Nils Leidel

O2 Reactions at the Six-iron Active Site (H-cluster) in [FeFe]-Hydrogenase

Irreversible inhibition by molecular oxygen (O2) complicates the use of [FeFe]-hydrogenases (HydA) for biotechnological hydrogen (H2) production. Modification by O2 of the active site six-iron complex denoted as the H-cluster ([4Fe4S]-2FeH) of HydA1 from the green alga Chlamydomonas reinhardtii was characterized by x-ray absorption spectroscopy at the iron K-edge. In a time-resolved approach, HydA1 protein samples were prepared after increasing O2 exposure periods at 0 °C. A kinetic analysis of changes in their x-ray absorption near edge structure and extended X-ray absorption fine structure spectra revealed three phases of O2 reactions. The first phase (τ1 ≤ 4 s) is characterized by the formation of an increased number of Fe–O,C bonds, elongation of the Fe–Fe distance in the binuclear unit (2FeH), and oxidation of one iron ion. The second phase (τ2 ≈ 15 s) causes a ∼50% decrease of the number of ∼2.7-Å Fe–Fe distances in the [4Fe4S] subcluster and the oxidation of one more iron ion. The final phase (τ3 ≤ 1000 s) leads to the disappearance of most Fe–Fe and Fe–S interactions and further iron oxidation. These results favor a reaction sequence, which involves 1) oxygenation at 2FeH+ leading to the formation of a reactive oxygen species-like superoxide (O2−), followed by 2) H-cluster inactivation and destabilization due to ROS attack on the [4Fe4S] cluster to convert it into an apparent [3Fe4S]+ unit, leading to 3) complete O2-induced degradation of the remainders of the H-cluster. This mechanism suggests that blocking of ROS diffusion paths and/or altering the redox potential of the [4Fe4S] cubane by genetic engineering may yield improved O2 tolerance in [FeFe]-hydrogenase.

Experimental and quantum chemical characterization of the water oxidation cycle catalysed by [RuII(damp)(bpy)(H2O)]2+

The water-oxidation catalytic activity of [RuII(damp)(bpy)(H2O)]2+ has been determined from manometric and mass spectroscopy studies. Mechanistic details of the catalytic cycle have been studied both experimentally and using DFT and CASSCF/CASPT2 calculations. Characterisation of this Ru(II) complex and more highly oxidized catalytic intermediates has been accomplished through UV-vis and XAS spectroscopy, as well as through electrochemical techniques. Comparison of XAS spectra with CASSCF/CASPT2 calculations provides insight into the electronic structures of the more highly oxidized species, especially the degree to which oxidation occurs over both atoms of the Ru–O fragment. 18O-labelling experiments indicate that the O–O bond formation step proceeds via a water nucleophilic attack mechanism, and a detailed DFT analysis of the catalytic cycle predicts that step to be rate-determining and to take place for a formal Ru(V)O species. A number of alternative higher energy pathways have also been characterised in order to provide a more complete vision of the whole system.

The [FeFe]‐hydrogenase maturation protein HydF contains a H‐cluster like [4Fe4S]–2Fe site

Formation of the catalytic six‐iron complex (H‐cluster) of [FeFe]‐hydrogenase (HydA) requires its interaction with a specific maturation protein, HydF. Comparison by X‐ray absorption spectroscopy at the Fe K‐edge of HydF from Clostridium acetobutylicum and HydA1 from Chlamydomonas reinhardtii revealed that the overall structure of the iron site in both proteins is highly similar, comprising a [4Fe4S] cluster (Fe–Fe distances of ∼2.7 Å) and a di‐iron unit (Fe–Fe distance of ∼2.5 Å). Thus, a precursor of the whole H‐cluster is assembled on HydF. Formation of the core structures of both the 4Fe and 2Fe units may require only the housekeeping [FeS] cluster assembly machinery of the cell. Presumably, only the 2Fe cluster is transferred from HydF to HydA1, thereby forming the active site.

Hydride binding to the active site of [FeFe]-hydrogenase.

[FeFe]-hydrogenase from green algae (HydA1) is the most efficient hydrogen (H2) producing enzyme in nature and of prime interest for (bio)technology. Its active site is a unique six-iron center (H-cluster) composed of a cubane cluster, [4Fe4S]H, cysteine-linked to a diiron unit, [2Fe]H, which carries unusual carbon monoxide (CO) and cyanide ligands and a bridging azadithiolate group. We have probed the molecular and electronic configurations of the H-cluster in functional oxidized, reduced, and super-reduced or CO-inhibited HydA1 protein, in particular searching for intermediates with iron-hydride bonds. Site-selective X-ray absorption and emission spectroscopy were used to distinguish between low- and high-spin iron sites in the two subcomplexes of the H-cluster. The experimental methods and spectral simulations were calibrated using synthetic model complexes with ligand variations and bound hydride species. Distinct X-ray spectroscopic signatures of electronic excitation or decay transitions in [4Fe4S]H and [2Fe]H were obtained, which were quantitatively reproduced by density functional theory calculations, thereby leading to specific H-cluster model structures. We show that iron-hydride bonds are absent in the reduced state, whereas only in the super-reduced state, ligand rotation facilitates hydride binding presumably to the Fe-Fe bridging position at [2Fe]H. These results are in agreement with a catalytic cycle involving three main intermediates and at least two protonation and electron transfer steps prior to the H2 formation chemistry in [FeFe]-hydrogenases.

Electronic structure of oxidized complexes derived from cis-[Ru II(bpy) 2(H 2O) 2] 2+ and its photoisomerization mechanism

The geometry and electronic structure of cis-[Ru(II)(bpy)(2)(H(2)O)(2)](2+) and its higher oxidation state species up formally to Ru(VI) have been studied by means of UV-vis, EPR, XAS, and DFT and CASSCF/CASPT2 calculations. DFT calculations of the molecular structures of these species show that, as the oxidation state increases, the Ru-O bond distance decreases, indicating increased degrees of Ru-O multiple bonding. In addition, the O-Ru-O valence bond angle increases as the oxidation state increases. EPR spectroscopy and quantum chemical calculations indicate that low-spin configurations are favored for all oxidation states. Thus, cis-[Ru(IV)(bpy)(2)(OH)(2)](2+) (d(4)) has a singlet ground state and is EPR-silent at low temperatures, while cis-[Ru(V)(bpy)(2)(O)(OH)](2+) (d(3)) has a doublet ground state. XAS spectroscopy of higher oxidation state species and DFT calculations further illuminate the electronic structures of these complexes, particularly with respect to the covalent character of the O-Ru-O fragment. In addition, the photochemical isomerization of cis-[Ru(II)(bpy)(2)(H(2)O)(2)](2+) to its trans-[Ru(II)(bpy)(2)(H(2)O)(2)](2+) isomer has been fully characterized through quantum chemical calculations. The excited-state process is predicted to involve decoordination of one aqua ligand, which leads to a coordinatively unsaturated complex that undergoes structural rearrangement followed by recoordination of water to yield the trans isomer.

Electronic and molecular structures of the active-site H-cluster in [FeFe]-hydrogenase determined by site-selective X-ray spectroscopy and quantum chemical calculations

The [FeFe]-hydrogenase (HydA1) from green algae is the minimal enzyme for efficient biological hydrogen (H2) production. Its active-site six-iron center (H-cluster) consists of a cubane, [4Fe4S]H, cysteine-linked to a diiron site, [2Fe]H. We utilized the spin-polarization of the iron Kβ X-ray fluorescence emission to perform site-selective X-ray absorption experiments for spectral discrimination of the two sub-complexes. For the H-cluster in reduced HydA1 protein, XANES and EXAFS spectra, Kβ emission lines (3p → 1s transitions), and core-to-valence (pre-edge) absorption (1s → 3d) and valence-to-core (Kβ2,5) emission (3d → 1s) spectra were obtained, individually for [4Fe4S]H and [2Fe]H. Iron–ligand bond lengths and intermetal distances in [2Fe]H and [4Fe4S]H were resolved, as well as fine structure in the high-spin iron containing cubane. Density functional theory calculations reproduced the X-ray spectral features and assigned the molecular orbital configurations, emphasizing the asymmetric d-level degeneracy of the proximal (Fep) and distal (Fed) low-spin irons in [2Fe]H in the non-paramagnetic state. This yielded a specific model structure of the H-cluster with a bridging carbon monoxide ligand and an apical open coordination site at Fed in [2Fe]H. The small HOMO–LUMO gap (∼0.3 eV) enables oxidation and reduction of the active site at similar potentials for reversible H2 turnover by HydA1, the LUMO spread over [4Fe4S]H supports its role as an electron transfer relay, and Fed carrying the HOMO is prepared for transient hydride binding. These features and the accessibility of Fed from the bulk phase can account for regio-specific redox transitions as well as H2-formation and O2-inhibition at the H-cluster. We provide a conceptual and experimental framework for site-selective studies on catalytic mechanisms in inhomogeneous materials.

Rapid X-ray Photoreduction of Dimetal-Oxygen Cofactors in Ribonucleotide Reductase

Background: Typical FeFe and MnFe cofactors bind to numerous enzymes such as ribonucleotide reductases. Crystallographic data suggest x-ray photoreduction (XPR) effects. Results: Rapid XPR-induced cofactor changes were monitored using time-resolved x-ray absorption spectroscopy. Conclusion: The XPR-induced cofactor states differ significantly from the native configurations, but comply with crystallographic structures. Significance: Structure determination for high-valent dimetal-oxygen cofactors requires free electron-laser protein crystallography combined with x-ray spectroscopy. Prototypic dinuclear metal cofactors with varying metallation constitute a class of O2-activating catalysts in numerous enzymes such as ribonucleotide reductase. Reliable structures are required to unravel the reaction mechanisms. However, protein crystallography data may be compromised by x-ray photoreduction (XRP). We studied XPR of Fe(III)Fe(III) and Mn(III)Fe(III) sites in the R2 subunit of Chlamydia trachomatis ribonucleotide reductase using x-ray absorption spectroscopy. Rapid and biphasic x-ray photoreduction kinetics at 20 and 80 K for both cofactor types suggested sequential formation of (III,II) and (II,II) species and similar redox potentials of iron and manganese sites. Comparing with typical x-ray doses in crystallography implies that (II,II) states are reached in <1 s in such studies. First-sphere metal coordination and metal-metal distances differed after chemical reduction at room temperature and after XPR at cryogenic temperatures, as corroborated by model structures from density functional theory calculations. The inter-metal distances in the XPR-induced (II,II) states, however, are similar to R2 crystal structures. Therefore, crystal data of initially oxidized R2-type proteins mostly contain photoreduced (II,II) cofactors, which deviate from the native structures functional in O2 activation, explaining observed variable metal ligation motifs. This situation may be remedied by novel femtosecond free electron-laser protein crystallography techniques.

Identification of a bis-molybdopterin intermediate in molybdenum cofactor biosynthesis in Escherichia coli

Background: Some molybdoenzymes in prokaryotes contain the bis-molybdopterin guanine dinucleotide cofactor. Results: The bis-Mo-MPT cofactor is a novel intermediate in Moco biosynthesis in E. coli. Conclusion: Bis-MGD formed by MobA is fully functional and restores the catalytic activity in apoTorA. Significance: Bis-Mo-MPT assembles spontaneously on MobA prior to forming bis-MGD. The molybdenum cofactor is an important cofactor, and its biosynthesis is essential for many organisms, including humans. Its basic form comprises a single molybdopterin (MPT) unit, which binds a molybdenum ion bearing three oxygen ligands via a dithiolene function, thus forming Mo-MPT. In bacteria, this form is modified to form the bis-MPT guanine dinucleotide cofactor with two MPT units coordinated at one molybdenum atom, which additionally contains GMPs bound to the terminal phosphate group of the MPTs (bis-MGD). The MobA protein catalyzes the nucleotide addition to MPT, but the mechanism of the biosynthesis of the bis-MGD cofactor has remained enigmatic. We have established an in vitro system for studying bis-MGD assembly using purified compounds. Quantification of the MPT/molybdenum and molybdenum/phosphorus ratios, time-dependent assays for MPT and MGD detection, and determination of the numbers and lengths of Mo–S and Mo–O bonds by X-ray absorption spectroscopy enabled identification of a novel bis-Mo-MPT intermediate on MobA prior to nucleotide attachment. The addition of Mg-GTP to MobA loaded with bis-Mo-MPT resulted in formation and release of the final bis-MGD product. This cofactor was fully functional and reconstituted the catalytic activity of apo-TMAO reductase (TorA). We propose a reaction sequence for bis-MGD formation, which involves 1) the formation of bis-Mo-MPT, 2) the addition of two GMP units to form bis-MGD on MobA, and 3) the release and transfer of the mature cofactor to the target protein TorA, in a reaction that is supported by the specific chaperone TorD, resulting in an active molybdoenzyme.

High-valent [MnFe] and [FeFe] cofactors in ribonucleotide reductases

Ribonucleotide reductases (RNRs) are essential for DNA synthesis in most organisms. In class-Ic RNR from Chlamydia trachomatis (Ct), a MnFe cofactor in subunit R2 forms the site required for enzyme activity, instead of an FeFe cofactor plus a redox-active tyrosine in class-Ia RNRs, for example in mouse (Mus musculus, Mm). For R2 proteins from Ct and Mm, either grown in the presence of, or reconstituted with Mn and Fe ions, structural and electronic properties of higher valence MnFe and FeFe sites were determined by X-ray absorption spectroscopy and complementary techniques, in combination with bond-valence-sum and density functional theory calculations. At least ten different cofactor species could be tentatively distinguished. In Ct R2, two different Mn(IV)Fe(III) site configurations were assigned either L(4)Mn(IV)(μO)(2)Fe(III)L(4) (metal-metal distance of ~2.75Å, L = ligand) prevailing in metal-grown R2, or L(4)Mn(IV)(μO)(μOH)Fe(III)L(4) (~2.90Å) dominating in metal-reconstituted R2. Specific spectroscopic features were attributed to an Fe(IV)Fe(III) site (~2.55Å) with a L(4)Fe(IV)(μO)(2)Fe(III)L(3) core structure. Several Mn,Fe(III)Fe(III) (~2.9-3.1Å) and Mn,Fe(III)Fe(II) species (~3.3-3.4Å) likely showed 5-coordinated Mn(III) or Fe(III). Rapid X-ray photoreduction of iron and shorter metal-metal distances in the high-valent states suggested radiation-induced modifications in most crystal structures of R2. The actual configuration of the MnFe and FeFe cofactors seems to depend on assembly sequences, bound metal type, valence state, and previous catalytic activity involving subunit R1. In Ct R2, the protonation of a bridging oxide in the Mn(IV)(μO)(μOH)Fe(III) core may be important for preventing premature site reduction and initiation of the radical chemistry in R1.

Structural differences of oxidized iron-sulfur and nickel-iron cofactors in O2-tolerant and O2-sensitive hydrogenases studied by X-ray absorption spectroscopy.

The class of [NiFe]-hydrogenases comprises oxygen-sensitive periplasmic (PH) and oxygen-tolerant membrane-bound (MBH) enzymes. For three PHs and four MBHs from six bacterial species, structural features of the nickel-iron active site of hydrogen turnover and of the iron-sulfur clusters functioning in electron transfer were determined using X-ray absorption spectroscopy (XAS). Fe-XAS indicated surplus oxidized iron and a lower number of ~2.7 Å Fe-Fe distances plus additional shorter and longer distances in the oxidized MBHs compared to the oxidized PHs. This supported a double-oxidized and modified proximal FeS cluster in all MBHs with an apparent trimer-plus-monomer arrangement of its four iron atoms, in agreement with crystal data showing a [4Fe3S] cluster instead of a [4Fe4S] cubane as in the PHs. Ni-XAS indicated coordination of the nickel by the thiol group sulfurs of four conserved cysteines and at least one iron-oxygen bond in both MBH and PH proteins. Structural differences of the oxidized inactive [NiFe] cofactor of MBHs in the Ni-B state compared to PHs in the Ni-A state included a ~0.05 Å longer Ni-O bond, a two times larger spread of the Ni-S bond lengths, and a ~0.1 Å shorter Ni-Fe distance. The modified proximal [4Fe3S] cluster, weaker binding of the Ni-Fe bridging oxygen species, and an altered localization of reduced oxygen species at the active site may each contribute to O2 tolerance.