogen. The reaction takes place at a specialized metal center that dramatically increases the acidity of H2 and leads to a heterolytic splitting of the molecule which is strongly accelerated by the presence of a nearby base. Hydrogenases are widespread in nature; they occur in bacteria, archaea, and some eukarya and can be classified according to the metal ion composition of their active sites in [NiFe], [FeFe], and [Fe] hydrogenases. The use of hydrogenase or hydrogenase models as catalysts (to replace Pt) in fuel cells or in electrolytic H 2 production will depend strongly on new concepts how to overcome the O2 sensitivity of many hydrogenases. It is to be hoped that the great progress made in the understanding of O2 tolerance in [NiFe] hydrogenases and in the artificial maturation of the [FeFe] hydrogenases.
... Recently, this Na 2 S inhibition effect and reductive reactivation has been shown for several standard Ni-Fe hydrogenases by protein film voltammetry. 279 These results are understood in terms of the X-ray crystal structure of D. Vulgaris Miyazaki F hydrogenase in the oxidized state, in which a sulfur species was assigned as a bridging ligand between both metals of the active site. 126 This observation offers a possible explanation as to why formation of H 2 S is detected upon reductive activation of this hydrogenase. ...
... The function of the [NiFe] hydrogenases can be inhibited in the presence of oxygen [12][13][14], carbon monoxide [15,16] and other substances [17,18]. Thus, aerobic isolation of the enzyme results in inactive states with oxygen-based ligands bound to the bimetallic site. ...
The [NiFe] hydrogenase from the sulphate-reducing bacterium Desulfovibrio vulgaris Miyazaki F is reversibly inhibited in the presence of molecular oxygen. A key intermediate in the reactivation process, Ni-SIr, provides the link between fully oxidized (Ni-A, Ni-B) and active (Ni-SIa, Ni-C and Ni-R) forms of hydrogenase. In this work Ni-SIr was found to be light-sensitive (T ≤ 110 K), similar to the active Ni-C and the CO-inhibited states. Transition to the final photoproduct state (Ni-SL) was shown to involve an additional transient light-induced state (Ni-SI1961). Rapid scan kinetic infrared measurements provided activation energies for the transition from Ni-SL to Ni-SIr in protonated as well as in deuterated samples. The inhibitor CO was found not to react with the active site of the Ni-SL state. The wavelength dependence of the Ni-SIr photoconversion was examined in the range between 410 and 680 nm. Light-induced effects were associated with a nickel-centred electronic transition, possibly involving a change in the spin state of nickel (Ni2+). In addition, at T ≤ 40 K the CN− stretching vibrations of Ni-SL were found to be dependent on the colour of the monochromatic light used to irradiate the species, suggesting a change in the interaction of the hydrogen-bonding network of the surrounding amino acids. A possible mechanism for the photochemical process, involving displacement of the oxygen-based ligand, is discussed.
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The online version of this article (doi:10.1007/s00775-009-0566-9) contains supplementary material, which is available to authorized users.
... The effects of these mutations were investigated in terms of cell growth characteristics and the catalytic properties of the isolated enzymes. The isolated enzymes were studied electrochemically using the suite of techniques known as protein film voltammetry (PFV), which has proved to be very useful in studying hydrogenases from various organisms (9,10,20,23,24). The enzyme is adsorbed onto an electrode as a sub-monolayer film such that the electrode replaces physiological electron donors and acceptors. ...
Knallgas bacteria such as certain Ralstonia spp. are able to obtain metabolic energy by oxidizing trace levels of H2 using O2 as the terminal electron acceptor. The [NiFe] hydrogenases produced by these organisms are unusual in their ability to oxidize
H2 in the presence of O2, which is a potent inactivator of most hydrogenases through attack at the active site. To probe the origin of this unusual
O2 tolerance, we conducted a study on the membrane-bound hydrogenase from Ralstonia eutropha H16 and that of the closely related organism Ralstonia metallidurans CH34, which was purified using a new heterologous overproduction system. Direct electrochemical methods were used to determine
apparent inhibition constants for O2 inhibition of H2 oxidation () for each enzyme. These values were at least 2 orders of magnitude higher than those of “standard” [NiFe] hydrogenases. Amino
acids close to the active site were exchanged in the membrane-bound hydrogenase of R. eutropha H16 for those from standard hydrogenases to probe the role of individual residues in conferring O2 sensitivity. Michaelis constants for H2 () were determined, and for some mutants these were increased more than 20-fold relative to the wild type. Mutations resulting
in membrane-bound hydrogenase enzymes with increased or decreased ) values were associated with impaired lithoautotrophic growth in the presence of high O2 concentrations.
The hydrogen-based economy will require not only sustainable hydrogen production but also sensitive and cheap hydrogen sensors. Commercially available H2 sensors are limited by either use of noble metals or elevated temperatures. In nature, hydrogenase enzymes present high affinity and selectivity for hydrogen, while being able to operate in mild conditions. This study aims at evaluating the performance of an electrochemical sensor based on carbon nanomaterials with immobilised hydrogenase from the hyperthermophilic bacterium Aquifex aeolicus for H2 detection. The effect of various parameters, including the surface chemistry, dispersion degree and amount of deposited carbon nanotubes, enzyme concentration, temperature and pH on the H2 oxidation are investigated. Although the highest catalytic response is obtained at a temperature around 60 °C, a noticeable current can be obtained at room temperature with a low amount of protein less than 1 μM. An original pulse-strategy to ensure H2 diffusion to the bioelectrode allows to reach H2 sensitivity of 4 μA cm-2 per % H2 and a linear range between 1 and 20%. Sustainable hydrogen was then produced through dark fermentation performed by a synthetic bacterial consortium in an up-flow anaerobic packed-bed bioreactor. Thanks to the outstanding properties of the A. aeolicus hydrogenase, the biosensor was demonstrated to be quite insensitive to CO2 and H2S produced as the main co-products of the bioreactor. Finally, the bioelectrode was used for the in situ measurement of H2 produced in the bioreactor in steady-state.
Selenium-derived electrocatalysts have been well explored for electrocatalytic hydrogen evolution reactions to mimic hydrogenase-like activity; however, the stability of these synthetic mimics is yet to be enhanced. In this study, we report the synthesis and characterization of a series of 1,10-phenanthroline-cobalt(II) phenolate selenoether complexes using 1,10-phenanthroline and 6-nitro-1,10-phenanthroline-Co(II)-dichloride and substituted bis-selenophenolate ligands. The synthesized cobalt(II) phenolate selenoether complexes have been characterized by CHN analysis, mass spectrometry, single crystal XRD, and UV-visible absorption spectroscopy. These complexes show electrocatalytic proton reduction from acetic acid at an overpotential of 0.45-0.56 V vs. Fc+/Fc and surpass previously reported selenium and sulfur-containing electrocatalysts. Furthermore, gas analysis from control potential electrolysis confirms that the cobalt(II) selenoethers act as electrocatalysts to produce H2 with a faradaic efficiency of 43-83% and show a turnover number of 3.24-58.60 molcat-1. The hydrogen evolution reaction (HER) was probed using deuterated acetic acid, which demonstrates an inverse kinetic isotopic effect (KIE) and is consistent with the formation of metal hydride intermediates. Furthermore, control experiments (post-dip analysis and multiple CV studies) have been performed to support the catalysis being due to a homogeneous process. Acid titration using UV-visible spectroscopy reveals that protonation is the prior step for electrocatalysis and assists in the formation of a cobalt hydride intermediate, which upon reaction with a proton generates hydrogen gas.
Hydrothermal vents host a vast microbial diversity, both at the taxonomic and metabolic levels. These ecosystems are qualified as extreme, because they harbor harsh physico-chemical gradients. Sulfur is omnipresent in these environments, and it can be used by a large diversity of microorganisms for oxidation or reduction reactions.However, the sulfur cycle remains partially unknown in these ecosystems. The objective of this thesis was to study the poorly documented or thermodynamically predicted metabolisms of the sulfur cycle in hydrothermal ecosystems, namely the dismutation of inorganic sulfur compounds, the catabolism of organosulfur compounds and the comproportionation of sulfur. Four new inorganic sulfur compound disproportionating taxa were discovered during this study and extensive genomic analyses were conducted to decipher the pathways of inorganic sulfur compound dismutation. Comparative genomics analyses identified a gene cluster potentially involved in elemental sulfur dismutation in marine hydrothermal bacteria, but this result will need to be confirmed by functional approaches.Finally, the microbial communities of the geographically isolated hot springs from the Kerguelen Islands were studied by metagenomics, revealing the presence of many new lineages of bacteria and archaea in these previously unstudied habitats.
Cu2ZnSnS4-based heterostructure materials present broad spectral absorption and high absorption coefficient in the visible region; however, their photocatalytic activity and stability are still impeded due to photochemical corrosion. In this...
This book aims to introduce the reader to the cellular effects of molecular hydrogen (H2) in both plant and animal species. It contains a brief introduction to H2 and a collection of academic papers undertaken as an early career researcher.
World demand for energy is rapidly increasing and finding sufficient supplies of clean energy for the future is one of the major scientific challenges of today. This book presents the latest knowledge and chemical prospects in developing hydrogen as a solar fuel. Using oxygenic photosynthesis and hydrogenase enzymes for bio-inspiration, it explores strategies for developing photocatalysts to produce a molecular solar fuel. The book begins with perspective of solar energy utilization and the role that synthetic photocatalysts can play in producing solar fuels. It then summarizes current knowledge with respect to light capture, photochemical conversion, and energy storage in chemical bonds. Following chapters on the natural systems, the book then summarizes the latest developments in synthetic chemistry of photo- and reductive catalysts. Finally, important future research goals for the practical utilization of solar energy are discussed. The book is written by experts from various fields working on the biological and synthetic chemical side of molecular solar fuels to facilitate advancement in this area of research.
In this study, we report the electrocatalytic behavior of the neutral, monomeric Ni(II) complex of diacetyl-bis( N-4-methyl-3-thiosemicarbazonato), NiL1, for ligand-assisted metal-centered hydrogen evolution in acetonitrile (ACN) and dimethylformamide (DMF). Using foot-of-the-wave analysis (FOWA), NiL1 displays a maximum turnover frequency (TOF) of 4200 and 1200 s-1 for acetic acid (CH3COOH) in ACN and DMF, whereas for trifluoroacetic acid (CF3COOH) the TOFs are 1300 and 120 s-1 in ACN and DMF, respectively. In ACN, the overpotentials are 0.53 and 0.67 V for CH3COOH and CF3COOH, respectively. In DMF, the overpotential is 0.85 V for CH3COOH. First-order dependence with respect to the catalyst is established. NiL1 displays a minimum Faradaic efficiency of 87% from controlled potential electrolysis. Gas analysis from controlled potential electrolysis in both ACN and DMF using CH3COOH and CF3COOH confirms NiL1 as an electrocatalyst to produce H2. In ACN, TONs of 48 and 24 were obtained for CH3COOH and CF3COOH, respectively in 4 h. In DMF, TONs of 13 and 3 were obtained for CH3COOH and CF3COOH, respectively. The H2 evolution reaction was evaluated using deuterated acid, demonstrating an inverse kinetic isotope, which is consistent with formation of a metal hydride intermediate. A proposed ligand-assisted metal-centered mechanism for HER is supported by computational investigations. All catalytic intermediates in the proposed mechanism were structurally and energetically characterized using density functional theory (DFT), with the B3LYP/6-311g(d,p) and BP86/TZV/P in solution modeled via polarizable continuum model. The final step of catalysis involves the reaction of [HNi(L1·)]- with H+ generating H2. The correctness of proposed mechanism was confirmed by location of corresponding transition state (TS) having single imaginary frequency ( i1786 cm-1).
[FeFe] hydrogenases catalyze proton reduction and hydrogen oxidation with high rates and efficiency under physiological conditions, but are highly oxygen sensitive. The [FeFe] hydrogenase from Desulfovibrio desulfuricans (DdHydAB) can be purified under air in an oxygen stable inactive state Hoxair. The formation of the Hoxair state in vitro allows the handling of hydrogenases in air, making their implementation in biotechnological applications more feasible. Here, we report a simple and robust protocol for the formation of the Hoxair state in DdHydAB and the [FeFe] hydrogenase from Chlamydomonas reinhardtii, which is based on high potential inactivation in the presence of sulfide.
Standard [NiFe]-hydrogenase from Desulfovibrio vulgaris Miyazaki F (DvMF-H2ase) catalyzes the uptake and production of hydrogen (H2) and is a promising biocatalyst for future energy devices. However, DvMF-H2ase experiences oxidative inactivation under oxidative stress to generate Ni-A and Ni-B states. It takes a long time to reactivate the Ni-A state by chemical reduction, whereas the Ni-B state is quickly reactivated under reducing conditions. Oxidative inhibition limits the application of DvMF-H2ase in practical devices. In this research, we constructed a mediated-electron-transfer system by co-immobilizing DvMF-H2ase and a viologen redox polymer (VP) on electrodes. The system can avoid oxidative inactivation into the Ni-B state at high electrode potentials and rapidly reactivate the Ni-A state by electrochemical reduction of VP. H2 oxidation and H+ reduction were realized by adjusting the pH from a thermodynamic viewpoint. Using carbon felt as a working-electrode material, high current densities-up to (200 ± 70) and -(100 ± 9) mA cm-3 for the H2-oxidation and H+-reduction reactions, respectively-were attained.
A new series of the structural and functional models for the active site of [NiFe]-H2ases has been prepared by a simple and convenient synthetic route. Thus, treatment of diphosphines RN(PPh2)2 (1a, R = p-MeC6H4CH2; 1b, R = EtO2CCH2) with an equimolar NiCl26H2O, NiBr23H2O, and NiI2 in refluxing CH2Cl2/MeOH or EtOH gave the mononuclear Ni complexes RN(PPh2)2NiX2 (2a, R = p-MeC6H4CH2, X = Cl; 2b, R = EtO2CCH2, X = Cl; 3a, R = p-MeC6H4CH2, X = Br; 3b, R = EtO2CCH2, X = Br; 4a, R = p-MeC6H4CH2, X = I; 4b, R = EtO2CCH2, X = I) in 67-97% yields. Further treatment of complexes 2a,b-4a,b with an equimolar mononuclear Fe complex (dppv)(CO)2Fe(pdt) and NaBF4 resulted in formation of the targeted model complexes [RN(PPh2)2Ni(µ-pdt)(µ-X)Fe(CO)(dppv)](BF4) (5a, R = p-MeC6H4CH2, X = Cl; 5b, R = EtO2CCH2, X = Cl; 6a, R = p-MeC6H4CH2, X = Br; 6b, R = EtO2CCH2, X = Br; 7a, R = p-MeC6H4CH2, X = I; 7b, R = EtO2CCH2, X = I) in 60-96% yields. All the new complexes 3a,b-4a,b and 5a,b-7a,b have been characterized by elemental analysis and spectroscopy, and particularly for some of them (3a,b/4a,b and 5b/6b) by X-ray crystallography. More interestingly, the electrochemical and electrocatalytic properties of such halogenido-bridged model complexes are first studied systematically and particularly they have been found to be catalysts for proton reduction to H2 under CV conditions.
Tetra-coordinate Ni(II) and Zn(II) complexes employing the PS chelates 2-(diphenylphosphino)benzenethiol (HL1) and 2-(diisopropylphosphino)benzenethiol (HL2) have been synthesized and characterized by spectroscopic, structural, and electrochemical methods. All complexes were screened for electrocatalytic activity for hydrogen evolution with acetic acid and hydrochloric acid and hyrdogen oxidation in the presence of triethylamine. The nickel complex Ni(L1)2 (1) was found to reduce protons from external acids to generate hydrogen with a turnover frequency of 140 s-1 at an overpotential of 1.09 V and cleave dihydrogen using redox active base triethylamine (Et3N) with a turnover frequency of 23 s-1 at an overpotential of 0.33 V. Ni(L2)2 (3) was also found to be an active catalyst for dihydrogen oxidation, but inefficient for proton reduction due to inaccessible Ni (II/I) reduction in the potential window. Zn(L1)2 (2) and Zn(L2)2 (4) complexes were found to be inadequate for their electrocatalytic behaviour towards both the reactions.
Through modulation of its coordination environment, Nature has found ways to utilize nickel in biology. In this chapter, the relevant coordination chemistry, toxicology, and essential uses of nickel in biology are discussed, including in plants, animals, and particularly in microbes. Nickel plays important roles as a catalytic center in both redox and nonredox enzymes, where it has important ramifications in human health (e.g., urease), energy science (e.g., hydrogenase), and the environment (e.g., carbon monoxide dehydrogenases). To supply nickel for these functions, while avoiding toxicity, bacteria have developed complex pathways to maintain nickel homeostasis. The structure/function relationships in the proteins involved in maintaining nickel homeostasis are also discussed.
Iron-sulfur clusters are ubiquitous and ancient prosthetic groups that are present in all kingdoms of life. They are flexible in terms of coordination and redox properties. The first function of these proteins to be identified was electron transfer back in the 1960s, but since then other functions have been discovered. Iron-sulfur centers are directly involved in catalysis, as sensors of gases (nitric oxide and oxygen), iron, and other cellular compounds, and also participate in biosynthetic pathways of iron-sulfur clusters from the basic to the more complex ones. The role of iron-sulfur clusters is emerging in DNA repair, as the driving force for DNA lesion recognition. In recent years, more and more enzymes containing iron-sulfur clusters have been identified, and it is now known that these centers catalyze a wide range of diverse reactions.
We describe a new approach to selective H2-driven hydrogenation that exploits a sequence of enzymes immobilised on carbon particles. We used a catalyst system that comprised alcohol dehydrogenase, hydrogenase and an NAD+ reductase on carbon black to demonstrate a greater than 98 % conversion of acetophenone to phenylethanol. Oxidation of H2 by the hydrogenase provides electrons through the carbon for NAD+ reduction to recycle the NADH cofactor required by the alcohol dehydrogenase. This biocatalytic system operates over the pH range 6-8 or in un-buffered water, and can function at low concentrations of the cofactor (10 μm NAD+) and at H2 partial pressures below 1 bar. Total turnover numbers >130 000 during acetophenone reduction indicate high enzyme stability, and the immobilised enzymes can be recovered by a simple centrifugation step and re-used several times. This offers a route to convenient, atom-efficient operation of NADH-dependent oxidoreductases for selective hydrogenation catalysis. © 2015 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.
Hydrogenases catalyze reversible oxidation/reduction of molecular-hydrogen/protons in nature, and the enzymes are classified into three groups, namely, the [NiFe], [FeFe], and [Fe] hydrogenases. We herein summarize our structural and functional model studies on the [NiFe] hydrogenase. Aseires of (OC)3Fe(I0-Ni(I0, (OC)2 (gNC)2Fe(II)-Ni(I0, and (OC)(NC)2Fe(n)-Ni(II) complexes bridged by thiolato ligands have been synthesized as models of the [NiFe] hydrogenase active site. The investigations of dihydrogen activation at the chalcogenido bridged Ge-Ru and W-Ru complexes, and coordinatively unsaturated Ir and Rh thiolato complexes provide clues to understand the mechanism of the [NiFe] hydrogenase function.
Catalytically inactive oxidized O2-sensitive [NiFe]-hydrogenases are characterized by a mixture of the paramagnetic Ni-A and Ni-B states. Upon O2 exposure, enzymes in a partially reduced state preferentially form the unready Ni-A state. Because partial O2 reduction should generate a peroxide intermediate, this species was previously assigned to the elongated Ni-Fe bridging electron density observed for preparations of [NiFe]-hydrogenases known to contain the Ni-A state. However, this proposition has been challenged based on the stability of this state to UV light exposure and the possibility of generating it anaerobically under either chemical or electrochemical oxidizing conditions. Consequently, we have considered alternative structures for the Ni-A species including oxidation of thiolate ligands to either sulfenate or sulfenic acid. Here, we report both new and revised [NiFe]-hydrogenases structures and conclude, taking into account corresponding characterizations by Fourier transform infrared spectroscopy (FTIR), that the Ni-A species contains oxidized cysteine and bridging hydroxide ligands instead of the peroxide ligand we proposed earlier. Our analysis was rendered difficult by the typical formation of mixtures of unready oxidized states that, furthermore, can be reduced by X-ray induced photoelectrons. The present study could be carried out thanks to the use of Desulfovibrio fructosovorans [NiFe]-hydrogenase mutants with special properties. In addition to the Ni-A state, crystallographic results are also reported for two diamagnetic unready states, allowing the proposal of a revised oxidized inactive Ni-SU model and a new structure characterized by a persulfide ion that is assigned to an Ni-'Sox' species.
Hydrogenases catalyze the reversible oxidation of H2, which is crucial for the anaerobic metabolism of microorganisms. They attract growing interest in connection with H2-based energy systems. [NiFe] hydrogenase is the most common type among the currently known hydrogenases, and its active site consists of an “organometallic” Fe–Ni complex supported by cysteinyl thiolate ligands. This review presents an overview of the synthesis, properties, and reactions of thiolate-bridged iron–nickel complexes that model the active site of [NiFe] hydrogenase.
Cyanide reacts rapidly with [NiFe]-hydrogenases (hydrogenase-1 and hydrogenase-2 from Escherichia coli) under mild oxidizing conditions, inhibiting the electrocatalytic oxidation of hydrogen as recorded by protein film electrochemistry. Electrochemical, EPR, and FTIR measurements show that the final enzyme product, formed within a second (even under 100% H2), is the resting state known as Ni-B, which contains a hydroxido-bridged species, Ni(III)-μ(OH)-Fe(II), at the active site. "Cyanide inhibition" is easily reversed because it is simply the reductive activation of Ni-B. This paper brings back into focus an observation originally made in the 1940s that cyanide inhibits microbial H2 oxidation and addresses the interesting mechanism by which cyanide promotes the formation of Ni-B. As a much stronger nucleophile than hydroxide, cyanide binds more rapidly and promotes oxidation of Ni(II) to Ni(III); however, it is quickly replaced by hydroxide which is a far superior bridging ligand.
This article summarizes the development of a range of organometallic, biomimetic analogues of [NiFe]hydrogenases and their employment in a new generation of H2-O2 fuel cells. It begins with a summary of O2-sensitive and O2-tolerant enzyme chemistry before detailing the properties and functionality of our biomimetic complexes, including: the first ever fully functional model, selective H2 and O2 activation, and the first catalyst using only common metals. These systems are centered on Ni–Fe, Ni–Ru, Ir–Ir, and Rh–Rh cores and use a range of ligands that all follow a set of design principles described herein.
Hydrogenases catalyze the conversion between 2H+ + 2e− and H2. Most of these enzymes are inhibited by O2, which represents a major drawback for their use in biotechnological applications. Improving hydrogenase O2 tolerance is therefore a major contemporary challenge to allow the implementation of a sustainable hydrogen economy. A few bacteria, however, contain hydrogenases that activate H2 even in the presence of O2. Intriguingly, kinetic and spectroscopic studies lead to assuming that different mechanisms might be responsible for the resistance, depending on the enzyme type. The various hypotheses that emerged from these studies are still a matter of debate. In order to better understand the molecular bases of resistance to O2 inhibition, we explored different methods to improve the O2-tolerance of the O2-sensitive [Ni–Fe] hydrogenase from Desulfovibrio fructosovorans. A whole bunch of mutants has been studied and fully characterized, which revealed that actually, different mechanisms can lead to O2 tolerance. These mechanisms are described in this review and compared to the current hypothesis of O2 tolerance.
EPR studies of the [NiFe] hydrogenases are reviewed. These enzymes contain a heterobimetallic [NiFe] center as the active
site. The nickel is ligated to four cysteine residues, two of which form a bridge to the iron. The iron carries additionally
3 small inorganic diatomic ligands (2CN−, CO). A third small ligand X is situated in the bridge between Ni and Fe. In the catalytic cycle the enzyme passes through
a number of redox states, several of which are paramagnetic. The iron remains in the divalent low-spin (FeII, S = 0) state, whereas the nickel changes its valence and spin state during this cycle. Nickel is believed to bind the hydrogen
and to be directly involved in the catalytic process.
This review is focused on the basic principles, the main applications, and the theoretical models developed for various redox mechanisms in protein film voltammetry, with a special emphasis to square-wave voltammetry as a working technique. Special attention is paid to the thermodynamic and kinetic parameters of relevant enzymes studied in the last decade at various modified electrodes, and their use as a platform for the detection of reactive oxygen species is also discussed. A set of recurrent formulas for simulations of different redox mechanisms of lipophilic enzymes is supplied together with representative simulated voltammograms that illustrate the most relevant voltammetric features of proteins studied under conditions of square-wave voltammetry.
The O-2-tolerant, NAD(+)-reducing soluble [NiFe] hydrogenase (SH) from Ralstonia eutropha H16, HoxHYFUI(2), is a complex enzyme, harboring multiple redox cofactors: a [NiFe] active site, an electron relay of iron-sulfur clusters, and two noncovalently bound flavin mononucleotides (FMN). The interplay and functional role of these cofactors is so far not understood in detail. In the present study, the isolated HoxHY module was investigated, which represents the smallest active sub-complex of a [NiFe] hydrogenase. Direct electrochemical studies and solution assays showed that the as-isolated HoxHY is initially catalytically inactive, but after reductive activation at low potentials, exhibits both H-2 oxidation and H+ reduction, consistent with the role of the SH in bidirectional catalysis. The overpotential relative to E(2H(+)/H-2) is minimal, facilitating coupling of the closely spaced 2H(+)/H-2 and NAD(+)/NADH half reactions in the SH. Methyl viologen reduction assays revealed that H-2 oxidation by HoxHY is enhanced on addition of excess FMN, in line with results from optical spectroscopy which indicate that FMN is present at substoichiometric levels in as-isolated HoxHY. X-ray absorption spectroscopy suggested one 4Fe4S cluster in addition to the active site in HoxHY. FTIR investigations confirmed that the active site iron atom has a "standard" ligation, i.e., one CO and two cyanide ligands. At least two novel oxidized states were detected by FTIR, both of which could be reductively activated by artificial electron donors, such as dithionite, and by the native electron donor H-2 in the presence of additional FMN. The flavin cofactor also appears to stabilize the active site, providing further evidence for its importance in HoxHY. All reduced states of the [NiFe] site previously identified for standard [NiFe] hydrogenases and for the native SH within living cells were detected in FTIR spectra of HoxHY with the exception of the intermediate Ni-a-C species. Electrochemical experiments show that incubation of active HoxHY with O-2 at high potentials causes slow inactivation, but activity is recovered within seconds at potentials below -170 mV at 30 degrees C, even in the presence of 2% O-2. This behavior is consistent with the HoxHY moiety of the SH remaining active in the presence of O-2 at the potential of the NAD(+)/NADH pool in vivo.
Organic syntheses catalyzed by iron complexes have attracted considerable attention because iron is an abundant, inexpensive,
and environmentally benign metal. It has been documented that various iron hydride complexes play important roles in catalytic
cycles such as hydrogenation, hydrosilylation, hydroboration, hydrogen generation, and element–element bond formation. This
chapter summarizes the recent developments, mainly from 2000 to 2009, of iron catalysts involving hydride ligand(s) and the
role of Fe–H species in catalytic cycles.
KeywordsCatalysis-Electrochemical reduction-Hydroboration-Hydrogenation-Hydrosilylation-Iron hydride complex-Photochemical reduction
Histamine dehydrogenase from Nocardioides simplex (HmDH) belongs to the family of soluble iron–sulfur flavoproteins having one [4Fe–4S] cluster and one 6-S-cysteinyl flavin mononucleotide per monomer. Direct electrochemistry of HmDH was studied using several carbon particle-modified glassy carbon electrodes (GCEs) and indium tin oxide (ITO) electrodes. HmDH gave a clear catalytic wave of the histamine oxidation without any mediator at a GCE modified with Ketjen Black (KB) with an average particle diameter of 39.5 nm, although redox signal of the cofactors itself was not clearly recognized. Experimental data supported the irreversible adsorption of HmDH on the KB particles and the importance of the size of the carbon particle as well as the surface area as factors determining the current density of the direct electron transfer (DET)-type bioelectrocatalysis. On the other hand, HmDH was adsorbed on ITO electrodes as a monolayer, as evidenced by quartz crystal microbalance measurement, and showed a clear redox wave ascribed to the [4Fe–4S] cluster. However, some mediators were required to observe catalytic wave of histamine oxidation at ITO electrodes, indicating that the interaction between the two redox cofactors seems to be disrupted in the monomer HmDH adsorbed on the planar and hydrophilic surfaces of ITO electrodes. Surface properties of electrodes favorable for DET-type bioelectrocatalysis of HmDH are discussed.
We have developed complexes of CdS nanorods capped with 3-mercaptopropionic acid (MPA) and Clostridium acetobutylicum [FeFe]-hydrogenase I (CaI) that photocatalyze reduction of H(+) to H(2) at a CaI turnover frequency of 380-900 s(-1) and photon conversion efficiencies of up to 20% under illumination at 405 nm. In this paper, we focus on the compositional and mechanistic aspects of CdS:CaI complexes that control the photochemical conversion of solar energy into H(2). Self-assembly of CdS with CaI was driven by electrostatics, demonstrated as the inhibition of ferredoxin-mediated H(2) evolution by CaI. Production of H(2) by CdS:CaI was observed only under illumination and only in the presence of a sacrificial donor. We explored the effects of the CdS:CaI molar ratio, sacrificial donor concentration, and light intensity on photocatalytic H(2) production, which were interpreted on the basis of contributions to electron transfer, hole transfer, or rate of photon absorption, respectively. Each parameter was found to have pronounced effects on the CdS:CaI photocatalytic activity. Specifically, we found that under 405 nm light at an intensity equivalent to total AM 1.5 solar flux, H(2) production was limited by the rate of photon absorption (~1 ms(-1)) and not by the turnover of CaI. Complexes were capable of H(2) production for up to 4 h with a total turnover number of 10(6) before photocatalytic activity was lost. This loss correlated with inactivation of CaI, resulting from the photo-oxidation of the CdS capping ligand MPA.
Direct electrochemical methods have been productive in revealing mechanistic details of catalysis by a range of metalloenzymes including hydrogenases and carbon and nitrogen cycling enzymes. In this approach, termed protein film electrochemistry, the protein is attached or adsorbed on the electrode surface and exchanges electrons directly, providing precise control over redox states or catalysis and avoiding diffusion-limited electron transfer. The 'edge' surface of pyrolytic graphite has proved to be a particularly good surface for adsorption of proteins in electroactive conformations. We now describe development of an approach that combines the precise control achieved in direct electrochemical measurements at a graphite electrode with surface infrared (IR) spectroscopic analysis of chemistry occurring at metallocentres in proteins. Hydrogenases are of particular interest: their unusual organo-metallic active sites--iron or nickel-iron centres coordinated by CO and CN(-)--give rise to IR v(CO) and v(CN) bands that are detected readily because these ligands are strong vibrational oscillators and are sensitive to changes in electron density and coordination at the metals. Small diatomic species also bind as exogenous ligands (as substrate, product, activator or inhibitor) to a range of other important metalloproteins, and understanding their reactivity and binding selectivity is critical in building up a multidimensional picture of enzyme chemistry and evolutionary history. The surface IR spectroelectrochemical approach we describe is based around Attenuated Total Reflectance (ATR) mode sampling of a film of pyrolytic graphite particles modified with a protein of interest. The particle network extends the electrode into three-dimensional space, providing sufficient adsorbed protein for spectroscopic analysis under precise electrochemical control. This strategy should open up new opportunities for detection of redox-dependent chemistry at metal centres in proteins, including short-lived catalytic intermediates and time-resolved details of catalysis and inhibition.
The crystal structure of the membrane-associated [NiFe] hydrogenase from Allochromatium vinosum has been determined to 2.1 Å resolution. Electron paramagnetic resonance (EPR) and Fourier transform infrared spectroscopy on dissolved crystals showed that it is present in the Ni-A state (>90%). The structure of the A. vinosum [NiFe] hydrogenase shows significant similarities with [NiFe] hydrogenase structures derived from Desulfovibrio species. The amino acid sequence identity is ∼ 50%. The bimetallic [NiFe] active site is located in the large subunit of the heterodimer and possesses three diatomic non-protein ligands coordinated to the Fe (two CN(-) , one CO). Ni is bound to the protein backbone via four cysteine thiolates; two of them also bridge the two metals. One of the bridging cysteines (Cys64) exhibits a modified thiolate in part of the sample. A mono-oxo bridging ligand was assigned between the metal ions of the catalytic center. This is in contrast to a proposal for Desulfovibrio sp. hydrogenases that show a di-oxo species in this position for the Ni-A state. The additional metal site located in the large subunit appears to be a Mg(2+) ion. Three iron-sulfur clusters were found in the small subunit that forms the electron transfer chain connecting the catalytic site with the molecular surface. The calculated anomalous Fourier map indicates a distorted proximal iron-sulfur cluster in part of the crystals. This altered proximal cluster is supposed to be paramagnetic and is exchange coupled to the Ni(3+) ion and the medial [Fe(3)S(4)](+) cluster that are both EPR active (S=1/2 species). This finding of a modified proximal cluster in the [NiFe] hydrogenase might explain the observation of split EPR signals that are occasionally detected in the oxidized state of membrane-bound [NiFe] hydrogenases as from A. vinosum.
The [NiFe] hydrogenase from the anaerobic sulphate reducing bacterium Desulfovibrio vulgaris Miyazaki F is an excellent model for constructing a mechanism for the function of the so-called 'oxygen-sensitive' hydrogenases. The present review focuses on spectroscopic investigations of the active site intermediates playing a role in the activation/deactivation and catalytic cycle of this enzyme as well as in the inhibition by carbon monoxide or molecular oxygen and the light-sensitivity of the hydrogenase. The methods employed include magnetic resonance and vibrational (FTIR) techniques combined with electrochemistry that deliver information about details of the geometrical and electronic structure of the intermediates and their redox behaviour. Based on these data a mechanistic scheme is developed.
This review aims at presenting the principles of water-oxidation in photosystem II and of hydrogen production by the two major classes of hydrogenases in order to facilitate application for the design of artificial catalysts for solar fuel production.
Hydrogen is a good energy vector, and its production from renewable sources is a requirement for its widespread use. [NiFeSe] hydrogenases (Hases) are attractive candidates for the biological production of hydrogen because they are capable of high production rates even in the presence of moderate amounts of O(2), lessening the requirements for anaerobic conditions. The three-dimensional structure of the [NiFeSe] Hase from Desulfovibrio vulgaris Hildenborough has been determined in its oxidised "as-isolated" form at 2.04-A resolution. Remarkably, this is the first structure of an oxidised Hase of the [NiFe] family that does not contain an oxide bridging ligand at the active site. Instead, an extra sulfur atom is observed binding Ni and Se, leading to a SeCys conformation that shields the NiFe site from contact with oxygen. This structure provides several insights that may explain the fast activation and O(2) tolerance of these enzymes.
The catalytic cycle of the anaerobic [NiFe] hydrogenase from Desulfovibrio vulgaris Miyazaki F (DvMF) both in solution and immobilized on an Au electrode was studied by IR spectroscopic and electrochemical methods. IR spectroelectrochemistry in solution at different pH values allows the identification of the various redox-states of the active site and the determination of the midpoint potentials, as well as their acid-base equilibria. The spectroscopic characterization was based on the unique marker bands of the CN and CO stretching modes of the Ni-Fe center and served as reference for the surface-enhanced IR absorption (SEIRA) study of the immobilized enzyme. Using structural models of hydrogenases from DvMF and Desulfovibrio gigas , dipole moment calculations were carried out to guide the immobilization strategy. In view of the high dipole moment of about 1100 D pointing through the negatively charged area surrounding the distal [FeS] cluster, the Au electrode was coated by a self-assembled monolayer of amino-terminated mercaptanes which, due to the positively charged head groups, permit a durable electrostatic binding of the protein. SEIRA spectroscopy revealed a structurally and functionally intact active site as demonstrated by the reversible activation and inactivation under hydrogen and argon, respectively. Cyclic voltammetry on the immobilized enzyme demonstrate a reversible anaerobic inactivation upon changing the applied potential. The "switch" potential (E(switch)) associated with the reductive reactivation was determined to be -33 mV (vs normal hydrogen electrode). However, the catalytic current decreased on the time scale of hours during continuous cycling. SEIRA experiments demonstrate that the loss of catalytic activity is not due to protein desorption but is rather related to a slow degradation of the active site, possibly initiated by the attack of reactive species electrochemically generated from residual traces of oxygen in solution.
[NiFe] hydrogenases catalyze the reversible oxidation of dihydrogen. For this simple reaction the molecule has developed a complex catalytic mechanism, during which the enzyme passes through various redox states. The [NiFe] hydrogenase contains several metal centres, including the bimetallic Ni-Fe active site, iron-sulfur clusters and a Mg(2+) ion. The Ni-Fe active site is located in the inner part of the protein molecule, therefore a number of pathways are involved in the catalytic reaction route. These consist of an electron transfer pathway, a proton transfer pathway and a gas-access channel. Over the last 10-15 years we have been investigating the crystal structures of the [NiFe] hydrogenase from Desulfovibrio vulgaris Miyazaki F, which is a sulfate-reducing anaerobic bacterium. So far the crystal structures of the oxidized, H(2)-reduced and carbon monoxide inhibited states have been determined at high resolution and have revealed a rather unique structure of the hetero-bimetallic Ni-Fe active site. Furthermore, intensive spectroscopic studies have been performed on the enzyme. Based on the crystal structure, a water-soluble Ni-Ru complex has been synthesized as a functional model for the [NiFe] hydrogenases. The present review gives an overview of the catalytic reaction mechanism of the [NiFe] hydrogenases.
This tutorial review describes studies of hydrogen production and oxidation by biological catalysts--metalloenzymes known as hydrogenases--attached to electrodes. It explains how the electrocatalytic properties of hydrogenases are studied using specialised electrochemical techniques and how the data are interpreted to allow assessments of catalytic rates and performance under different conditions, including the presence of O2, CO and H2S. It concludes by drawing some comparisons between the enzyme active sites and platinum catalysts and describing some novel proof-of-concept applications that demonstrate the high activities and selectivities of these 'alternative' catalysts for promoting H2 as a fuel.
Desulfovibrio vulgaris Hildenborough is a model organism for studying the energy metabolism of sulfate-reducing bacteria (SRB) and for understanding the economic impacts of SRB, including biocorrosion of metal infrastructure and bioremediation of toxic metal ions. The 3,570,858 base pair (bp) genome sequence reveals a network of novel c-type cytochromes, connecting multiple periplasmic hydrogenases and formate dehydrogenases, as a key feature of its energy metabolism. The relative arrangement of genes encoding enzymes for energy transduction, together with inferred cellular location of the enzymes, provides a basis for proposing an expansion to the 'hydrogen-cycling' model for increasing energy efficiency in this bacterium. Plasmid-encoded functions include modification of cell surface components, nitrogen fixation and a type-III protein secretion system. This genome sequence represents a substantial step toward the elucidation of pathways for reduction (and bioremediation) of pollutants such as uranium and chromium and offers a new starting point for defining this organism's complex anaerobic respiration.
[NiFe] hydrogenases catalyze the reversible heterolytic cleavage of molecular hydrogen. Several oxidized, inactive states of these enzymes are known that are distinguishable by their very different activation properties. So far, the structural basis for this difference has not been understood because of lack of relevant crystallographic data. Here, we present the crystal structure of the ready Ni-B state of Desulfovibrio fructosovorans [NiFe] hydrogenase and show it to have a putative mu-hydroxo Ni-Fe bridging ligand at the active site. On the other hand, a new, improved refinement procedure of the X-ray diffraction data obtained for putative unready Ni-A/Ni-SU states resulted in a more elongated electron density for the bridging ligand, suggesting that it is a diatomic species. The slow activation of the Ni-A state, compared with the rapid activation of the Ni-B state, is therefore proposed to result from the different chemical nature of the ligands in the two oxidized species. Our results along with very recent electrochemical studies suggest that the diatomic ligand could be hydro-peroxide.
Use of hydrogen in fuel cells requires catalysts that are tolerant to oxygen and are able to function in the presence of poisons such as carbon monoxide. Hydrogen-cycling catalysts are widespread in the bacterial world in the form of hydrogenases, enzymes with unusual active sites composed of iron, or nickel and iron, that are buried within the protein. We have established that the membrane-bound hydrogenase from the β-proteobacterium Ralstonia eutropha H16, when adsorbed at a graphite electrode, exhibits rapid electrocatalytic oxidation of hydrogen that is completely unaffected by carbon monoxide [at 0.9 bar (1 bar = 100 kPa), a 9-fold excess] and is inhibited only partially by oxygen. The practical significance of this discovery is illustrated with a simple fuel cell device, thus demonstrating the feasibility of future hydrogen-cycle technologies based on biological or biologically inspired electrocatalysts having high selectivity for hydrogen.
• biohydrogen
• electron transfer
• energy
• fuel cell
• hydrogenase
Crystallographic data on the [NiFe] hydrogenase from Desulfovibrio gigas are presented that provide new information on the structure and mode of action of its dihydrogen activating metal center. Recently we found this center to contain, besides Ni, a second metal ion which was tentatively assigned to Fe (Volbeda, A.; Charon, M. H.; Piras, C.; Hatchikian, E. C.; Frey, M.; Fontecilla-Camps, J. C. Nature 1995, 373, 580−587). This assignment is now unambiguously confirmed by a crystallographic analysis using 3 Å resolution X-ray data collected at wavelengths close to either side of the Fe absorption edge. Moreover, we report the structure of another crystal form of the as-purified D. gigas hydrogenase refined at 2.54 Å resolution, showing that the active site Fe binds three diatomic ligands. The electron density map shows an additional small peak at a position bridging the two active site metal ions, which may be assigned to some form of oxygen. This bridging oxygen species is proposed to be the signature of the inactive form of the enzyme. An infrared analysis similar to the one reported for Chromatium vinosum hydrogenase (Bagley, K. A.; Duin, E. C.; Roseboom, W.; Albracht, S. P. J.; Woodruff, W. H. Biochemistry 1995, 34, 5527−5535) shows the existence of three bands at exceptionally high frequencies, that shift their position in a concerted fashion depending on the redox state of the enzyme. Based on these high frequencies, the diatomic Fe ligands may be assigned to nonexchangeable triply bonded molecules, possible candidates being CO, CN- and NO. The frequency shifts of the infrared bands suggest a redox role for the Fe center during catalysis. Based on the new crystal structure and a number of spectroscopic results, possible modes of hydrogen binding to the active site are discussed.
The primary and three-dimensional structures of a [NiFe] hydrogenase isolated from D. desulfuricans ATCC 27774 were determined, by nucleotide analysis and single-crystal X-ray crystallography. The three-dimensional structural model was refined to R=0.167 and R
free=0.223 using data to 1.8 Å resolution. Two unique structural features are observed: the [4Fe-4S] cluster nearest the [NiFe] centre has been modified [4Fe-3S-3O] by loss of one sulfur atom and inclusion of three oxygen atoms; a three-fold disorder was observed for Cys536 which binds to the nickel atom in the [NiFe] centre. Also, the bridging sulfur atom that caps the active site was found to have partial occupancy, thus corresponding to a partly activated enzyme. These structural features may have biological relevance. In particular, the two less-populated rotamers of Cys536 may be involved in the activation process of the enzyme, as well as in the catalytic cycle. Molecular modelling studies were carried out on the interaction between this [NiFe] hydrogenase and its physiological partner, the tetrahaem cytochrome c
3 from the same organism. The lowest energy docking solutions were found to correspond to an interaction between the haem IV region in tetrahaem cytochrome c
3 with the distal [4Fe-4S] cluster in [NiFe] hydrogenase. This interaction should correspond to efficient electron transfer and be physiologically relevant, given the proximity of the two redox centres and the fact that electron transfer decay coupling calculations show high coupling values and a short electron transfer pathway. On the other hand, other docking solutions have been found that, despite showing low electron transfer efficiency, may give clues on possible proton transfer mechanisms between the two molecules.
Dynamic electrochemical studies, incorporating catalytic voltammetry and detailed potential-step manipulations, provide compelling evidence that the oxidized inactive state of [NiFe]-hydrogenases termed Unready (or Ni-A) contains a product of partial reduction of O(2) that is trapped in the active site.
Oxygen, either molecular oxygen or a reduction adduct, can tightly bind in the vicinity of the two forms of trivalent nickel occurring in hydrogenase from Chromatium vinosum, as evident from studies with 17O-enriched O2. This oxygen is not in the first coordination sphere of nickel. As has been reported earlier for hydrogenase from Desulfovibrio gigas (Fernandez, V.M., Hatchikian, A.C., Patil, D.S. and Cammack, R. (1986) Biochim. Biophys. Acta 883, 145-154), also the relative activity of the C.vinosum enzyme correlates well with the presence of only one of the two Ni(III) forms in the oxidized preparation. These results make it less likely that a specific oxygenation of only one of the Ni(III) forms would be the reason for the reversible inactivation of nickel hydrogenases by oxygen. Reaction of H2-reduced enzyme with 13CO now demonstrated beyond doubt that: (i) One 13CO molecule is a direct ligand to nickel in axial position; and (ii) hydrogen binds at the same coordination site as CO. It can also be concluded that hydrogen is not bound as a hydride ion, but presumably as molecular hydrogen. A simple way to explain the EPR spectra from the 13CO-adduct of the enzyme is to assume a monovalent state for the nickel.
The X-ray structure of the heterodimeric Ni-Fe hydrogenase from Desulfovibrio gigas, the enzyme responsible for the metabolism of molecular hydrogen, has been solved at 2.85 A resolution. The active site, which appears to contain, besides nickel, a second metal ion, is buried in the 60K subunit. The 28K subunit, which coordinates one [3Fe-4S] and two [4Fe-4S] clusters, contains an amino-terminal domain with similarities to the redox protein flavodoxin. The structure suggests plausible electron and proton transfer pathways.
The 2.54 A resolution structure of Ni-Fe hydrogenase has revealed the existence of hydrophobic channels connecting the molecular surface to the active site. A crystallographic analysis of xenon binding together with molecular dynamics simulations of xenon and H2 diffusion in the enzyme interior suggest that these channels serve as pathways for gas access to the active site.
The hydrogenase of Desulfovibrio sp. catalyzes the reversible oxidoreduction of molecular hydrogen, in conjunction with a specific electron acceptor, cytochrome c3. The Ni-Fe active center of Desulfovibrio hydrogenase has an unusual ligand structure with non-protein ligands. An atomic model at high resolution is required to make concrete assignment of the ligands which coordinate the Ni-Fe center. These in turn will provide insight into the mechanism of electron transfer, during the reaction catalysed by hydrogenase.
The X-ray structure of the hydrogenase from Desulfovibrio vulgaris Miyazaki has been solved at 1.8 A resolution and refined to a crystallographic R factor of 0.229. The overall folding pattern and the spatial arrangement of the metal centers are very similar to those found in Desulfovibrio gigas hydrogenase. This high resolution crystal structure enabled us to assign the non-protein ligands to the Fe atom in the Ni-Fe site and revealed the presence of a Mg center, located approximately 13 A from the Ni-Fe active center.
From the nature of the electron-density map, stereochemical geometry and atomic parameters of the refined structure, the most probable candidates for the four ligands, coordinating the Ni-Fe center, have been proposed to be diatomic S=O, C triple bond O and C triple bond N molecules and one sulfur atom. The assignment was supported by pyrolysis mass spectrometry measurements. These ligands may have a role as an electron sink during the electron transfer reaction between the hydrogenase and its biological counterparts, and they could stabilize the redox state of Fe(II), which may not change during the catalytic cycle and is independent of the redox transition of the Ni. The hydrogen-bonding system between the Ni-Fe and the Mg centers suggests the possible.
The active site of [NiFe] hydrogenase from Desulfovibrio species is composed of a binuclear Ni-Fe complex bearing three diatomic nonprotein ligands to Fe and three bridges between the two metals, two of which are thiolate side chains of the protein moiety. The third bridging atom in the enzyme isolated from D. vulgaris Miyazaki F was suggested to be sulfur species, but was suggested to be oxygen species in D. gigas enzyme. When the hydrogenase from D. vulgaris Miyazaki F was incubated under the atmosphere of H2, H2S was liberated from the enzyme only in the presence of its electron carrier, cytochrome c3 or methylviologen. The amount of H2S liberation was little in the absence of electron carrier or essentially null when the enzyme was incubated under N2. The amount of H2S liberated was about 37% of the hydrogenase contained in the reaction vial in molar basis. These observations are in agreement with the recent observation that the third bridging site at the Ni-Fe active site is vacant in the reduced form of the enzyme revealed by X-ray crystallography.
The active site of [NiFe] hydrogenase, a heterodimeric protein, is suggested to be a binuclear Ni-Fe complex having three diatomic ligands to the Fe atom and three bridging ligands between the Fe and Ni atoms in the oxidized form of the enzyme. Two of the bridging ligands are thiolate sidechains of cysteinyl residues of the large subunit, but the third bridging ligand was assigned as a non-protein monatomic sulfur species in Desulfovibrio vulgaris Miyazaki F hydrogenase.
The X-ray crystal structure of the reduced form of D. vulgaris Miyazaki F [NiFe] hydrogenase has been solved at 1.4 A resolution and refined to a crystallographic R factor of 21.8%. The overall structure is very similar to that of the oxidized form, with the exception that the third monatomic bridge observed at the Ni-Fe site in the oxidized enzyme is absent, leaving this site unoccupied in the reduced form.
The unusual ligand structure found in the oxidized form of D. vulgaris Miyazaki F [NiFe] hydrogenase was confirmed in the reduced form of the enzyme, with the exception that the electron density assigned to the monatomic sulfur bridge had almost disappeared. On the basis of this finding, as well as the observation that H2S is liberated from the oxidized enzyme under an atmosphere of H2 in the presence of its electron carrier, it was postulated that the monatomic sulfur bridge must be removed for the enzyme to be activated. A possible mechanism for the catalytic action of the hydrogenase is proposed.
Crystallographic studies of the hydrogenases (Hases) from Desulfovibrio gigas (Dg) and Desulfovibrio vulgaris Miyazaki (DvM) have revealed heterodinuclear nickel-iron active centers in both enzymes. The structures, which represent the as-isolated (unready) Ni-A (S = (1)/(2)) enzyme state, disclose a nonprotein ligand (labeled as X) bridging the two metals. The bridging atom was suggested to be an oxygenic (O(2)(-) or OH(-)) species in Dg Hase and an inorganic sulfide in DvM Hase. To determine the nature and chemical characteristics of the Ni-X-Fe bridging ligand in Dg Hase, we have performed 35 GHz CW (17)O ENDOR measurements on the Ni-A form of the enzyme, exchanged into H(2)(17)O, on the active Ni-C (S = (1)/(2)) form prepared by H(2)-reduction of Ni-A in H(2)(17)O, and also on Ni-A formed by reoxidation of Ni-C in H(2)(17)O. In the native state of the protein (Ni-A), the bridging ligand does not exchange with the H(2)(17)O solvent. However, after a reduction/reoxidation cycle (Ni-A --> Ni-C --> Ni-A), an (17)O label is introduced at the active site, as seen by ENDOR. Detailed analysis of a 2-D field-frequency plot of ENDOR spectra taken across the EPR envelope of Ni-A((17)O) shows that the incorporated (17)O has a roughly axial hyperfine tensor, A((17)O) approximately [5, 7, 20] MHz, discloses its orientation relative to the g tensor, and also yields an estimate of the quadrupole tensor. The substantial isotropic component (a(iso)((17)O) approximately 11 MHz) of the hyperfine interaction indicates that a solvent-derived (17)O is indeed a ligand to Ni and thus that the bridging ligand X in the Ni-A state of Dg Hase is indeed an oxygenic (O(2)(-) or OH(-)) species; comparison with earlier EPR results by others indicates that the same holds for Ni-B. The small (57)Fe hyperfine coupling seen previously for Ni-A (A((57)Fe) approximately 0.9 MHz) is now shown to persist in Ni-C, A((57)Fe) approximately 0.8 MHz. However, the (17)O signal is lost upon reductive activation to the Ni-C state; reoxidation to Ni-A leads to the reappearance of the signal. Consideration of the electronic structure of the EPR-active states of the dinuclear center leads us to suggest that the oxygenic bridge in Ni-A(B) is lost in Ni-C and is re-formed from solvent upon reoxidation to Ni-A. This implies that the reductive activation to Ni-C opens Ni/Fe coordination sites which may play a central role in the enzyme's activity.
The cycling between active and inactive states of the catalytic center of [NiFe]-hydrogenase from Allochromatium vinosum has been investigated by dynamic electrochemical techniques. Adsorbed on a rotating disk pyrolytic graphite "edge" electrode, the enzyme is highly electroactive: this allows precise manipulations of the complex redox chemistry and facilitates quantitative measurements of the interconversions between active catalytic states and the inactive oxidized form Ni(r) (also called Ni-B or "ready") as functions of pH, H(2) partial pressure, temperature, and electrode potential. Cyclic voltammograms for catalytic H(2) oxidation (current is directly related to turnover rate) are highly asymmetric (except at pH > 8 and high temperature) due to inactivation being much slower than activation. Controlled potential-step experiments show that the rate of oxidative inactivation increases at high pH but is independent of potential, whereas the rate of reductive activation increases as the potential becomes more negative. Indeed, at 45 degrees C, activation takes just a few seconds at -288 mV. The cyclic asymmetry arises because interconversion is a two-stage reaction, as expected if the reduced inactive Ni(r)-S state is an intermediate. The rate of inactivation depends on a chemical process (rearrangement and uptake of a ligand) that is independent of potential, but sensitive to pH, while activation is driven by an electron-transfer process, Ni(III) to Ni(II), that responds directly to the driving force. The potentials at which fast activation occurs under different conditions have been analyzed to yield the potential-pH dependence and the corresponding entropies and enthalpies. The reduced (active) enzyme shows a pK of 7.6; thus, when a one-electron process is assumed, reductive activation at pH < 7 involves a net uptake of one proton (or release of one hydroxide), whereas, at pH > 8, there is no net exchange of protons with solvent. Activation is favored by a large positive entropy, consistent with the release of a ligand and/or relaxation of the structure around the active site.
We have used protein film voltammetry to study the NiFe hydrogenase from Desulfovibrio fructosovorans. We show how measurements of transient activity following the addition in the electrochemical cell of H(2), CO, or O(2) allow simple and virtually instantaneous determinations of the Michaelis constant, inhibition constant, or rate of inactivation, respectively, thus opening new opportunities to study the active site of NiFe hydrogenases. The binding and release of CO occur within a fraction of a second, and we determine and discuss how its affinity for the active site changes as the driving force for the H(+)/H(2) reaction is continuously varied. Inactivation by O(2) is a slow, bimolecular process (with pH-independent rate constant approximately 3 x 10(4) s(-1) M(-1) at 40 degrees C, under one atm of H(2)) that leads to a mixture of fully oxidized states, and unlike the case of CO inhibition, the active site is not fully protected by H(2). This experimental approach could be used to study the reaction of other multicentered metalloenzymes with their gaseous substrates or inhibitors.
Protein film voltammetry is a powerful method for probing the chemistry of redox-active sites in metalloproteins. The technique affords precise potential control over a tiny quantity of material that is manipulated on an electrode surface, providing information on ligand- or metal-exchange reactions coupled to electron transfer. This is illustrated by examples of transformations of the iron-sulfur clusters in ferredoxins. Protein film voltammetry is particularly advantageous in studies of metalloenzymes for which the current response is proportional to catalytic activity: kinetic data of extremely high signal/noise ratio are obtained for highly active enzymes. We present a series of interesting examples in which catalytic activity varies in unusual ways with applied potential, surveying information that can be obtained from cyclic voltammetry and then looking beyond this method to controlled potential-step experiments that yield kinetic and mechanistic details. Recent results on the voltammetry of the highly active [NiFe]-hydrogenase from Allochromatium vinosum illustrate how it is possible to use the precise kinetic information from potential-step experiments to diagnose subtle details of transformations between catalytically active and inactive states of an enzyme. Protein film voltammetry thus complements spectroscopic techniques and other physical methods, revealing the chemistry of systems that might appear intractable or convoluted by other means.
Hydrogenases catalyze oxidoreduction of molecular hydrogen and have potential applications for utilizing dihydrogen as an energy source. [NiFe] hydrogenase has two different oxidized states, Ni-A (unready, exhibits a lag phase in reductive activation) and Ni-B (ready). We have succeeded in converting Ni-B to Ni-A with the use of Na2S and O2 and determining the high-resolution crystal structures of both states. Ni-B possesses a monatomic nonprotein bridging ligand at the Ni-Fe active site, whereas Ni-A has a diatomic species. The terminal atom of the bridging species of Ni-A occupies a similar position as C of the exogenous CO in the CO complex (inhibited state). The common features of the enzyme structures at the unready (Ni-A) and inhibited (CO complex) states are proposed. These findings provide useful information on the design of new systems of biomimetic dihydrogen production and fuel cell devices.
The catalytic center of the [NiFe] hydrogenase of Desulfovibrio vulgaris Miyazaki F in the oxidized states was investigated by electron paramagnetic resonance and electron-nuclear double resonance spectroscopy applied to single crystals of the enzyme. The experimental results were compared with density functional theory (DFT) calculations. For the Ni-B state, three hyperfine tensors could be determined. Two tensors have large isotropic hyperfine coupling constants and are assigned to the beta-CH2 protons of the Cys-549 that provides one of the bridging sulfur ligands between Ni and Fe in the active center. From a comparison of the orientation of the third hyperfine tensor with the tensor obtained from DFT calculations an OH- bridging ligand has been identified in the Ni-B state. For the Ni-A state broader signals were observed. The signals of the third proton, as observed for the "ready" state Ni-B, were not observed at the same spectral position for Ni-A, confirming a structural difference involving the bridging ligand in the "unready" state of the enzyme.
A new strategy is described for comparing, quantitatively, the ability of hydrogenases to tolerate exposure to O2 and anoxic oxidizing conditions. Using protein film voltammetry, the inherent sensitivities to these challenges (thermodynamic potentials and rates of reactions) have been measured for enzymes from a range of mesophilic microorganisms. In the absence of O2, all the hydrogenases undergo reversible inactivation at various potentials above that of the H+/H2 redox couple, and H2 oxidation activities are thus limited to characteristic "potential windows". Reactions with O2 vary greatly; the [FeFe]-hydrogenase from Desulfovibrio desulfuricans ATCC 7757, an anaerobe, is irreversibly damaged by O2, surviving only if exposed to O2 in the anaerobically oxidized state (which therefore affords protection). In contrast, the membrane-bound [NiFe]-hydrogenase from the aerobe, Ralstonia eutropha, reacts reversibly with O2 even during turnover and continues to catalyze H2 oxidation in the presence of O2.