Structure of the Ni Sites in Hydrogenases by X-ray Absorption Spectroscopy. Species Variation and the Effects of Redox Poise

Effect of Redox-Inactive Metal Ion-Nickel(III) Interactions on the Redox Properties and Proton-Coupled Electron Transfer Reactivity

Mononuclear nickel(II) and nickel(III) complexes of a bisamidate-bisalkoxide ligand, (NMe₄)₂[Ni^II(HMPAB)] (1) and (NMe₄)[Ni^III(HMPAB)] (2), respectively, have been synthesized and characterized by various spectroscopic techniques including X-ray crystallography. The reaction of redox-inactive metal ions (Mⁿ⁺ = Ca²⁺, Mg²⁺, Zn²⁺, Y³⁺, and Sc³⁺) with 2 resulted in 2-Mⁿ⁺ adducts, which was assessed by an array of spectroscopic techniques including X-ray absorption spectroscopy (XAS), electron paramagnetic resonance (EPR), and reactivity studies. The X-ray structure of Ca²⁺ coordinated to Ni(III) complexes, 2-Ca²⁺T, was determined and exhibited an average Ni-Ca distance of 3.1253 Å, close to the metal ions' covalent radius. XAS analysis of 2-Ca²⁺ and 2-Y³⁺ in solution further revealed an additional coordination to Ca and Y in the 2-Mⁿ⁺ adducts with shortened Ni-M distances of 2.15 and 2.11 Å, respectively, implying direct bonding interactions between Ni and Lewis acids (LAs). Such a short interatomic distance between Ni(III) and M is unprecedented and was not observed before. EPR analysis of 2 and 2-Mⁿ⁺ species, moreover, displayed rhombic signals with g_av > 2.12 for all complexes, supporting the +III oxidation state of Ni. The Ni^III/Ni^II redox potential of 2 and 2-Mⁿ⁺ species was determined, and a plot of E_1/2 of 2-Mⁿ⁺ versus pK_a of [M(H₂O)_n]^m+ exhibited a linear relationship, implying that the Ni^III/Ni^II potential of 2 can be tuned with different redox-inactive metal ions. Reactivity studies of 2 and 2-Mⁿ⁺ with different 4-X-2,6-ditert-butylphenol (4-X-DTBP) and other phenol derivatives were performed, and based on kinetic studies, we propose the involvement of a proton-coupled electron transfer (PCET) pathway. Analysis of the reaction products after the reaction of 2 with 4-OMe-DTBP showed the formation of a Ni(II) complex (1a) where one of the alkoxide arms of the ligand is protonated. A pK_a value of 24.2 was estimated for 1a. The reaction of 2-Mⁿ⁺ species was examined with 4-OMe-DTBP, and it was observed that the k₂ values of 2-Mⁿ⁺ species increase by increasing the Lewis acidity of redox-inactive metal ions. However, the obtained k₂ values for 2-Mⁿ⁺ species are much lower compared to the k₂ value for 2. Such a variation of PCET reactivity between 2 and 2-Mⁿ⁺ species may be attributed to the interactions between Ni(III) and LAs. Our findings show the significance of the secondary coordination sphere effect on the PCET reactivity of Ni(III) complexes and furnish important insights into the reaction mechanism involving high-valent nickel species, which are frequently invoked as key intermediates in Ni-mediated enzymatic reactions, solar-fuel catalysis, and biomimetic/synthetic transformation reactions.

Cyclic Heterometallic Interactions formed from a Flexible Tripeptide Complex Showing Effective Antiferromagnetic Spin Coupling

Developing tunable motifs for heterometallic interactions should be beneficial for fabricating functional materials based on cooperative electronic communications between metal centers. Reported here is the efficient formation of cyclic heterometallic interactions from a complex containing an artificial tripeptide with metal binding sites on its main chain and side chains. X-ray structural analysis and X-ray absorption spectroscopy revealed that the cyclic metal-metal arrangements arise from the amide groups connecting four square-planar Cu^II centers and four octahedral Ni^II centers in a cyclic manner. UV/Vis spectral studies suggested that this efficient formation was achieved by the selective formation of the square-planar Cu^II centers and a crystallization process. Magnetic measurements using SQUID clarified that the cyclic complex represented the S=2 spin state at low temperatures due to effective antiferromagnetic interactions between the Ni^II and Cu^II centers.

Redesign of a Copper Storage Protein into an Artificial Hydrogenase

We report the construction of an artificial hydrogenase (ArH) by reengineering a Cu storage protein (Cspl) into a Ni-binding protein (NBP) employing rational metalloprotein design. The hypothesis driven design approach involved deleting existing Cu sites of Csp1 and identification of a target tetrathiolate Ni binding site within the protein scaffold followed by repacking the hydrophobic core. Guided by modeling, the NBP was expressed and purified in high purity. NBP is a well-folded and stable construct displaying native-like unfolding behavior. Spectroscopic and computational studies indicated that the NBP bound nickel in a distorted square planar geometry that validated the design. Ni(II)-NBP is active for photo-induced H₂ evolution following a reductive quenching mechanism. Ni(II)-NBP catalyzed H⁺ reduction to H₂ gas electrochemically as well. Analysis of the catalytic voltammograms established a proton-coupled electron transfer (PCET) mechanism. Electrolysis studies confirmed H₂ evolution with quantitative Faradaic yields. Our studies demonstrate an important scope of rational metalloprotein design that allows imparting functions into protein scaffolds that have natively not evolved to possess the same function of the target metalloprotein constructs.

Hydrogenases

Hydrogenases catalyze the simple yet important interconversion between H₂ and protons and electrons. Found throughout prokaryotes, lower eukaryotes, and archaea, hydrogenases are used for a variety of redox and signaling purposes and are found in many different forms. This diverse group of metalloenzymes is divided into [NiFe], [FeFe], and [Fe] variants, based on the transition metal contents of their active sites. A wide array of biochemical and spectroscopic methods has been used to elucidate hydrogenases, and this along with a general description of the main enzyme types and catalytic mechanisms is discussed in this chapter.

In search of metal hydrides: an X-ray absorption and emission study of [NiFe] hydrogenase model complexes

Insight into the factors that favor metal–hydride interactions in NiFe-hydrogenase models is obtained through X-ray spectroscopic and quantum chemical studies.

Reversible active site sulfoxygenation can explain the oxygen tolerance of a NAD+-reducing [NiFe] hydrogenase and its unusual infrared spectroscopic properties

Oxygen-tolerant [NiFe] hydrogenases are metalloenzymes that represent valuable model systems for sustainable H2 oxidation and production. The soluble NAD(+)-reducing [NiFe] hydrogenase (SH) from Ralstonia eutropha couples the reversible cleavage of H2 with the reduction of NAD(+) and displays a unique O2 tolerance. Here we performed IR spectroscopic investigations on purified SH in various redox states in combination with density functional theory to provide structural insights into the catalytic [NiFe] center. These studies revealed a standard-like coordination of the active site with diatomic CO and cyanide ligands. The long-lasting discrepancy between spectroscopic data obtained in vitro and in vivo could be solved on the basis of reversible cysteine oxygenation in the fully oxidized state of the [NiFe] site. The data are consistent with a model in which the SH detoxifies O2 catalytically by means of an NADH-dependent (per)oxidase reaction involving the intermediary formation of stable cysteine sulfenates. The occurrence of two catalytic activities, hydrogen conversion and oxygen reduction, at the same cofactor may inspire the design of novel biomimetic catalysts performing H2-conversion even in the presence of O2.

Nickel L-edge and K-edge X-ray absorption spectroscopy of non-innocent Ni[S₂C₂(CF₃)₂]₂(n) series (n = -2, -1, 0): direct probe of nickel fractional oxidation state changes

A series of nickel dithiolene complexes Ni[S2C2(CF3)2]2(n) (n = -2, -1, 0) has been investigated using Ni L- and K-edge X-ray absorption spectroscopy (XAS). The L3 centroid shifts about 0.3 eV for a change of one unit in the formal oxidation state (or 0.3 eV per oxi), corresponding to ~33% of the shift for Ni oxides or fluorides (about 0.9 eV per oxi). The K-edge XAS edge position shifts about 0.7 eV per oxi, corresponding to ~38% of that for Ni oxides (1.85 eV per oxi). In addition, Ni L sum rule analysis found the Ni(3d) ionicity in the frontier orbitals being 50.5%, 44.0% and 38.5% respectively (for n = -2, -1, 0), in comparison with their formal oxidation states (of Ni(II), Ni(III), and Ni(IV)). For the first time, direct and quantitative measurement of the Ni fractional oxidation state changes becomes possible for Ni dithiolene complexes, illustrating the power of L-edge XAS and L sum rule analysis in such a study. The Ni L-edge and K-edge XAS can be used in a complementary manner to better assess the oxidation states for Ni.

Atomic partitioning of M-H2 bonds in [NiFe] hydrogenase--a test case of concurrent binding

The possibility of simultaneous addition of η(2)-H2 to both the metals (Ni and Fe) in the active site of the as isolated state of the enzyme (Ni-SI) is examined here by an atom-by-atom electronic energy partitioning based on the QTAIM method. Results show that the 4LS state prefers H2 removal than addition. Destabilization of the atomic basins of the thiolate bridges and decrease of the electrophilicity of the Fe and Ni, resulting in poor back donation to the CO ligand, are the bottlenecks that hamper dihydrogen activation simultaneously. The study helps to understand why such states are seldom accessed in the activation of dihydrogen. Moreover, Ni has been found to be the natural choice for the dihydrogen binding.

Synchrotron ultrafast techniques for photoactive transition metal complexes

In the last decade, the use of time-resolved X-ray techniques has revealed the structure of light-generated transient species for a wide range of samples, from small organic molecules to proteins. Time resolutions of the order of 100 ps are typically reached, allowing one to monitor thermally equilibrated excited states and capture their structure as a function of time. This review aims at providing a general overview of the application of time-resolved X-ray solution scattering (TR-XSS) and time-resolved X-ray absorption spectroscopy (TR-XAS), the two techniques prevalently employed in the investigation of light-triggered structural changes of transition metal complexes. In particular, we herein describe the fundamental physical principles for static XSS and XAS and illustrate the theory of time-resolved XSS and XAS together with data acquisition and analysis strategies. Selected pioneering examples of photoactive transition metal complexes studied by TR-XSS and TR-XAS are discussed in depth.

[NiFe] hydrogenases: a common active site for hydrogen metabolism under diverse conditions

Hydrogenase proteins catalyze the reversible conversion of molecular hydrogen to protons and electrons. The most abundant hydrogenases contain a [NiFe] active site; these proteins are generally biased towards hydrogen oxidation activity and are reversibly inhibited by oxygen. However, there are [NiFe] hydrogenase that exhibit unique properties, including aerobic hydrogen oxidation and preferential hydrogen production activity; these proteins are highly relevant in the context of biotechnological devices. This review describes four classes of these "nonstandard" [NiFe] hydrogenases and discusses the electrochemical, spectroscopic, and structural studies that have been used to understand the mechanisms behind this exceptional behavior. A revised classification protocol is suggested in the conclusions, particularly with respect to the term "oxygen-tolerance". This article is part of a special issue entitled: metals in bioenergetics and biomimetics systems.

NAD(H)-coupled hydrogen cycling - structure-function relationships of bidirectional [NiFe] hydrogenases

Hydrogenases catalyze the activation or production of molecular hydrogen. Due to their potential importance for future biotechnological applications, these enzymes have been in the focus of intense research for the past decades. Bidirectional [NiFe] hydrogenases are of particular interest as they couple the reversible cleavage of hydrogen to the redox conversion of NAD(H). In this account, we review the current state of knowledge about mechanistic aspects and structural determinants of these complex multi-cofactor enzymes. Special emphasis is laid on the oxygen-tolerant NAD(H)-linked bidirectional [NiFe] hydrogenase from Ralstonia eutropha.

Dipeptide-based models of nickel superoxide dismutase: solvent effects highlight a critical role to Ni-S bonding and active site stabilization

Nickel superoxide dismutase (Ni-SOD) catalyzes the disproportionation of the superoxide radical to O(2) and H(2)O(2) utilizing the Ni(III/II) redox couple. The Ni center in Ni-SOD resides in an unusual coordination environment that is distinct from other SODs. In the reduced state (Ni-SOD(red)), Ni(II) is ligated to a primary amine-N from His1, anionic carboxamido-N/thiolato-S from Cys2, and a second thiolato-S from Cys6 to complete a NiN(2)S(2) square-planar coordination motif. Utilizing the dipeptide N(2)S(2-) ligand, H(2)N-Gly-l-Cys-OMe (GC-OMeH(2)), an accurate model of the structural and electronic contributions provided by His1 and Cys2 in Ni-SOD(red), we constructed the dinuclear sulfur-bridged metallosynthon, [Ni(2)(GC-OMe)(2)] (1). From 1 we prepared the following monomeric Ni(II)-N(2)S(2) complexes: K[Ni(GC-OMe)(SC(6)H(4)-p-Cl)] (2), K[Ni(GC-OMe)(S(t)Bu)] (3), K[Ni(GC-OMe)(SC(6)H(4)-p-OMe)] (4), and K[Ni(GC-OMe)(SNAc)] (5). The design strategy in utilizing GC-OMe(2-) is analogous to one which we reported before (see Inorg. Chem. 2009, 48, 5620 and Inorg. Chem. 2010, 49, 7080) where Ni-SOD(red) active site mimics can be assembled at will with electronically variant RS(-) ligands. Discussed herein is our initial account pertaining to the aqueous behavior of isolable, small-molecule Ni-SOD model complexes (non-maquette based). Spectroscopic (FTIR, UV-vis, ESI-MS, XAS) and electrochemical (CV) measurements suggest that 2-5 successfully simulate many of the electronic features of Ni-SOD(red). Furthermore, the aqueous studies reveal a dynamic behavior with regard to RS(-) lability and bridging interactions, suggesting a stabilizing role brought about by the protein architecture.

Structural models of the manganese complex of photosystem II and mechanistic implications

Photosynthetic water oxidation and O₂ formation are catalyzed by a Mn₄Ca complex bound to the proteins of photosystem II (PSII). The catalytic site, including the inorganic Mn₄CaO(n)H(x) core and its protein environment, is denoted as oxygen-evolving complex (OEC). Earlier and recent progress in the endeavor to elucidate the structure of the OEC is reviewed, with focus on recent results obtained by (i) X−ray spectroscopy (specifically by EXAFS analyses), and (ii) X-ray diffraction (XRD, protein crystallography). Very recently, an impressive resolution of 1.9Å has been achieved by XRD. Most likely however, all XRD data on the Mn₄CaO(n)H(x) core of the OEC are affected by X-ray induced modifications (radiation damage). Therefore and to address (important) details of the geometric and electronic structure of the OEC, a combined analysis of XRD and XAS data has been approached by several research groups. These efforts are reviewed and extended using an especially comprehensive approach. Taking into account XRD results on the protein environment of the inorganic core of the Mn complex, 12 alternative OEC models are considered and evaluated by quantitative comparison to (i) extended-range EXAFS data, (ii) polarized EXAFS of partially oriented PSII membrane particles, and (iii) polarized EXAFS of PSII crystals. We conclude that there is a class of OEC models that is in good agreement with both the recent crystallographic models and the XAS data. On these grounds, mechanistic implications for the O−O bond formation chemistry are discussed. This article is part of a Special Issue entitled: Photosystem II.

The crystal structure of the [NiFe] hydrogenase from the photosynthetic bacterium Allochromatium vinosum: characterization of the oxidized enzyme (Ni-A state)

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.

Intermediates in the catalytic cycle of [NiFe] hydrogenase: functional spectroscopy of the active site

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.

Introduction of methionines in the gas channel makes [NiFe] hydrogenase aero-tolerant

Hydrogenases catalyze the conversion between 2H(+) + 2e(-) and H(2)(1). Most of these enzymes are inhibited by O(2), which represents a major drawback for their use in biotechnological applications. Improving hydrogenase O(2) tolerance is therefore a major contemporary challenge to allow the implementation of a sustainable hydrogen economy. We succeeded in improving O(2) tolerance, which we define here as the ability of the enzyme to resist for several minutes to O(2) exposure, by substituting with methionines small hydrophobic residues strongly conserved in the gas channel. Remarkably, the mutated enzymes remained active in the presence of an O(2) concentration close to that found in aerobic solutions in equilibrium with air, while the wild type enzyme is inhibited in a few seconds. Crystallographic and spectroscopic studies showed that the structure and the chemistry at the active site are not affected by the mutations. Kinetic studies demonstrated that the inactivation is slower and reactivation faster in these mutants. We propose that in addition to restricting O(2) diffusion to the active site of the enzyme, methionine may also interact with bound peroxide and provide an assisted escape route for H(2)O(2) toward the gas channel. These results show for the first time that it is possible to improve O(2)-tolerance of [NiFe] hydrogenases, making possible the development of biohydrogen production systems.

Mononuclear nickel(III) complexes [Ni(III)(OR)(P(C6H3-3-SiMe3-2-S)3)](-) (R = Me, Ph) containing the terminal alkoxide ligand: relevance to the nickel site of oxidized-form [NiFe] hydrogenases

The unprecedented nickel(III) thiolate [Ni (III)(OR)(P(C 6H 3-3-SiMe 3-2-S) 3)] (-) [R = Ph ( 1), Me ( 3)] containing the terminal Ni (III)-OR bond, characterized by UV-vis, electron paramagnetic resonance, cyclic voltammetry, and single-crystal X-ray diffraction, were isolated from the reaction of [Ni (III)(Cl)(P(C 6H 3-3-SiMe 3-2-S) 3)] (-) with 3 equiv of [Na][OPh] in tetrahydrofuran (THF)-CH 3CN and the reaction of complex 1 with 1 equiv of [Bu 4N][OMe] in THF-CH 3OH, respectively. Interestingly, the addition of complex 1 into the THF-CH 3OH solution of [Me 4N][OH] also yielded complex 3. In contrast to the inertness of complex [Ni (III)(Cl)(P(C 6H 3-3-SiMe 3-2-S) 3)] (-) toward 1 equiv of [Na][OPh], the addition of 1 equiv of [Na][OMe] into a THF-CH 3CN solution of [Ni (III)(Cl)(P(C 6H 3-3-SiMe 3-2-S) 3)] (-) yielded the known [Ni (III)(CH 2CN)(P(C 6H 3-3-SiMe 3-2-S) 3)] (-) ( 4). At 77 K, complexes 1 and 3 exhibit a rhombic signal with g values of 2.31, 2.09, and 2.00 and of 2.28, 2.04, and 2.00, respectively, the characteristic g values of the known trigonal-bipyramidal Ni (III) [Ni (III)(L)(P(C 6H 3-3-SiMe 3-2-S) 3)] (-) (L = SePh, SEt, Cl) complexes. Compared to complexes [Ni (III)(EPh)(P(C 6H 3-3-SiMe 3-2-S) 3)] (-) [E = S ( 2), Se] dominated by one intense absorption band at 592 and 590 nm, respectively, the electronic spectrum of complex 1 coordinated by the less electron-donating phenoxide ligand displays a red shift to 603 nm. In a comparison of the Ni (III)-OMe bond length of 1.885(2) A found in complex 3, the longer Ni (III)-OPh bond distance of 1.910(3) A found in complex 1 may be attributed to the absence of sigma and pi donation from the [OPh]-coordinated ligand to the Ni (III) center.

Proton pathways in a [NiFe]-hydrogenase: A theoretical study

We present here a theoretical study to investigate possible proton pathways in the [NiFe]-hydrogenase from Desulfovibrio gigas. The approach used in this study consists of a combination of Poisson-Boltzmann and Monte Carlo simulations together with a distance-based network analysis to find possible groups involved in the proton transfer. Results obtained at different pH values show a reasonable number of proton active residues distributed by the protein interior and surface, with a concentration around the metal centres. The electrostatic interactions in this protein are strong, as shown by the unusual shape of the titration curves of several sites. Some residue pairs show strongly correlated protonations, indicating the sharing and probably exchange of a proton between them. The conjugation of the PB and MC simulations with the distance-based analysis allows a detailed characterization of the possible proton pathways. We discuss previous suggestions and propose a new complete pathway for the proton transfer between the active site and the surface. This pathway is mainly composed of histidines and glutamic acid residues.

A Dinuclear Ni( -H)Ru Complex Derived from H2

Models of the active site in [NiFe]hydrogenase enzymes have proven challenging to prepare. We isolated a paramagnetic dinuclear nickel-ruthenium complex with a bridging hydrido ligand from the heterolytic cleavage of H2 by a dinuclear NiRu aqua complex in water under ambient conditions (20 degrees C and 1 atmosphere pressure). The structure of the hexacoordinate Ni(mu-H)Ru complex was unequivocally determined by neutron diffraction analysis, and it comes closest to an effective analog for the core structure of the proposed active form of the enzyme.

Characterization of a HoxEFUYH type of [NiFe] hydrogenase from Allochromatium vinosum and some EPR and IR properties of the hydrogenase module

A soluble hydrogenase from Allochromatium vinosum was purified. It consisted of a large (M (r) = 52 kDa) and a small (M (r) = 23 kDa) subunit. The genes encoding for both subunits were identified. They belong to an open reading frame where they are preceded by three more genes. A DNA fragment containing all five genes was cloned and sequenced. The deduced amino acid sequences of the products characterized the complex as a member of the HoxEFUYH type of [NiFe] hydrogenases. Detailed sequence analyses revealed binding sites for eight Fe-S clusters, three [2Fe-2S] clusters and five [4Fe-4S] clusters, six of which are also present in homologous subunits of [FeFe] hydrogenases and NADH:ubiquione oxidoreductases (complex I). This makes the HoxEFUYH type of hydrogenases the one that is evolutionary closest to complex I. The relative positions of six of the potential Fe-S clusters are predicted on the basis of the X-ray structures of the Clostridium pasteurianum [FeFe] hydrogenase I and the hydrophilic domain of complex I from Thermus thermophilus. Although the HoxF subunit contains binding sites for flavin mononucleotide and NAD(H), cell-free extracts of A. vinosum did not catalyse a H(2)-dependent reduction of NAD(+). Only the hydrogenase module (HoxYH) could be purified. Its electron paramagnetic resonance (EPR) and IR spectral properties showed the presence of a Ni-Fe active site and a [4Fe-4S] cluster. Its activity was sensitive to carbon monoxide. No EPR signals from a light-sensitive Ni(a)-C* state could be observed. This study presents the first IR spectroscopic data on the HoxYH module of a HoxEFUYH type of [NiFe] hydrogenase.

Pathways of H2 toward the active site of [NiFe]-hydrogenase

Hydrogenases catalyze the reversible oxidation of molecular hydrogen (H(2)), but little is known about the diffusion of H(2) toward the active site. Here we analyze pathways for H(2) permeation using molecular dynamics (MD) simulations in explicit solvent. Various MD simulation replicates were done, to improve the sampling of the system states. H(2) easily permeates hydrogenase in every simulation and it moves preferentially in channels. All H(2) molecules that reach the active site made their approach from the side of the Ni ion. H(2) is able to reach distances of <4 A from the active site, although after 6 A permeation is difficult. In this region we mutated Val-67 into alanine and perform new MD simulations. These simulations show an increase of H(2) inside the protein and at lower distances from the active site. This valine can be a control point in the H(2) access to the active center.

Density functional study of the catalytic cycle of nickel–iron [NiFe] hydrogenases and the involvement of high-spin nickel(II)

In light of recent experiments suggesting high-spin (HS) Ni(II) species in the catalytic cycle of [NiFe] hydrogenase, a series of models of the Ni(II) forms Ni-SI(I,II), SI-CO and Ni-R(I,II,III) were examined in their high-spin states via density functional calculations. Because of its importance in the catalytic cycle, the Ni-C form was also included in this study. Unlike the Ni(II) forms in previous studies, in which a low-spin (LS) state was assumed and a square-planar structure found, the optimized geometries of these HS Ni(II) forms resemble those observed in the crystal structures: a distorted tetrahedral to distorted pyramidal coordination for the NiS4. This resemblance is particularly significant because the LS state is 20-30 kcal/mol less stable than the HS state for the geometry of the crystal structure. If these Ni(II) forms in the enzyme are not high spin, a large change in geometry at the active site is required during the catalytic cycle. Furthermore, only the HS state for the CO-inhibited form SI-CO has CO stretching frequencies that match the experimental results. As in the previous work, these new results show that the heterolytic cleavage reaction of dihydrogen (where H2 is cleaved with the metal acting as a hydride acceptor and a cysteine as the proton acceptor) has a lower energy barrier and is more exothermic when the active site is oxidized to Ni(III). The enzyme models described here are supported by a calibrated correlation of the calculated and measured CO stretching frequencies of the forms of the enzyme. The correlation coefficient for the final set of models of the forms of [NiFe] hydrogenase is 0.8.

An improved purification procedure for the soluble [NiFe]-hydrogenase of Ralstonia eutropha: new insights into its (in)stability and spectroscopic properties

Infrared (IR) spectra in combination with chemical analyses have recently shown that the active Ni-Fe site of the soluble NAD(+)-reducing [NiFe]-hydrogenase from Ralstonia eutropha contains four cyanide groups and one carbon monoxide as ligands. Experiments presented here confirm this result, but show that a variable percentage of enzyme molecules loses one or two of the cyanide ligands from the active site during routine purification. For this reason the redox conditions during the purification have been optimized yielding hexameric enzyme preparations (HoxFUYHI(2)) with aerobic specific H(2)-NAD(+) activities of 150-185 mumol/min/mg of protein (up to 200% of the highest activity previously reported in the literature). The preparations were highly homogeneous in terms of the active site composition and showed superior IR spectra. IR spectro-electrochemical studies were consistent with the hypothesis that only reoxidation of the reduced enzyme with dioxygen leads to the inactive state, where it is believed that a peroxide group is bound to nickel. Electron paramagnetic resonance experiments showed that the radical signal from the NADH-reduced enzyme derives from the semiquinone form of the flavin (FMN-a) in the hydrogenase module (HoxYH dimer), but not of the flavin (FMN-b) in the NADH-dehydrogenase module (HoxFU dimer). It is further demonstrated that the hexameric enzyme remains active in the presence of NADPH and air, whereas NADH and air lead to rapid destruction of enzyme activity. It is proposed that the presence of NADPH in cells keeps the enzyme in the active state.

Structural differences between the ready and unready oxidized states of [NiFe] hydrogenases

[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.

A theoretical study of spin states in Ni-S4 complexes and models of the [NiFe] hydrogenase active site

We have applied density functional theory, using both pure (BP86) and hybrid (B3LYP and B3LYP*) functionals, to investigate structural parameters and reaction energies for nickel(II)-sulfur coordination compounds, as well as for small cluster models of the Ni-SI and Ni-R redox state of [NiFe] hydrogenases. Results obtained investigating experimentally well-characterized complexes show that BP86 is well suited to describe the structural features of this class of compounds. However, the singlet-triplet energy splitting and even the computed ground state are strongly dependent on the applied functional. Results for the cluster models of [NiFe] hydrogenases lead to the conclusion that in the reduced protein structures characterized by X-ray diffraction a hydride bridges the two metal centres. The energy splitting of the singlet and triplet states in Ni-R and Ni-SI models is calculated to be very small and may be overcome at room temperature to allow a spin crossover. Moreover, the relative stability of the Ni-SI and Ni-R structures adopted in the present investigation is fully compatible with their involvement in the reversible heterolytic cleavage of H(2).

The auxiliary protein HypX provides oxygen tolerance to the soluble [NiFe]-hydrogenase of ralstonia eutropha H16 by way of a cyanide ligand to nickel

The hypX gene of the facultative lithoautotrophic bacterium Ralstonia eutropha is part of a cassette of accessory genes (the hyp cluster) required for the proper assembly of the active site of the [NiFe]-hydrogenases in the bacterium. A deletion of the hypX gene led to a severe growth retardation under lithoautotrophic conditions with 5 or 15% oxygen, when the growth was dependent on the activity of the soluble NAD+ -reducing hydrogenase. The enzymatic and infrared spectral properties of the soluble hydrogenase purified from a HypX-negative strain were compared with those from an enzyme purified from a HypX-positive strain. In activity assays under anaerobic conditions both enzyme preparations behaved the same. Under aerobic conditions, however, the mutant enzyme became irreversibly inactivated during H2 oxidation with NAD+ or benzyl viologen as the electron acceptor. Infrared spectra and chemical determination of cyanide showed that one of the four cyanide groups in the wild-type enzyme was missing in the mutant enzyme. The data are consistent with the proposal that the HypX protein is specifically involved in the biosynthetic pathway that delivers the nickel-bound cyanide. The data support the proposal that this cyanide is crucial for the enzyme to function under aerobic conditions.

A Stable Monomeric Nickel Borohydride

A stable discrete nickel borohydride complex (Tp*NiBH(4) or Tp*NiBD(4)) was prepared using the nitrogen-donor ligand hydrotris(3,5-dimethylpyrazolyl)borate (Tp*-). This complex represents one of the best characterized nickel(II) borohydrides to date. Tp*NiBH(4) and Tp*NiBD(4) are stable toward air, boiling water, and high temperatures (mp > 230 degrees C dec). X-ray crystallographic measurements for Tp*NiBH(4) showed a six-coordinate geometry for the complex, with the nickel(II) center facially coordinated by three bridging hydrogen atoms from borohydride and a tridentate Tp(-) ligand. For Tp*NiBH(4), the empirical formula is C(15)H(26)B(2)N(6)Ni, a = 13.469(9) A, b = 7.740(1) A, c = 18.851(2) A, beta = 107.605(9) degrees, the space group is monoclinic P2(1)/c, and Z = 4. Infrared measurements confirmed the presence of bridging hydrogen atoms; both nu(B[bond]H)(terminal) and nu(B[bond]H)(bridging) are assignable and shifted relative to nu(B-D) of Tp*NiBD(4) by amounts in agreement with theory. Despite their hydrolytic stability, Tp*NiBH(4) and Tp*NiBD(4) readily reduce halocarbon substrates, leading to the complete series of Tp*NiX complexes (X = Cl, Br, I). These reactions showed a pronounced hydrogen/deuterium rate dependence (k(H)/k(D) approximately 3) and sharp isosbestic points in progressive electronic spectra. Nickel K-edge X-ray absorption spectroscopy (XAS) measurements of a hydride-rich nickel center were obtained for Tp*NiBH(4), Tp*NiBD(4), and Tp*NiCl. X-ray absorption near-edge spectroscopy results confirmed the similar six-coordinate geometries for Tp*NiBH(4) and Tp*NiBD(4). These contrasted with XAS results for the crystallographically characterized pseudotetrahedral Tp*NiCl complex. The stability of Tp*Ni-coordinated borohydride is significant given this ion's accelerated decomposition and hydrolysis in the presence of transition metals and simple metal salts.

Refinement of the nickel site structure in Desulfovibrio gigas hydrogenase using range-extended EXAFS spectroscopy

We have reexamined the Ni EXAFS of oxidized, inactive (as-isolated) and H(2) reduced Desulfovibrio gigas hydrogenase. Better spatial resolution was achieved by analyzing the data over a 50% wider k-range than was previously available. A lower k(min) was obtained using the FEFF code for phase shifts and amplitudes. A higher k(max) was obtained by removing an interfering Cu signal from the raw spectra using multiple energy fluorescence detection. The larger k-range allowed us to better resolve the Ni-S bond lengths and to define more accurately the Ni-O and Ni-Fe bond lengths. We find that as-isolated, hydrogenase has two Ni-S bonds at approximately 2.2 A, but also 1-2 Ni-S bonds in the 2.35+/-0.05 A range. A Ni-O interaction is evident at 1.91 A. The as-isolated Ni-Fe distance cannot be unambiguously determined. Upon H(2) reduction, two short Ni-S bonds persist at approximately 2.2 A, but the remaining Ni-S bonds lengthen to 2.47+/-0.05 A. Good simulations are obtained with a Ni-Fe distance at 2.52 A, in agreement with crystal structures of the reduced enzyme. Although not evident in the crystal structures, an improvement in the fit is obtained by inclusion of one Ni-O interaction at 2.03 A. Implications of these distances for the spin-state of H(2) reduced H(2)ase are discussed.

Six-coordinate and five-coordinate Fe(II)(CN)(2)(CO)(x) thiolate complexes (x = 1, 2): synthetic advances for iron sites of [NiFe] hydrogenases

The dicyanodicarbonyliron(II) thiolate complexes trans,cis-[(CN)(2)(CO)(2)Fe(S,S-C-R)](-) (R = OEt (2), N(Et)(2) (3)) were prepared by the reaction of [Na][S-C(S)-R] and [Fe(CN)(2)(CO)(3)(Br)](-) (1). Complex 1 was obtained from oxidative addition of cyanogen bromide to [Fe(CN)(CO)(4)](-). In a similar fashion, reaction of complex 1 with [Na][S,O-C(5)H(4)N], and [Na][S,N-C(5)H(4)] produced the six-coordinate trans,cis-[(CN)(2)(CO)(2)Fe(S,O-C(5)H(4)N)](-) (6) and trans,cis-[(CN)(2)(CO)(2)Fe(S,N-C(5)H(4))](-) (7) individually. Photolysis of tetrahydrofuran (THF) solution of complexes 2, 3, and 7 under CO led to formation of the coordinatively unsaturated iron(II) dicyanocarbonyl thiolate compounds [(CN)(2)(CO)Fe(S,S-C-R)](-) (R = OEt (4), N(Et)(2) (5)) and [(CN)(2)(CO)Fe(S,N-C(5)H(4))](-) (8), respectively. The IR v(CN) stretching frequencies and patterns of complexes 4, 5, and 8 have unambiguously identified two CN(-) ligands occupying cis positions. In addition, density functional theory calculations suggest that the architecture of five-coordinate complexes 4, 5, and 8 with a vacant site trans to the CO ligand and two CN(-) ligands occupying cis positions serves as a conformational preference. Complexes 2, 3, and 7 were reobtained when the THF solution of complexes 4, 5, and 8 were exposed to CO atmosphere at 25 degrees C individually. Obviously, CO ligand can be reversibly bound to the Fe(II) site in these model compounds. Isotopic shift experiments demonstrated the lability of carbonyl ligands of complexes 2, 3, 4, 5, 7, and 8. Complexes [(CN)(2)(CO)Fe(S,S-C-R)](-) and NiA/NiC states [NiFe] hydrogenases from D. gigas exhibit a similar one-band pattern in the v(CO) region and two-band pattern in the v(CN) region individually, but in different positions, which may be accounted for by the distinct electronic effects between [S,S-C-R](-) and cysteine ligands. Also, the facile formations of five-coordinate complexes 4, 5, and 8 imply that the strong sigma-donor, weak pi-acceptor CN(-) ligands play a key role in creating/stabilizing five-coordinate iron(II) [(CN)(2)(CO)Fe(S,S-C-R)](-) complexes with a vacant coordination site trans to the CO ligand.

High-spin Ni(II), a surprisingly good structural model for [NiFe] hydrogenase

The first density functional calculations on high-spin (HS) Ni(II) models for the active site of the [NiFe] hydrogenases predict a ligand arrangement about Ni that is in better agreement with the crystal structures than previous predictions for low-spin (LS) Ni(II) models. With the crystal structures' geometry, the HS form is approximately 20 kcal/mol lower in energy than the LS one.