A single-crystal ENDOR and density functional theory study of the oxidized states of the [NiFe] hydrogenase from Desulfovibrio vulgaris Miyazaki F

Membrane-bound hydrogenase I from the hyperthermophilic bacterium Aquifex aeolicus: enzyme activation, redox intermediates and oxygen tolerance

The membrane-bound hydrogenase (Hase I) of the hyperthermophilic bacterium Aquifex aeolicus belongs to an intriguing class of redox enzymes that show enhanced thermostability and oxygen tolerance. Protein film electrochemistry is employed here to portray the interaction of Hase I with molecular oxygen and obtain an overall picture of the catalytic activity. Fourier transform infrared (FTIR) spectroscopy integrated with in situ electrochemistry is used to identify structural details of the [NiFe] site and the intermediate states involved in its redox chemistry. We found that the active site coordination is similar to that of standard hydrogenases, with a conserved Fe(CN)(2)CO moiety. However, only four catalytic intermediates could be detected; these correspond structurally to the Ni-B, Ni-SI(a), Ni-C, and Ni-R states of standard hydrogenases. The Ni-SI/Ni-C and Ni-C/Ni-R midpoint potentials are approximately 100 mV more positive than those observed in mesophilic hydrogenases, which may be the reason that A. aeolicus Hase I is more suitable as a catalyst for H(2) oxidation than production. Protein film electrochemistry shows that oxygen inhibits the enzyme by reacting at the active site to form a single species (Ni-B); the same inactive state is obtained under oxidizing, anaerobic conditions. The mechanism of anaerobic inactivation and reactivation in A. aeolicus Hase I is similar to that in standard hydrogenases. However, the reactivation of the former is more than 2 orders of magnitude faster despite the fact that reduction of Ni-B is not thermodynamically more favorable. A scheme for the enzymatic mechanism of A. aeolicus Hase I is presented, and the results are discussed in relation to the proposed models of oxygen tolerance.

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.

How Escherichia coli is equipped to oxidize hydrogen under different redox conditions

The enterobacterium Escherichia coli synthesizes two H(2) uptake enzymes, Hyd-1 and Hyd-2. We show using precise electrochemical kinetic measurements that the properties of Hyd-1 and Hyd-2 contrast strikingly, and may be individually optimized to function under distinct environmental conditions. Hyd-2 is well suited for fast and efficient catalysis in more reducing environments, to the extent that in vitro it behaves as a bidirectional hydrogenase. In contrast, Hyd-1 is active for H(2) oxidation under more oxidizing conditions and cannot function in reverse. Importantly, Hyd-1 is O(2) tolerant and can oxidize H(2) in the presence of air, whereas Hyd-2 is ineffective for H(2) oxidation under aerobic conditions. The results have direct relevance for physiological roles of Hyd-1 and Hyd-2, which are expressed in different phases of growth. The properties that we report suggest distinct technological applications of these contrasting enzymes.

Interaction of radical pairs through-bond and through-space: scope and limitations of the point-dipole approximation in electron paramagnetic resonance spectroscopy

The validity of the popular point-dipole approximation for interpretation of the zero-field splitting (ZFS) parameter (D-value) in EPR spectroscopy is studied. This approximation is of central importance for the determination of distances by analysis of EPR data. In this work, a detailed experimental (EPR spectroscopy and X-ray crystallography) and theoretical study for a model system (2,2',5,5'-tetra(tert-butyl)-4,4'-bis(ethoxy-carbonyl)-3,3'-bipyrrolyl-1,1'-dioxyl) was performed to understand the scope and limitations of the point-dipole model in EPR spectroscopy. For this diradical, the radical-radical distance derived with the point-dipole approximation deviates significantly (by approximately 40%) from the results derived from the X-ray analysis. Explicit quantum chemical calculation of the D-value on the basis of B3LYP density functional calculations leads to excellent quantitative agreement with the measured D-value. The quantitative accuracy of the employed methodology was confirmed for two additional systems that have previously been experimentally characterized. We therefore analyzed the contributions to the D-value of the target system in detail. This analysis leads to insight into the reasons for the failure of the point-dipole approximation. The analysis was then extended to an in silico study of five classes of model systems. Linkers of varying length and bond saturation were introduced between the radical-carrying groups. This allows for the analysis of the distance dependence of the D-parameter as well as the through-bond and through-space spin-spin interaction. From these results we established the limitations of the point-dipole approximation. The results of this analysis demonstrate that even very modest amounts of spin delocalization can cause significant deviations from pure point-dipole behavior and consequently cause the EPR derived distances to deviate from the N-O midpoint distance by up to several angstroms. If unsaturated linkers are used, the distance dependence of D does not follow the inverse cubic behavior predicted by the point-dipole model. However, for commonly used nonaromatic nitroxide rings connected by a saturated linker, the point-dipole approximation works well. Among the various point-dipole variants tested in this work for delocalized spins, the most successful one is based on distributed point-dipoles with spin populations derived from quantum chemical calculations. The distance dependence of the isotropic Heisenberg exchange parameter J has also been studied theoretically. The decay was found to be monoexponential with a decay constant of approximately 1 A(-1). Thus at linker lengths between 6-8 carbon atoms between a nitroxide radical pair, a switch from the strong to the weak exchange limit is predicted.

Probing intermediates in the activation cycle of [NiFe] hydrogenase by infrared spectroscopy: the Ni-SIr state and its light sensitivity

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-SI_r, provides the link between fully oxidized (Ni-A, Ni-B) and active (Ni-SI_a, Ni-C and Ni-R) forms of hydrogenase. In this work Ni-SI_r 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-SI_r 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-SI_r 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.

Spectroscopic insights into the oxygen-tolerant membrane-associated [NiFe] hydrogenase of Ralstonia eutropha H16

This study provides the first spectroscopic characterization of the membrane-bound oxygen-tolerant [NiFe] hydrogenase (MBH) from Ralstonia eutropha H16 in its natural environment, the cytoplasmic membrane. The H2-converting MBH is composed of a large subunit, harboring the [NiFe] active site, and a small subunit, capable in coordinating one [3Fe4S] and two [4Fe4S] clusters. The hydrogenase dimer is electronically connected to a membrane-integral cytochrome b. EPR and Fourier transform infrared spectroscopy revealed a strong similarity of the MBH active site with known [NiFe] centers from strictly anaerobic hydrogenases. Most redox states characteristic for anaerobic [NiFe] hydrogenases were identified except for one remarkable difference. The formation of the oxygen-inhibited Niu-A state was never observed. Furthermore, EPR data showed the presence of an additional paramagnetic center at high redox potential (+290 mV), which couples magnetically to the [3Fe4S] center and indicates a structural and/or redox modification at or near the proximal [4Fe4S] cluster. Additionally, significant differences regarding the magnetic coupling between the Nia-C state and [4Fe4S] clusters were observed in the reduced form of the MBH. The spectroscopic properties are discussed with regard to the unusual oxygen tolerance of this hydrogenase and in comparison with those of the solubilized, dimeric form of the MBH.

Thiolate-bridged dinuclear iron(tris-carbonyl)-nickel complexes relevant to the active site of [NiFe] hydrogenase

The reaction of NiBr(2)(EtOH)(4) with a 1:2-3 mixture of FeBr(2)(CO)(4) and Na(SPh) generated a linear trinuclear Fe-Ni-Fe cluster (CO)(3)Fe(mu-SPh)(3)Ni(mu-SPh)(3)Fe(CO)(3), 1, whereas the analogous reaction system FeBr(2)(CO)(4)/Na(S(t)Bu)/NiBr(2)(EtOH)(4) (1:2-3:1) gave rise to a linear tetranuclear Fe-Ni-Ni-Fe cluster [(CO)(3)Fe(mu-S(t)Bu)(3)Ni(mu-Br)](2), 2. By using this tetranuclear cluster 2 as the precursor, we have developed a new synthetic route to a series of thiolate-bridged dinuclear Fe(CO)(3)-Ni complexes, the structures of which mimic [NiFe] hydrogenase active sites. The reactions of 2 with SC(NMe(2))(2) (tmtu), Na{S(CH(2))(2)SMe} and ortho-NaS(C(6)H(4))SR (R = Me, (t)Bu) led to isolation of (CO)(3)Fe(mu-S(t)Bu)(3)NiBr(tmtu), 3, (CO)(3)Fe(S(t)Bu)(mu-S(t)Bu)(2)Ni{S(CH(2))(2)SMe}, 4, and (CO)(3)Fe(S(t)Bu)(mu-S(t)Bu)(2)Ni{S(C(6)H(4))SR}, 5a (R = Me) and 5b (R = (t)Bu), respectively. On the other hand, treatment of 2 with 2-methylthio-phenolate (ortho-O(C(6)H(4))SMe) in methanol resulted in (CO)(3)Fe(mu-S(t)Bu)(3)Ni(MeOH){O(C(6)H(4))SMe}, 6a. The methanol molecule bound to Ni is labile and is readily released under reduced pressure to afford (CO)(3)Fe(S(t)Bu)(mu-S(t)Bu)(2)Ni{O(C(6)H(4))SMe}, 6b, and the coordination geometry of nickel changes from octahedral to square planar. Likewise, the reaction of 2 with NaOAc in methanol followed by crystallization from THF gave (CO)(3)Fe(mu-S(t)Bu)(3)Ni(THF)(OAc), 7. The dinuclear complexes, 3-7, are thermally unstable, and a key to their successful isolation is to carry out the reactions and manipulations at -40 degrees C.

Direct electrochemical study of the multiple redox centers of hydrogenase from Desulfovibrio gigas

Direct electrochemical response was first time observed for the redox centers of Desulfovibrio gigas [NiFe]-Hase, in non-turnover conditions, by cyclic voltammetry, in solution at glassy carbon electrode. The activation of the enzyme was achieved by reduction with H(2) and by electrochemical control and electrocatalytic activity was observed. The inactivation of the [NiFe]-Hase was also attained through potential control. All electrochemical data was obtained in the absence of enzyme inhibitors. The results are discussed in the context of the proposed mechanism currently accepted for activation/inactivation of [NiFe]-Hases.

The strength of EPR and ENDOR techniques in revealing structure-function relationships in metalloproteins

Recent technological and methodological advances have strongly increased the potential of electron paramagnetic resonance (EPR) and electron nuclear double resonance (ENDOR) techniques to characterize the structure and dynamics of metalloproteins. These developments include the introduction of powerful pulsed EPR/ENDOR methodologies and the development of spectrometers operating at very high microwave frequencies and high magnetic fields. This overview focuses on how valuable information about metalloprotein structure-function relations can be obtained using a combination of EPR and ENDOR techniques. After an overview of the historical development and a limited theoretical description of some of the key EPR and ENDOR techniques, their potential will be highlighted using selected examples of applications to iron-, nickel-, cobalt-, and copper-containing proteins. We will end with an outlook of future developments.

Characterization of a cyanobacterial-like uptake [NiFe] hydrogenase: EPR and FTIR spectroscopic studies of the enzyme from Acidithiobacillus ferrooxidans

Electron paramagnetic resonance (EPR) and Fourier transform IR studies on the soluble hydrogenase from Acidithiobacillus ferrooxidans are presented. In addition, detailed sequence analyses of the two subunits of the enzyme have been performed. They show that the enzyme belongs to a group of uptake [NiFe] hydrogenases typical for Cyanobacteria. The sequences have also a close relationship to those of the H(2)-sensor proteins, but clearly differ from those of standard [NiFe] hydrogenases. It is concluded that the structure of the catalytic centre is similar, but not identical, to that of known [NiFe] hydrogenases. The active site in the majority of oxidized enzyme molecules, 97% in cells and more than 50% in the purified enzyme, is EPR-silent. Upon contact with H(2) these sites remain EPR-silent and show only a limited IR response. Oxidized enzyme molecules with an EPR-detectable active site show a Ni(r)*-like EPR signal which is light-sensitive at cryogenic temperatures. This is a novelty in the field of [NiFe] hydrogenases. Reaction with H(2) converts these active sites to the well-known Ni(a)-C* state. Illumination below 160 K transforms this state into the Ni(a)-L* state. The reversal, in the dark at 200 K, proceeds via an intermediate Ni EPR signal only observed with the H(2)-sensor protein from Ralstonia eutropha. The EPR-silent active sites in as-isolated and H(2)-treated enzyme are also light-sensitive as observed by IR spectra at cryogenic temperatures. The possible origin of the light sensitivity is discussed. This study represents the first spectral characterization of an enzyme of the group of cyanobacterial uptake hydrogenases.

Spectroelectrochemical Characterization of the [NiFe] Hydrogenase of Desulfovibrio vulgaris Miyazaki F

The active site in the [NiFe] hydrogenase of Desulfovibrio vulgaris Miyazaki F has been investigated by Fourier transform infrared (FTIR) spectroscopy. Analysis of the spectra allowed the three diatomic inorganic ligands to Fe in this enzyme to be identified as one CO molecule and two CN(-) molecules. Furthermore, pH-dependent redox titrations were performed to determine the midpoint potentials as well as the pK value of the respective reactions and revealed that each single-electron redox transition is accompanied by a single-proton transfer step. The comparison of these spectra with those published for other [NiFe] hydrogenases shows that the electronic structure of the active sites of these enzymes and their redox processes are essentially the same. Nevertheless, differences with respect to the frequency of the CO band and the pH dependence of the Ni-R states have been observed. Finally, the frequency shifts of the bands in the IR spectra were interpreted with respect to the electronic configuration of the redox intermediates in the catalytic cycle.

Rapid and Reversible Reactions of [NiFe]-Hydrogenases with Sulfide

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.

Hydrogen Bonding Affects the [NiFe] Active Site of Desulfovibrio vulgaris Miyazaki F Hydrogenase: A Hyperfine Sublevel Correlation Spectroscopy and Density Functional Theory Study

Pulse electron paramagnetic resonance and hyperfine sublevel correlation spectroscopy have been used to investigate nitrogen coordination of the active site of [NiFe] hydrogenase of Desulfovibrio vulgaris Miyazaki F in its oxidized "ready" state. The obtained (14)N hyperfine (A = [+1.32, +1.32, +2.07] MHz) and nuclear quadrupole (e(2)qQ/h = -1.9 MHz, eta = 0.37) coupling constants were assigned to the N(epsilon) of a highly conserved histidine (His88) by studying a hydrogenase preparation in which the histidines were (15)N labeled. The histidine is hydrogen-bonded via its N(epsilon)-H to the nickel-coordinating sulfur of a cysteine (Cys549) that carries an appreciable amount of spin density. Through the hydrogen bond a small fraction of the spin density ( approximately 1%) is delocalized onto the histidine ring giving rise to an isotropic (14)N hyperfine coupling constant of about 1.6 MHz. These conclusions are supported by density functional calculations. The measured (14)N quadrupole coupling constants are related to the polarization of the N(epsilon)-H bond, and the respective hydrogen bond can be classified as being weak.

How are the ready and unready states of nickel–iron hydrogenase activated by H2? A density functional theory study

We have explored possible mechanisms for the formation of the catalytically active Ni(a)-S state of the enzyme, nickel iron hydrogenase, from the Ni*(r) (ready) or Ni*(u) (unready) state, by reaction with H(2), using density functional theory calculations with the BP86 functional in conjunction with a DZVP basis set. We find that for the reaction of the ready state, which is taken to have an -OH bridge, the rate determining step is the cleavage of H(2) at the Ni(3+) centre with a barrier of approximately 15 kcal mol(-1). We take the unready state to have a -OOH bridge, and find that reaction with H(2) to form the Ni(r)-S state can proceed by two possible routes. One such path has a number of steps involving electron transfer, which is consistent with experiment, as is the calculated barrier of approximately 19 kcal mol(-1). The alternative pathway, with a lower barrier, may not be rate determining. Overall, our predictions give barriers in line with experiment, and allow details of the mechanism to be explored which are inaccessible from experiment.