High-frequency (140-GHz) time domain EPR and ENDOR spectroscopy: the tyrosyl radical-diiron cofactor in ribonucleotide reductase from yeast

High-frequency pulsed EPR and ENDOR have been employed to characterize the tyrosyl radical (Y*)-diiron cofactor in the Y2-containing R2 subunit of ribonucleotide reductase (RNR) from yeast. The present work represents the first use of 140-GHz time domain EPR and ENDOR to examine this system and demonstrates the capabilities of the method to elucidate the electronic structure and the chemical environment of protein radicals. Low-temperature spin-echo-detected EPR spectra of yeast Y* reveal an EPR line shape typical of a tyrosyl radical; however, when compared with the EPR spectra of Y* from E. coli RNR, a substantial upfield shift of the g(1)-value is observed. The origin of the shift in g(1) was investigated by 140-GHz (1)H and (2)H pulsed ENDOR experiments of the Y2-containing subunit in protonated and D(2)O-exchanged buffer. (2)H ENDOR spectra and simulations provide unambiguous evidence for one strongly coupled (2)H arising from a bond between the radical and an exchangeable proton of an adjacent residue or a water molecule. Orientation-selective 140-GHz ENDOR spectra indicate the direction of the hydrogen bond with respect to the molecular symmetry axes and the bond length (1.81 A). Finally, we have performed saturation recovery experiments and observed enhanced spin lattice relaxation rates of the Y* above 10 K. At temperatures higher than 20 K, the relaxation rates are isotropic across the EPR line, a phenomenon that we attribute to isotropic exchange interaction between Y* and the first excited paramagnetic state of the diiron cluster adjacent to it. From the activation energy of the rates, we determine the exchange interaction between the two irons of the cluster, J(exc) = -85 cm(-)(1). The relaxation mechanism and the presence of the hydrogen bond are discussed in terms of the differences in the structure of the Y*-diiron cofactor in yeast Y2 and other class I R2s.     

Characterization of the Fe site in iron-sulfur cluster-free hydrogenase (Hmd) and of a model compound via nuclear resonance vibrational spectroscopy (NRVS)

We have used (57)Fe nuclear resonance vibrational spectroscopy (NRVS) to study the iron site in the iron-sulfur cluster-free hydrogenase Hmd from the methanogenic archaeon Methanothermobacter marburgensis. The spectra have been interpreted by comparison with a cis-(CO)2-ligated Fe model compound, Fe(S2C2H4)(CO)2(PMe3)2, as well as by normal mode simulations of plausible active site structures. For this model complex, normal mode analyses both from an optimized Urey-Bradley force field and from complementary density functional theory (DFT) calculations produced consistent results. For Hmd, previous IR spectroscopic studies found strong CO stretching modes at 1944 and 2011 cm(-1), interpreted as evidence for cis-Fe(CO)2 ligation. The NRVS data provide further insight into the dynamics of the Fe site, revealing Fe-CO stretch and Fe-CO bend modes at 494, 562, 590, and 648 cm(-1), consistent with the proposed cis-Fe(CO)2 ligation. The NRVS also reveals a band assigned to Fe-S stretching motion at approximately 311 cm(-1) and another reproducible feature at approximately 380 cm(-1). The (57)Fe partial vibrational densities of states (PVDOS) for Hmd can be reasonably well simulated by a normal mode analysis based on a Urey-Bradley force field for a five-coordinate cis-(CO)2-ligated Fe site with additional cysteine, water, and pyridone cofactor ligands. A "truncated" model without a water ligand can also be used to match the NRVS data. A final interpretation of the Hmd NRVS data, including DFT analysis, awaits a three-dimensional structure for the active site.     

57Fe ENDOR spectroscopy and 'electron inventory' analysis of the nitrogenase E4 intermediate suggest the metal-ion core of FeMo-cofactor cycles through only one redox couple

N(2) binds to the active-site metal cluster in the nitrogenase MoFe protein, the FeMo-cofactor ([7Fe-9S-Mo-homocitrate-X]; FeMo-co) only after the MoFe protein has accumulated three or four electrons/protons (E(3) or E(4) states), with the E(4) state being optimally activated. Here we study the FeMo-co (57)Fe atoms of E(4) trapped with the α-70(Val→Ile) MoFe protein variant through use of advanced ENDOR methods: 'random-hop' Davies pulsed 35 GHz ENDOR; difference triple resonance; the recently developed Pulse-Endor-SaTuration and REcovery (PESTRE) protocol for determining hyperfine-coupling signs; and Raw-DATA (RD)-PESTRE, a PESTRE variant that gives a continuous sign readout over a selected radiofrequency range. These methods have allowed experimental determination of the signed isotropic (57)Fe hyperfine couplings for five of the seven iron sites of the reductively activated E(4) FeMo-co, and given the magnitude of the coupling for a sixth. When supplemented by the use of sum-rules developed to describe electron-spin coupling in FeS proteins, these (57)Fe measurements yield both the magnitude and signs of the isotropic couplings for the complete set of seven Fe sites of FeMo-co in E(4). In light of the previous findings that FeMo-co of E(4) binds two hydrides in the form of (Fe-(μ-H(-))-Fe) fragments, and that molybdenum has not become reduced, an 'electron inventory' analysis assigns the formal redox level of FeMo-co metal ions in E(4) to that of the resting state (M(N)), with the four accumulated electrons residing on the two Fe-bound hydrides. Comparisons with earlier (57)Fe ENDOR studies and electron inventory analyses of the bio-organometallic intermediate formed during the reduction of alkynes and the CO-inhibited forms of nitrogenase (hi-CO and lo-CO) inspire the conjecture that throughout the eight-electron reduction of N(2) plus 2H(+) to two NH(3) plus H(2), the inorganic core of FeMo-co cycles through only a single redox couple connecting two formal redox levels: those associated with the resting state, M(N), and with the one-electron reduced state, M(R). We further note that this conjecture might apply to other complex FeS enzymes.     

Effect of structure on the reduction potentials of films of constitutional isomers of iron-sulfur cluster core dendrimers

The thermodynamic redox potentials of films of constitutional isomers of iron-sulfur cluster core dendrimers were measured and compared. It was determined that the primary structure of the dendrimer influences its reduction potential. Dendrimers containing so-called backfolded linkages were more difficult to reduce than their extended analogues. This behavior is rationalized by suggesting that the backfolded isomers pack more tightly around the iron-sulfur cluster, creating a more hydrophobic local microenvironment. Also, all of these molecules are easier to reduce in the film than in dimethyl formamide solution. The variation in redox potential between film and solution environment was compared to that of dendrimers of differing generations and correlated with the amount of hydrophobic dendron surrounding the cluster.     

Comparing the electronic properties of the low-spin cyano-ferric [Fe(N4)(Cys)] active sites of superoxide reductase and p450cam using ENDOR spectroscopy and DFT calculations

Superoxide reductase (SOR) and P450 enzymes contain similar [Fe(N)4(SCys)] active sites and, although they catalyze very different reactions, are proposed to involve analogous low-spin (hydro)peroxo-Fe(III) intermediates in their respective mechanisms that can be modeled by cyanide binding. The equatorial FeN4 ligation by four histidine ligands in CN-SOR and the heme in CN-P450cam is directly compared by 14N ENDOR, while the axial Fe-CN and Fe-S bonding is probed by 13C ENDOR of the cyanide ligand and 1Hbeta ENDOR measurements to determine the spin density delocalization onto the cysteine sulfur. There are small, but notable, differences in the bonding between Fe(III) and its ligands in the two enzymes. The ENDOR measurements are complemented by DFT computations that support the semiempirical equation used to compute spin densities on metal-coordinated cysteinyl and shed light on bonding changes as the Fe-C-N linkage bends. They further indicate that H bonds to the cysteinyl thiolate sulfur ligand reduce the spin density on the sulfur in both active sites to a degree that exceeds the difference induced by the alternative sets of "in-plane" nitrogen ligands.     

Single-molecule-magnet behavior in a Fe(12)Sm(4) cluster

Through the combination of Sm(III) spin carriers with a Fe(III) system, the largest Fe-Ln cluster so far has been synthesized. To our knowledge, the new complex, Fe(12)Sm(4), is the first Sm(III) single-molecule magnet. Furthermore, Fe(12)La(4) and Fe(12)Gd(4) have also been synthesized to help understand the magnetic exchange interactions and origin of magnetic anisotropy in Fe(12)Sm(4).     

Mössbauer spectroscopic study of 57Fe species produced by 56Fe(n,γ)57Fe reaction in iron disulfide

In order to investigate the physical and chemical effects of neutron capture reaction, a neutron in-beam Mössbauer spectroscopic study on two isomorphs of iron disulfide: pyrite and marcasite, were carried out with a parallel plate avalanche counter at room temperature. In both compounds only two major products accounted for the obtained spectrum: one with Mössbauer parameters close to the parent compound and the other one considered to be a new product. The yield of the parent-like species was different in the two isomorphs.     

Synthesis of Isotope Enriched (CN3H6)2[57Fe(CN)5NO] starting from 57Fe

A high‐yield, mmolar‐scale synthesis of pure guanidinium nitroprusside, (CN₃H₆)₂[⁽⁵⁷⁾Fe(CN)₅NO] (GNP) from iron metal is described. The iron metal contained pieces of 95.3% ⁵⁷Fe together with normal iron so that an isotope enrichment in ⁵⁷Fe of 25% was achieved. Single‐crystals of GNP could be grown in cubic shape and dimensions of about 3 × 4 × 4 mm³. The purity of the GNP product and the intermediates K₄[⁽⁵⁷⁾Fe(CN)₆] · 3 H₂O and Na₂[⁽⁵⁷⁾Fe(CN)₅NO] · 2 H₂O was ascertained by ⁵⁷Fe Mössbauer spectroscopy as well as ¹³C, ¹⁴N and ⁵⁷Fe NMR spectroscopy. The ⁵⁷Fe NMR chemical shift for [⁽⁵⁷⁾Fe(CN)₅NO]^2– in GNP was detected at +2004.0 ppm [vs Fe(CO)₅].     

Manganoan rockbridgeite Fe4.32Mn0.62Zn0.06(PO4)3(OH)5: structure analysis and 57Fe Mössbauer spectroscopy

The structure of the basic iron phosphate rockbridgeite [iron manganese zinc tris­(phosphate) penta­hydroxide] was reinvestigated with special emphasis on the cation distribution deduced from new X‐ray and ⁵⁷Fe Mössbauer data. Rockbridgeite is orthorhombic, space group Cmcm, and shows three different Fe sites, one with symmetry, another with m symmetry and the third in a general position. One phosphate group has the P atom on a site with m symmetry, while the other has the P atom at a site with mm symmetry. Two Fe sites are fully occupied by ferric iron, while Mn³⁺ and Fe²⁺ are situated at a third, principally Fe, site. Structural data, bond‐valence sums and polyhedral distortion parameters suggest a new inter­pretation of the rockbridgeite ⁵⁷Fe Mössbauer spectrum.     

On the spin relaxation of57Fe(III) species produced through EC-decay in diamagnetic57Co-labelled Co(III) compounds

Absorption Mössbauer spectra of high-spin⁵⁷Fe(acac)₃ incorporated in diamagnetic Co(acac)₃ and in paramagnetic Mn(acac)₃ and of the γ-ray irradiated (⁵⁷Fe, Co) (acac)₃ and (⁵⁷Fe, Mn) (acac)₃ were compared with emission spectra of⁵⁷Co-labelled Co(acac)₃. Magnetic hfs is found in the spectra of (⁵⁷Fe, Co) (acac)₃ at 78 to 195 K, whereas such hfs is observed neither for the spectrum of⁵⁷Co-labelled Co(acac)₃ nor for that of γ-ray irradiated (⁵⁷Fe, Co) (acac)₃). The absence of magnetic hfs in the spectrum of diamagnetic⁵⁷Co-labelled cobalt(III) compounds was ascribed to the spin-spin interaction due to the radicals produced in the vicinity of the decayed atom.     

A density functional evaluation of an Fe(III)-Fe(IV) model diiron cluster: comparisons with ribonucleotide reductase intermediate X

Using broken-symmetry density functional theory and spin-projection methods, we have examined the electronic structure and properties of a large mixed-valent Fe(III)-Fe(IV) diiron system that displays two bidentate carboxylates and a single mu-oxo moiety as bridging ligands. Two carboxylates and a single oxygen species have long been implicated as core elements of the elusive intermediate X in ribonucleotide reductase. Spectroscopic studies of X have also identified the presence of an additional terminal or bridging oxygen-based ligand. Introduction of a second oxygen and protonated variants thereof in the core of our structural model is favored as a bridging hydroxide based on the lowest energy structure. M?ssbauer measurements indicate clearly that the two iron sites of X are distinct and that there is significant electron delocalization onto the oxygen-based ligands. For several examined spin states of our model cluster, M?ssbauer parameters from density functional calculations are neither able to differentiate between the iron sites nor reproduce the strong spin delocalization onto the oxygen-based ligands observed experimentally. The combined comparison of the calculated geometries, spin states, spin densities, and M?ssbauer properties for our model clusters with available experimental data for X implies that intermediate X is significantly different from the diiron structural models examined herein.     

Fe4 cluster and a buckled macrocycle complex from the reduction of [(dmgBF2)2Fe(L)2] (L = MeCN, (t)Bu(i)NC)

We report the syntheses, X-ray structures, and reductive electrochemistry of the Fe(II) complexes [(dmgBF(2))(2)Fe(MeCN)(2)] (1; dmg = dimethylglyoxime, MeCN = acetonitrile) and [(dmgBF(2))Fe((t)Bu(i)NC)(2)] (2; (t)Bu(i)NC = tert-butylisocyanide). The reaction of 1 with Na/Hg amalgam led to isolation and the X-ray structure of [(dmgBF(2))(2)Fe(glyIm)] (3; glyIm = glyimine), wherein the (dmgBF(2))(2) macrocyclic frame is bent to accommodate the binding of a bidentate apical ligand. We also report the X-ray structure of a rare mixed-valence Fe(4) cluster with supporting dmg-type ligands. In the structure of [(dmg(2)BF(2))(3)Fe(3)((1)/(2)dmg)(3)Fe(O)(6)] (4), the (dmgBF(2))(2) macrocycle has been cleaved, eliminating BF(2) groups. Density functional theory calculations and electron paramagnetic resonance data are in accordance with a central Fe(III) ion surrounded by three formally Fe(II)dmg(2)BF(2) units.     

Spectroscopic characterization of site-specific [Fe(4)S(4)] cluster chemistry in ferredoxin:thioredoxin reductase: implications for the catalytic mechanism

Light regulation of enzyme activities in oxygenic photosynthesis is mediated by ferredoxin:thioredoxin reductase (FTR), a novel class of disulfide reductase with an active site comprising a [Fe(4)S(4)](2+) cluster and an adjacent disulfide, that catalyzes reduction of the thioredoxin disulfide in two sequential one-electron steps using a [Fe(2)S(2)](2+/+) ferredoxin as the electron donor. In this work, we report on spectroscopic (EPR, VTMCD, resonance Raman, and M?ssbauer) and redox characterization of the active site of FTR in various forms of the enzyme, including wild-type FTR, point-mutation variants at each of the active-site cysteine residues, and stable analogues of the one-electron-reduced FTR-Trx heterodisulfide intermediate. The results reveal novel site-specific Fe(4)S(4)-cluster chemistry in oxidized, one-electron-reduced, and two-electron-reduced forms of FTR. In the resting enzyme, a weak interaction between the Fe(4)S(4) cluster and the active-site disulfide promotes charge buildup at a unique Fe site and primes the active site to accept an electron from ferredoxin to break the disulfide bond. In one-electron-reduced analogues, cleavage of the active-site disulfide is accompanied by coordination of one of the cysteine residues that form the active-site disulfide to yield a [Fe(4)S(4)](3+) cluster with two cysteinate ligands at a unique Fe site. The most intriguing result is that two-electron-reduced FTR in which the disulfide is reduced to a dithiol contains an unprecedented electron-rich [Fe(4)S(4)](2+) cluster comprising both valence-delocalized and valence-localized Fe(2+)Fe(3+) pairs. These results provide molecular level insights into the catalytic mechanism of FTR, and two viable mechanisms are proposed.     

Preparation of57Fe enriched K4[Fe(CN)6] and K3[Fe(CN)6]

A simple method to prepare⁵⁷Fe enriched K₄[Fe(CN)₆] and K₃[Fe(CN)₆] is described. The yields of the products are much better than those reported in the literature so far. The enrichment is essential for⁵⁷Fe Mössbauer investigation in a variety of Prussiate type complexes and other inorganic compounds which are conveniently prepared from K₄[Fe(CN)₆] and K₃[Fe(CN)₆]. K₄[Fe(CN)₆] was obtained by reacting freshly prepared Fe(OH)₃ with glacial acetic acid and treating with iron acetate in boiling aqueous solution of KCN. The novel feature of the procedure to obtain K₃[Fe(CN)₆] is that the oxidation of K₄[Fe(CN)₆] has been carried out in the solid state by passing chlorine gas over the powdered specimen. K₃[Fe(CN)₆] was crystallised from alkaline solution of this oxidised powder. The compounds were characterised by Mössbauer spectroscopy.     

Mechanistic implications for the formation of the diiron cluster in ribonucleotide reductase provided by quantitative EPR spectroscopy

The small subunit of Escherichia coli ribonucleotide reductase (R2) is a homodimeric (betabeta) protein, in which each beta-peptide contains a diiron cluster composed of two inequivalent iron sites. R2 is capable of reductively activating O(2) to produce a stable tyrosine radical (Y122*), which is essential for production of deoxyribonucleotides on the larger R1 subunit. In this work, the paramagnetic Mn(II) ion is used as a spectroscopic probe to characterize the assembly of the R2 site with EPR spectroscopy. Upon titration of Mn(II) into samples of apoR2, we have been able to quantitatively follow three species (aquaMn(II), mononuclear Mn(II)R2, and dinuclear Mn(2)(II)R2) and fit each to a sequential two binding site model. As previously observed for Fe(II) binding within apoR2, one of the sites has a greater binding affinity relative to the other, K(1) = (5.5 +/- 1.1) x 10(5) M(-)(1) and K(2) = (3.9 +/- 0.6) x 10(4) M(-)(1), which are assigned to the B and A sites, respectively. In multiple titrations, only one dinuclear Mn(2)(II)R2 site was created per homodimer of R2, indicating that only one of the two beta-peptides of R2 is capable of binding Mn(II) following addition of Mn(II) to apoR2. Under anaerobic conditions, addition of only 2 equiv of Fe(II) to R2 (Fe(2)(II)R2) completely prevented the formation of any bound MnR2 species. Upon reaction of this sample with O(2) in the presence of Mn(II), both Y122* and Mn(2)(II)R2 were produced in equal amounts. Previous stopped-flow absorption spectroscopy studies have indicated that apoR2 undergoes a protein conformational change upon binding of metal (Tong et al. J. Am. Chem. Soc. 1996, 118, 2107-2108). On the basis of these observations, we propose a model for R2 metal incorporation that invokes an allosteric interaction between the two beta-peptides of R2. Upon binding the first equiv of metal to a beta-peptide (beta(I)), the aforementioned protein conformational change prevents metal binding in the adjacent beta-peptide (beta(II)) approximately 25 A away. Furthermore, we show that metal incorporation into beta(II) occurs only during the O(2) activation chemistry of the beta(I)-peptide. This is the first direct evidence of an allosteric interaction between the two beta-peptides of R2. Furthermore, this model can explain the generally observed low Fe occupancy of R2. We also demonstrate that metal uptake and this newly observed allosteric effect are buffer dependent. Higher levels of glycerol cause loss of the allosteric effect. Reductive cycling of samples in the presence of Mn(II) produced a novel mixed metal Fe(III)Mn(III)R2 species within the active site of R2. The magnitude of the exchange coupling (J) determined for both the Mn(2)(II)R2 and Fe(III)Mn(III)R2 species was determined to be -1.8 +/- 0.3 and -18 +/- 3 cm(-)(1), respectively. Quantitative spectral simulations for the Fe(III)Mn(III)R2 and mononuclear Mn(II)R2 species are provided. This work represents the first instance where both X- and Q-band simulations of perpendicular and parallel mode spectra were used to quantitatively predict the concentration of a protein bound mononuclear Mn(II) species.     

Biological activity of Fe(III) aquo-complexes towards ferric chelate reductase (FCR)

In this study we have obtained experimental evidence that confirms the high activity of aquo complexes III and IV towards the enzyme FCR, responsible for the reduction of Fe(III) to Fe(II) in the process of iron acquisition by plants. The in vivo FCR assays in roots of stressed cucumber plants have shown a higher efficiency of the family of complexes III and a striking structure-activity relationship with the nature of the substituent placed in a phenyl group far away from the metal center. The results obtained in this work demonstrate that all the aquo compounds tested interact efficiently with the enzyme FCR and hence constitute a new concept of iron chelates that could be of great use in agronomy.     

Kinetics of the Fe(II) reduction of trans-halogenopyridinebis(dimethylglyoximato)Co(III) complexes

The kinetics of the Fe(II) reduction of trans-chloro, bromo and iodopyridinebis(dimethylglyoximato)Co(III) have been studied at 30.0±0.1°C and I = 1.0 mol. dm⁻³(NaClO₄) in the [H⁺] range 0.0043–0.115 mol. dm⁻³. The reaction showed an inverse dependence on [H⁺]. The second order rate constant could be expressed in the form k_II = k₁ + k₂(1 + K_B[H⁺])^{−1. The kinetic data were found to be:} Co(DH)₂(py)Cl−k₁ = 0.051 ±0.003 dm³ mol⁻¹s⁻¹, 0.051±0.003 dm³ mol⁻¹ s⁻¹,k₂ = 0.76±0.04 dm³ mol⁻¹ s⁻¹ K_B = 325±8 dm³ mol⁻¹;Co(DH)₂(py)Br-k₁ = 0.071±0.004 dm³mol⁻¹ s⁻¹,k₂ = 1.21±0.04 dm³ mol⁻¹ s⁻¹ K_B = 460±15 dm³ mol⁻¹; Co(DH)₂(py)I-k₁ = 0.075±0.006 dm³ mol⁻¹ s⁻¹,k₂ = 1.91±0.09 dm³ mol⁻¹ s⁻¹ K_B = 625±30 dm³ mol⁻¹. The inverse dependence on [H⁺] suggests an inner-sphere mechanism involving protonated and unprotonated species of the complex. The order of rates for the three complexes was found to be Co(DH)₂(py)I > Co(DH)₂(py)Br > Co(DH)₂(py)Cl.     

Determination of the hydration number of gadolinium(III) complexes by high-field pulsed 17O ENDOR spectroscopy.

Pulsed 17O Mims electron-nuclear double resonance (ENDOR) spectroscopy at the W band (95 GHz) and D band (130 GHz) is used for the direct determination of the water coordination number (q) of gadolinium-based magnetic resonance imaging (MRI) contrast agents. Spectra of metal complexes in frozen aqueous solutions at approximately physiological concentrations can be obtained either in the presence or absence of protein targets. This method is an improvement over the 1H ENDOR method described previously, which involved the difference ENDOR spectrum of exchangeable protons from spectra taken in H2O and D2O. In addition to exchangeable water protons, the 1H ENDOR method is also sensitive to other exchangeable protons, and it is shown here that this method can overestimate hydration numbers for complexes with exchangeable protons at GdH distances similar to that of the coordinated water, for example, from NH groups. The 17O method does not suffer from this limitation. 17O ENDOR spectroscopy is applied to Gd(III) complexes containing zero, one, or two inner-sphere water molecules. In addition, 13C and 1H ENDOR studies were performed to assess the extent of methanol coordination, since methanol is used to produce a glass in these experiments. Under the experimental conditions used for the hydration number determination (30 mol % methanol), fewer than 15 % of the coordination sites were found to be occupied by methanol.