Optimization of pulsed DEER measurements for Gd-based labels: choice of operational frequencies, pulse durations and positions, and temperature.

In this work, the experimental conditions and parameters necessary to optimize the long-distance (≥ 60 Å) Double Electron-Electron Resonance (DEER) measurements of biomacromolecules labeled with Gd(III) tags are analyzed. The specific parameters discussed are the temperature, microwave band, the separation between the pumping and observation frequencies, pulse train repetition rate, pulse durations and pulse positioning in the electron paramagnetic resonance spectrum. It was found that: (i) in optimized DEER measurements, the observation pulses have to be applied at the maximum of the EPR spectrum; (ii) the optimal temperature range for Ka-band measurements is 14-17 K, while in W-band the optimal temperatures are between 6-9 K; (iii) W-band is preferable to Ka-band for DEER measurements. Recent achievements and the conditions necessary for short-distance measurements (<15 Å) are also briefly discussed.

Dielectric Resonator for Ka-Band Pulsed EPR Measurements at Cryogenic Temperatures: Probehead Construction and Applications.

The construction and performance of a Ka-band pulsed electron paramagnetic resonance (EPR) cryogenic probehead that incorporates dielectric resonator (DR) is presented. We demonstrate that the use of DR allows one to optimize pulsed double electron-electron resonance (DEER) measurements utilizing large resonator bandwidth and large amplitude of the microwave field B1 . In DEER measurements of Gd-based spin labels, use of this probe finally allows one to implement the potentials of Gd-based labels in distance measurements. Evidently, this DR is well suited to any applications requiring large B1-fields and resonator bandwidths, such as electron spin echo envelope modulation spectroscopy of nuclei having low magnetic moments and strong hyperfine interactions and double quantum coherence dipolar spectroscopy as was recently demonstrated in the application of a similar probe based on an loop-gap resonator and reported by Forrer et al. (J Magn Reson 190:280, 2008).

Pulsed dipolar spectroscopy distance measurements in biomacromolecules labeled with Gd(III) markers.

This work demonstrates the feasibility of using Gd(III) tags for long-range Double Electron Electron Resonance (DEER) distance measurements in biomacromolecules. Double-stranded 14- base pair Gd(III)-DNA conjugates were synthesized and investigated at K(a) band. For the longest Gd(III) tag the average distance and average deviation between Gd(III) ions determined from the DEER time domains was about 59±12Å. This result demonstrates that DEER measurements with Gd(III) tags can be routinely carried out for distances of at least 60Å, and analysis indicates that distance measurements up to 100Å are possible. Compared with commonly used nitroxide labels, Gd(III)-based labels will be most beneficial for the detection of distance variations in large biomacromolecules, with an emphasis on large scale changes in shape or distance. Tracking the folding/unfolding and domain interactions of proteins and the conformational changes in DNA are examples of such applications.

Electronic spectral studies of molybdenyl complexes. 2. MCD spectroscopy of [MoOS4]- centers.

Magnetic circular dichroism (MCD) and absorption spectroscopies have been used to probe the electronic structure of [PPh4][MoO(p-SC6H4X)4] (X = H, Cl, OMe) and [PPh4][MoO(edt)2] complexes (edt = ethane-1,2-dithiolate). The results of density functional calculations (DFT) on [MoO(SMe)4]- and [MoO(edt)2]- model complexes were used to provide a framework for the interpretation of the spectra. Our analysis shows that the lowest energy transitions in [MoVOS4] chromophores (S4 = sulfur donor ligand) result from S-->Mo charge transfer transitions from S valence orbitals that lie close to the ligand field manifold. The energies of these transitions are strongly dependent on the orientation of the S lone-pair orbitals with respect to the Mo atom that is determined by the geometry of the ligand backbone. Thus, the lowest energy transition in the MCD spectrum of [PPh4][MoO(p-SC6H4X)4] (X = H) occurs at 14,800 cm-1, while that in [PPh4][MoO(edt)2] occurs at 11,900 cm-1. The identification of three bands in the absorption spectrum of [PPh4][MoO(edt)2] arising from LMCT from S pseudo-sigma combinations to the singly occupied Mo 4d orbital in the xy plane suggests that there is considerable covalency in the ground-state electronic structures of [MoOS4] complexes. DFT calculations on [MoO(SMe)4]- reveal that the singly occupied HOMO is 53% Mo 4dxy and 35% S p for the equilibrium C4 geometry. For [MoO(edt)2]- the steric constraints imposed by the edt ligands result in the S pi orbitals being of similar energy to the Mo 4d manifold. Significant S pseudo-sigma and pi donation may also weaken the Mo identical to O bond in [MoOS4] centers, a requirement for facile active site regeneration in the catalytic cycle of the DMSO reductases. The strong dependence of the energies of the bands in the absorption and MCD spectra of [PPh4][MoO(p-SC6H4X)4] (X = H, Cl, OMe) and [PPh4][MoO(edt)2] on the ligand geometry suggests that the structural features of the active sites of the DMSO reductases may result in an electronic structure that is optimized for facile oxygen atom transfer.

An MCD spectroscopic study of the molybdenum active site in sulfite oxidase: insight into the role of coordinated cysteine.

Temperature-dependent magnetic circular dichroism (MCD) spectroscopy has been used for the first time to probe the electronic structure of the Mo active site in sulfite oxidase (SO). The enzyme was poised in the catalytically relevant [Mo(V):Fe(II)] state by anaerobic reduction of the enzyme with the natural substrate, sulfite, in the absence of the physiological oxidant cytochrome c. The [Mo(V):Fe(II)] state is of particular importance, as it is proposed to be a catalytic intermediate in the oxidative half reaction, where SO is reoxidized to the resting [Mo(VI):Fe(III)] state by two sequential one-electron transfers to cytochrome c. The MCD spectrum of the enzyme shows no charge transfer transitions below approximately 17000 cm(-1). This has been interpreted to result from (1) a severe reduction in ene-1,2-dithiolate sulfur in-plane and out-of-plane p orbital mixing, (2) a decrease in the dithiolate sulfur out-of-plane p-Mo d(xy) orbital overlap, and (3) an orthogonal orientation between the vertical cysteine sulfur p (perpendicular to the Mo-Scys sigma-bond) and Mo d(xy) orbitals. The spectroscopically determined cysteine sulfur p-Mo d(xy) bonding scheme in the [Mo(V):Fe(II)] state is consistent with the crystallographically determined O-Mo-Scys-C dihedral angle of approximately 90 degrees and precludes a covalent interaction between the vertical cysteine sulfur p orbital and Mo d(xy), effectively decoupling the cysteine from an effective through-bond electron transfer pathway. We have tentatively assigned a 22250 cm(-1) positive C-term feature in the MCD as the cysteine S(sigma)-->Mo d(xy) charge transfer that becomes allowed by a combination of configuration interaction and low-symmetry; however, the orbital overlap is anticipated to be quite small due to the near orthogonality of these orbitals. Therefore, we propose that the primary role of the coordinated cysteine is to decrease the effective nuclear charge on Mo by charge donation to the metal, statically poising the active site at more negative reduction potentials during electron transfer (ET) regeneration. Finally, the results of this study are consistent with the pyranopterin ene-1,2-dithiolate acting to couple the Mo site into efficient superexchange pathways for ET regeneration following oxygen atom transfer to the substrate.

Analogues for the molybdenum center of sulfite oxidase: oxomolybdenum(V) complexes with three thiolate sulfur donor atoms.

cis,trans-(L-N2S2)Mo(V)O(SR) [L-N2S2H2 = N,N'-dimethyl-N,N'-bis(mercaptophenyl)ethylenediamine; R = CH2Ph, CH2CH3, and p-C6H4-Y (Y = CF3, Cl, Br, F, H, CH3, CH2CH3, and OCH3)] are the first structurally characterized mononuclear Mo compounds with three thiolate donors, as occurs at the Mo active site in sulfite oxidase. X-ray crystal structures of the cis,trans-(L-N2S2)Mo(V)O(SR) compounds, where R = CH2Ph, CH2CH3, p-C6H4-OCH3, and p-C6H4-CF3, show a similar coordination geometry about the Mo atom with all three sulfur thiolate donors in the equatorial plane. This coordination geometry places two adjacent S ppi orbitals parallel to the Mo=O bond, analogous to the orientation in the ene-dithiolate ligand in sulfite oxidase; the third S ppi orbital lies in the equatorial plane. Charge-transfer transitions from the S p to the Mo d orbitals occur at approximately 28,000 cm(-1) (epsilon: 4,400-6,900 L mol(-1)] cm(-1)) and 15,500 cm(-1) (epsilon: 3,200-4,900 L mol(-1) cm(-1)). The EPR parameters are nearly identical for all the cis,trans-(L-N2S2)Mo(V)O(SR) compounds (g1 approximately 2.022, g2 approximately 1.963, g3 approximately 1.956, Al approximately 58.4 x 10(-4) cm(-1), A2 approximately 23.7 x 10(-4) cm(-1), A3 approximately 22.3 x 10(-4) cm(-1)) and are typical of an oxo-Mo(V) center coordinated by multiple thiolate donors. The g and A tensors are related by a 24 degrees rotation about the coincident g2 and A2 tensor elements, reflecting the approximate Cs coordination symmetry. These EPR parameters more closely mimic those of the low pH form of sulfite oxidase and the "very rapid" species of xanthine oxidase than previous model compounds with two or four thiolate donors. The cis,trans-(L-N2S2)Mo(V)O(SR) compounds undergo a quasi-reversible, one-electron reduction and an irreversible oxidation that show a linear dependence upon the Hammett parameter, sigmap, of the Y group. The cis,trans-(L-N2S2)Mo(V)O(SR) compounds provide a well-defined platform for the systematic investigation of the electronic structures of the Mo(V)OS3 centers and their implications for molybdoenzymes.

The pH dependence of intramolecular electron transfer rates in sulfite oxidase at high and low anion concentrations.

The individual rate constants for intramolecular electron transfer (IET) between the Mo(VI)Fe(II) and Mo(V)Fe(III) forms of chicken liver sulfite oxidase (SO) have been determined at a variety of pH values, and at high and low anion concentrations. Large anions such as EDTA do not inhibit IET as dramatically as do small anions such as SO4(2-) and Cl-, which suggests that specific anion binding at the sterically constrained Mo active site is necessary for IET inhibition to occur.IET may require that SO adopt a conformation in which the Mo and Fe centers are held in close proximity by electrostatic interactions between the predominantly positively charged Mo active site, and the negatively charged heme edge. Thus, small anions which can fit into the Mo active site will weaken this electrostatic attraction and disfavor IET. The rate constant for IET from Fe(II) to Mo(VI) decreases with increasing pH, both in the presence and absence of 50 mM SO4(2-) . However, the rate constant for the reverse process exhibits no significant pH dependence in the absence of SO4(2-), and increases with pH in the presence of 50 mM S04(2-). This behavior is consistent with a mechanism in which IET from Mo(V) to Fe(III) is coupled to proton transfer from Mo(V)-OH to OH-, and the reverse IET process is coupled to proton transfer from H2O to Mo(VI) = O. At high concentrations of small anions, direct access of H2O or OH- to the Mo-OH will be blocked, which provides a second possible mechanism for inhibition of IET by such anions. Inhibition by anions is not strictly competitive, however, and Tyr322 may play an important intermediary role in transferring the proton when an anion blocks direct access of H2O or OH- to the Mo-OH. Competing H-bonding interactions of the Mo-OH moiety with Tyr322 and with the anion occupying the active site may also be responsible for the well-known equilibrium between two EPR-distinct forms of SO that is observed for the two-electron reduced enzyme.

A chemical approach to systematically designate the pyranopterin centers of molybdenum and tungsten enzymes and synthetic models.

The recent growth in the chemistry of the oxo-molybdenum enzymes has demonstrated the need for developing systematic methods for naming and abbreviating the novel pterin cofactors that bind to the metal ion via the sulfur atoms of an ene-1,2-dithiolate moiety. Historically, the term "molybdopterin" was coined to designate a special pterin that binds molybdenum and the molybdenum-bound form was termed the "molybdenum cofactor". However, recent studies have demonstrated that this novel pterin also binds tungsten. Furthermore, considerable variation has been found in the pterin entity itself. Taken together, these facts show that molybdenum- and tungsten-containing enzymes possess a family of cofactors rather than a single "molybdenum cofactor". This article proposes a unified methodology for describing these cofactors and their metal-free pterin units in light of recent results from protein crystallography. The various numbering schemes that have been used for this heterocycle are considered, as well as the IUPAC rules which are currently being used for related tricyclic compounds. A unified methodology for uniquely designating and abbreviating each cofactor is proposed. The available chemical and spectroscopic information on the pyranopterin entities that are present in the molybdenum and tungsten enzymes, the precursors to these centers, and synthetic pyranopterins are in part the basis of the systematic names and simplifying abbreviations.

The active sites of molybdenum- and tungsten-containing enzymes.

Protein X-ray crystallography has revealed the structures of the active sites of several molybdenum- and tungsten-containing enzymes that catalyze formal hydroxylation and oxygen atom transfer reactions. Each molybdenum (or tungsten) atom is coordinated by one (or two) ene-dithiolate groups of a novel pterin (molybdopterin), and the active sites are further differentiated from one another by the number of terminal oxo and/or sulfido groups and by coordinated amino acid residues. These active-site structures have no precedent in the coordination chemistry of molybdenum and tungsten.

Molecular basis of sulfite oxidase deficiency from the structure of sulfite oxidase.

The molybdenum-containing enzyme sulfite oxidase catalyzes the conversion of sulfite to sulfate, the terminal step in the oxidative degradation of cysteine and methionine. Deficiency of this enzyme in humans usually leads to major neurological abnormalities and early death. The crystal structure of chicken liver sulfite oxidase at 1.9 A resolution reveals that each monomer of the dimeric enzyme consists of three domains. At the active site, the Mo is penta-coordinated by three sulfur ligands, one oxo group, and one water/hydroxo. A sulfate molecule adjacent to the Mo identifies the substrate binding pocket. Four variants associated with sulfite oxidase deficiency have been identified: two mutations are near the sulfate binding site, while the other mutations occur within the domain mediating dimerization.

Electron transfer in sulfite oxidase: effects of pH and anions on transient kinetics.

Intramolecular electron transfer (ET) rates in sulfite oxidase (SO) were measured using flavin semiquinone reductants [5-deazariboflavin (dRFH.) and lumiflavin (LFH.)] generated by laser flash photolysis. Rapid bimolecular reduction of the heme by the dRF semiquinone occurred (k = 4 x 10(8) M-1 s-1 at pH 6; 1 x 10(8) M-1 s-1 at pH 9), followed by heme Fe(II) reoxidation due to intramolecular electron transfer to Mo(VI). Flash-induced difference spectra indicated that only spectral processes due to reduction and oxidation of the b-type heme prosthetic group were observed, with no detectable spectral contribution from the Mo cofactor. The extent of reoxidation decreased greatly from pH 6 to 9 (50% to 3%), as expected from the shifts in the redox potentials of the heme and Mo cofactor with pH, consistent with an electron transfer equilibrium between the two redox centers. The observed rate constant for the Fe(II) to Mo(VI) electron transfer decreased from 1650 s-1 at pH 6 to 60 s-1 at pH 9 and showed a maximum of 2400 s-1 at pH 7. Increases in salt concentration greatly decreased intramolecular ET rate constants (direct reduction by flavin semiquinone was unchanged), due to the binding of anions. Titration with the sodium salts of Cl-, SO4(2-), and H2PO4-/HPO4(2-) resulted in decreases in rate constants of intramolecular ET from 1500 s-1 to < 100 s-1 at pH 6 and 7. Similar dissociation constants were measured for the binding of these anions by flash photolysis and by steady-state enzyme kinetics using the inhibition of the sulfite/cytochrome c assay reaction for sulfite oxidase. A mechanism is proposed in which anion binding to the enzyme inhibits the rate of intramolecular electron transfer.

Structure of bis(4-chlorophenolato)[hydrotris(3,5-dimethyl-1- pyrazolyl)borato]oxomolybdenum(V).

[Mo(C15H22BN6)(C6H4ClO)2O], M(r) = 664.24, triclinic, P1, a = 10.585 (2), b = 12.068 (3), c = 13.728 (3) A, alpha = 88.01, beta = 69.94, gamma = 65.78 degrees, V = 1490.8 A3, Z = 2, Dx = 1.48 g cm-3, Mo K alpha, lambda = 0.71073 A, mu = 6.5 cm-1, F(000) = 678, T = 296 (1) K, R = 0.034, wR = 0.049 for 4634 observed independent reflections with F2 greater than 3 sigma (F2). This is the second structurally characterized mononuclear monooxo transition-metal complex containing the phenolato ligand. The molecule exhibits a distorted octahedral coordination geometry, and the Mo atom is ligated by a terminal O atom, two p-chloro-substituted phenolato groups, and a tridentate facially coordinated hydrotris(3,5-dimethylpyrazolyl)borate ligand (L).

Bis(benzenethiolato)nitrosyl [tris(3,5-dimethyl-1-pyrazolyl)hydroborato]-molybdenum(II) .

[Mo(C15H22BN6)(C6H5S)2(NO)], Mr = 641.5, monoclinic, P2(1)/n, a = 10.898 (1), b = 18.484 (2), c = 15.989 (2) A, beta = 109.81 (1) degree, V = 3030.2 A3, Z = 4, Dx = 1.41, Dm = 1.41 g cm-3, lambda(Mo K alpha) = 0.7173 A, mu = 5.9 cm-1, F(000) = 1320, T = 293 K, wR = 0.047 for 3997 observed reflections. In each complex, the Mo atom is six-coordinate, ligated by a terminal NO group, a tridentate pyrazolylborate ligand and two benzenethiolate ligands. The structure is compared with that of similar complexes and the Mo-S bonding is discussed.

Structure of the active site of sulfite oxidase. X-ray absorption spectroscopy of the Mo(IV), Mo(V), and Mo(VI) oxidation states.

The active site of sulfite oxidase has been investigated by X-ray absorption spectroscopy at the molybdenum K-edge at 4 K. We have investigated all three accessible molybdenum oxidation states, Mo(IV), Mo(V), and Mo(VI), allowing comparison with the Mo(V) electron paramagnetic resonance data for the first time. Quantitative analysis of the extended X-ray absorption fine structure indicates that the Mo(VI) oxidation state possesses two terminal oxo (Mo = O) and approximately three thiolate-like (Mo-S-) ligands and is unaffected by changes in pH and chloride concentration. The Mo(IV) and Mo(V) oxidation states, however, each have a single oxo ligand plus one Mo-O- (or Mo-N less than) bond, most probably Mo--OH, and two to three thiolate-like ligands. Both reduced forms appear to gain a single chloride ligand under conditions of low pH and high chloride concentration.

Structure of oxobis(phenolato)[tris(3,5-dimethyl-1-pyrazolyl)-hydroborato]molybdenum (V).

C27H32BMoN6O3, Mr = 595.34, monoclinic, P2(1)/n, a = 16.376 (6), b = 10.438 (5), c = 17.016 (8) A, beta = 107.25 (3) degrees, V = 2777.8 A3, Z = 4, Dm = 1.37, Dx = 1.43 g cm-3, Mo K alpha,lambda = 0.71073 A, mu = 5.02 cm-1, F(000) = 1228, T = 296 K, R = 0.038, wR = 0.045 for 2457 reflections. This molecule is the first structurally characterized mononuclear molybdenum complex containing a terminal aryl oxide ligand. The central molybdenum atom adopts a distorted octahedral coordination geometry with one face of the octahedron occupied by the tridentate pyrazolylborate ligand and the opposite face by the oxo and the two phenolato ligands. The structure is compared with that of the analogous benzenethiolate complex.

Purification of prosthetically intact sulfite oxidase from chicken liver using a modified procedure.

A modified procedure was used to purify sulfite oxidase (sulfite:O2 oxidoreductase; EC 1.8.3.1) from chicken liver in high yield. The modifications included dialysis of the enzyme against a buffered solution containing sodium molybdate (prior to ion-exchange chromatography), which apparently reconstituted any demolybdo enzyme present in the extract, and phenyl-Sepharose column chromatography. Analysis showed that the purified enzyme contained Mo and heme in a 1.03:1.00 ratio, indicating that the enzyme was prosthetically intact; exogenous heme and other colored proteins were absent from the final pool. Treatment of the sulfite-reduced enzyme with 50 mM cyanide at pH 8.5 resulted in a gradual loss of catalytic activity with a half-life of 19.7 min. Analysis of the cyanide-inactivated enzyme gave a Mo:heme ratio of 1.02:1.00, providing the first direct evidence that the enzyme does not lose molybdenum when inactivated with cyanide. This modified purification procedure provides enzyme in high yield which is well-suited for experiments requiring prosthetically intact enzyme and which is not contaminated with extraneous heme or with other redox active proteins.

The nature of the phosphate complex of sulphite oxidase from electron-paramagnetic-resonance studies.

The phosphate complex of sulphite oxidase in the Mo(V) oxidation state was investigated by e.p.r. spectroscopy. Third-derivative spectra reveal a wealth of structural detail previously unobserved in this spectrum. Most notable is the presence of hyperfine coupling from two inequivalent I = 1/2 nuclei, which we tentatively attribute to two 31P nuclei. Unresolved hyperfine interactions from at least one exchangeable 1H nucleus are also present.

Chicken liver sulfite oxidase. Kinetics of reduction by laser-photoreduced flavins and intramolecular electron transfer.

Laser flash photolysis was used to study the reaction of photoproduced 5-deazariboflavin (dRFH.), lumiflavin (LFH.), and riboflavin (RFH.) semiquinone radicals with the redox centers of purified chicken liver sulfite oxidase. Kinetic studies of the native enzyme with dRFH. yielded a second-order rate constant of 4.0 X 10(8) M-1 s-1 for direct reduction of the heme and a first-order rate constant of 310 s-1 for intramolecular electron transfer from the Mo center to the heme. The reaction with LFH. gave a second-order rate constant of 2.9 X 10(7) M-1 s-1 for heme reduction. Reoxidation of the reduced heme due to intramolecular electron transfer to the Mo center gave a first-order rate constant of 155 s-1. The direction of intramolecular electron transfer using dRFH. and LFH. was independent of the buffer used for the experiment. The different first-order rate constants observed for intramolecular electron transfer using dRFH. and LFH. are proposed to result from chemical differences at the Mo site. Flash photolysis studies with cyanide-inactivated sulfite oxidase using dRFH. and LFH. resulted in second-order reduction of the heme center with rate constants identical with those obtained with the native enzyme, whereas the first-order intramolecular electron-transfer processes seen with the native enzyme were absent. The isolated heme peptide of sulfite oxidase gave only second-order kinetics upon laser photolysis and confirmed that the first-order processes observed with the native enzyme involve the Mo site.(ABSTRACT TRUNCATED AT 250 WORDS)

Stereochemical Control of Valence and Its Application to the Reduction of Coordinated NO and N(2).

The electronic structures of transition metal complexes of NO are controlled by the stereochemistry about the metal atom (stereochemical control of valence). The six-coordinate complex, trans-[CoNO(NCS)-(C(6)H(4) [As(CH(3))(2)](2))(2)](+), consists of [Co(III)-(N=O(-))](2+) (angle(Co-N-O) = 135 degrees ), while the pentacoordinate trigonal bipyramidal complex, [CoNO(C(6)H(4)[As(CH(3))(2)](2))(2)] (2+), is best formulated as [Co(I)-(N identical withO(+)](2+) (angle(Co-N-O) = 179 degrees ). Evidence indicates that complexes of (NO)(+) and N(2) are electronically similar. Hence, the principles of stereochemical control of valence may be applied to metal complexes of N(2). In a linearly coordinated M(n) m(N identical withN) complex, valence electrons can be transferred from the metal to the N(2) ligand producing a bent, protonated, and/or metallated M(n+2)-(N=N(2-)) complex. This reduction of N(2) can be effected by the addition of an appropriate ligand to M or by a change in the coordination geometry about M. Stereo-chemical control of valence leads to the rejection of one of the previously proposed mechanisms for reduction by nitrogenase.