Studying high-spin ferric heme proteins by pulsed EPR spectroscopy: Analysis of the ferric form of the E7Q mutant of human neuroglobin

In this work, the high-spin ferric form of the E7Q mutant of human neuroglobin (E7Q-NGB) is studied by X-band continuous-wave electron paramagnetic resonance (CW EPR) and hyperfine sublevel correlation (HYSCORE) spectroscopy. It is shown that the use of matched pulses in the HYSCORE experiment is essential to observe the nitrogen spectral contributions. The validity of approximating the high-spin Fe(III) system (S=5/2) as an effectiveS=1/2 system is tested and the consequences for the HYSCORE simulations are highlighted. Comparative HYSCORE experiments combined with deuterium exchange experiments for aquometmyoglobin and ferric E7Q-NGB clearly show that the heme iron of the latter protein is pentacoordinated, lacking the distal water. Furthermore, CW EPR experiments show that, at high pH, the E10K residue is coordinating to the heme iron in this globin. These observations are corroborated by resonance Raman experiments and could also be reproduced for other E7 mutants of human and mouse neuroglobin. Finally, the proton and nitrogen hyperfine and nuclear quadrupole parameters obtained for ferric E7Q-NGB are discussed in detail.     

Site-specific oxidation of the [Fe4S4] cubanes in high-potential iron sulfur proteins as probed by EPR and orientation-selective proton ENDOR spectroscopy:Ectothiorhodospira halophila I versusRhodocyclus tenuis

Electron paramagnetic resonance (EPR) and proton ENDOR (electron-nuclear double resonance) spectroscopies were used to analyze the structural and electronic parameters of the oxidized [Fe₄S₄] cubane clusters in high-potential iron sulfur proteins (HiPIPs) fromEctothiorhodospira halophila (HiPIP I) andRhodocyclus tenuis. TheE. halophila HiPIP I EPR spectra at X- and Q-band revealed a dominant species (simulated withg _max=2.1425,g _int=2.0315,g _min=2.0296) and a minor species (ca. 5–10% contribution) which was not analyzed further. ForR. tenuis HiPIP the EPR spectrum contained a single species only (g _max=2.1140,g _int=2.0392,g _min=2.0215), i.e., withg _max significantly smaller than that of theE. halophila protein. Orientation-selected proton ENDOR spectra of HiPIP I ofE. halophila were reconstructed by simulation with slight modifications of the crystal structure data. ENDOR from two mutants, F36S and F36G, ofE. halophila HiPIP I gave evidence for a common assignment of a HB2 proton of a phenylalanine residue (36 and 44, respectively, in isoenzymes I and II as reported earlier) interacting with the mixed-valence pair iron ions Fe2 and Fe3. ForR. tenuis HiPIP, the ENDOR spectra were assigned to arise from Fe3 and Fe4 as mixedvalence pair under the assumption of an unchanged intrinsicg-tensor symmetry. The resulting site specificity of the cubane oxidation was discussed in relation to structural requirements and redox potentials of the two HiPIPs.     

EPR and ENDOR Investigation of Rhodosemiquinone in Bacterial Reaction Centers Formed by B-Branch Electron Transfer

In photosynthetic bacteria, light-induced electron transfer takes place in a protein called the reaction center (RC) leading to the reduction of a bound ubiquinone molecule, Q_B, coupled with proton binding from solution. We used electron paramagnetic resonance (EPR) and electron-nuclear double resonance (ENDOR) to study the magnetic properties of the protonated semiquinone, an intermediate proposed to play a role in proton coupled electron transfer to Q_B. To stabilize the protonated semiquinone state, we used a ubiquinone derivative, rhodoquinone, which as a semiquinone is more easily protonated than ubisemiquinone. To reduce this low-potential quinone we used mutant RCs modified to directly reduce the quinone in the Q_B site via B-branch electron transfer (Paddock et al. in Biochemistry 44:6920–6928, 2005). EPR and ENDOR signals were observed upon illumination of mutant RCs in the presence of rhodoquinone. The EPR signals had g values characteristic of rhodosemiquinone (g _x  = 2.0057, g _y  = 2.0048, g _z  ~ 2.0018) at pH 9.5 and were changed at pH 4.5. The ENDOR spectrum showed couplings due to solvent exchangeable protons typical of hydrogen bonds similar to, but different from, those found for ubisemiquinone. This approach should be useful in future magnetic resonance studies of the protonated semiquinone.     

The ups and downs of Feher-style ENDOR

A new transient variation of the “Feher-style” electron-nuclear double resonance (ENDOR) method is examined. In this technique, the passage-mode electron paramagnetic resonance (EPR) signal is monitored following the application of a pulsed radio frequency (RF). Continuous-wave and transient proton ENDOR experiments have been conducted on the nonheme iron center from the protein nitrile hydratase. These experiments show that the transient ENDOR signal response exhibits a complex response with multiple phases in the time evolution of the ENDOR signal. Both increases and decreases in the passage-mode EPR signals are observed at different times following the RF pulse that induces an ENDOR transition. A simple model based on a packet-shifting ENDOR mechanism for a nonadiabatic passage EPR signal is proposed. This model describes many of the features seen in the transient ENDOR experiments and provides new insight into the traditional Feher-style ENDOR measurements. This new model shows that a packet-shifting mechanism can account for many of the “negative ENDOR” effects commonly seen in Feher-style ENDOR, which suggests that more exotic ENDOR mechanisms may not be required to explain these observations.     

Local structure of titanium pair centers in SrF2 crystals: EPR and ENDOR spectroscopic studies

The local structure of titanium pair centers in SrF₂: Ti crystals is investigated using electron paramagnetic resonance (EPR) and electron-nuclear double resonance (ENDOR) spectroscopy. It is found that titanium pair centers with spin moment S=2 and tetragonal symmetry of the magnetic properties are formed in SrF₂: Ti cubic crystals under certain growth conditions and during annealing. The tensor components of the fine and ligand hyperfine structures in the EPR and ENDOR spectra are determined. A model of the Ti⁺-Ti³⁺ paramagnetic dimer is proposed. This model provides an adequate interpretation of both the ferromagnetic nature of the exchange interaction and the observed displacements of four ligands in the first coordination sphere of titanium impurity ions in directions perpendicular to the impurity ion-ligand bonds.     

Angle-selective measurements of spin soliton in ladder polydiacetylene by pulsed 94 GHz EPR

Angle-selection experiments of a spin soliton in randomly oriented ladder polydiacetylene were carried out by pulsed electron paramagnetic resonance (EPR) at W-band. EPR measurement using 94 GHz microwaves increased the difference in the resonance field due tog anisotropy of the spin soliton to allow the orientation dependence of transient nutation, electron nuclear double resonance (ENDOR) and spin relaxations to be investigated. The shape of theg anisotropy-resolved nutation spectrum was discussed on the basis of the EPR transition moments and the differences between spin relaxation times. Reliable assignments of hyperfine couplings to the β protons (H_β) of the alkyl side chains were achieved with the support of W-band ENDOR measurements. No significant orientational dependence in theT ₁ andT ₂ processes was found in terms of isotropy of the H_β-hyperfine interaction.     

Probing electronic and structural properties of the reduced [2Fe−2S] cluster by orientation-selective1H ENDOR spectroscopy: Adrenodoxin versus rieske iron-sulfur protein

The¹H electron-nuclear double resonance (ENDOR) spectra in frozen buffer solutions of the reduced [2Fe?2S] clusters in adrenodoxin (Adx) and in the “Rieske” iron-sulfur protein (ISP) from the bovine mitochondrial bc1 complex were measured at low temperatures (5–20 K) and analyzed by spectra reconstruction. A single paramagnetic species with iron valence states (II) and (III) connected uniquely to the cluster irons was found in both proteins. For Adx, the experimental spectra from 23 field positions across the nearly axial (g _max=2.0241,g _int=1.9347, andg _min=1.9331) electron paramagnetic resonance (EPR) spectrum were analyzed. Four larger hyperfine couplings were assigned to the cysteine β-protons near the Fe(III) ion. Transfer into the crystal structure showed that the Fe(III) ion was coordinated to the residues Cys55 and Cys92. The spin density was estimated as +1.60 for the Fe(III) and ?0.6 for the Fe(II) ion, respectively. Theg-tensor direction with respect to the cluster showed strong similarities with the earlier assignment inArthospira platensis ferredoxin (Canne C., Ebelshauser M., Gay E., Shergill J.K., Cammack R., Kappl R., Hüttermann J.: J. Biol. Inorg. Chem. 5, 514, 2000). An Adx mutant (T54A) exhibiting a change (70 mV) in redox potential showed no significant influence at the [2Fe?2S] cluster. The Rieske ISP was subjected to the same analysis. The ENDOR spectra from 35 field positions across the rhombic (g _max=2.028,g _int=1.891, andg _min=1.757) EPR spectrum were simulated. Three major proton contributions were identified from the orientation behavior. Two were assigned to cysteine β-protons and one to a β-proton of His141. In contrast to Adx, the direction of theg _max-component was found to lie roughly in the FeS-core plane and the largest proton coupling occurred alongg _int. The spin population was estimated as about +1.6 for the oxidized and ?0.55 for the reduced iron.     

Pulse EPR spectroscopy of Cu2+-doped inorganic glasses

Two-frequency continuous-wave and pulse EPR (electron paramagnetic resonance) spectroscopical techniques are applied to determine static and dynamic EPR parameters of Cu²⁺ ions in oxide and fluoride glasses. The investigations are focussed on the analysis of strain effects in the glassy matrices, the identification of the magnetic nuclei in the vicinity of Cu²⁺ ions as well as the determination of the dependence of the phase memory timeT _M on temperature and resonance field. The results obtained by X-band continuous-wave EPR, X- and S-band echo-detected EPR, and X- and S-band electron spin echo envelope modulation studies of Cu²⁺-doped inorganic glasses yield information on the local symmetry of the Cu²⁺ coordination polyhedra, the chemical nature of the atoms in the second and higher coordination spheres, the distribution of the parameters of the static spin Hamiltonian and the low-temperature motions of the dopant-containing structural units. Special techniques like 2-D Mims ENDOR (electron nuclear double resonance) and hyperfine-correlated ENDOR are applied for the first time to doped inorganic glasses. From the spin relaxation measurements a stronger tendency of the Cu²⁺ ions to aggregate is found for fluoride glasses in comparison to aluminosilicate and phosphate glasses.     

Electron nuclear quadruple resonance for assignment of overlapping spectra

Multiple resonance methods are important tools in EPR for revealing the network of hyperfine levels of free radicals and paramagnetic centers. The variations of electron nuclear double resonance (ENDOR) or electron spin-echo envelope modulation (ESEEM) techniques help to correlate nuclear frequencies with each other. These methods have limited utility when there is extensive overlap or suspected overlap in the EPR spectrum between different species or different orientations. In the ENDOR spectrum, overlap and second-order shifts of lines also leads to ambiguity in assignment and interpretation. A new electron nuclear multiple resonance method is presented here that is based on population transfer ENDOR. It is a quadruple resonance method that correlates ENDOR lines and reveals the network of hyperfine levels in samples with unoriented paramagnetic species and in samples with overlapping EPR or ENDOR lines.     

Anomalous Phases in Cavity-Free 240 GHz Pulsed ENDOR Spectra of 1.44 GeV Xe-Irradiated LiF

Paramagnetic centers generated by swift heavy ion irradiation of LiF crystals could be identified as electrons trapped at regular anion vacancy sites (F centers). Well-resolved electron-nuclear double resonance (ENDOR) spectra resulting from the hyperfine interaction with ⁷Li and ¹⁹F nuclei located in six different shells could be recorded. In order to preserve the millimeter-sized crystals, a cavity-free setup was used for the ENDOR experiments at an electronic Larmor frequency of 240 GHz. Apparently even under conditions of extremely high local energy loss in the ion track, the local density of persistent F centers is still sufficiently low to prevent distortions of the ionic crystal. The spread of hyperfine coupling constants was less than 5 %. Neither in electron paramagnetic resonance (EPR) nor in ENDOR spectra there was evidence for different types of paramagnetic centers. When performing ENDOR by applying the radiofrequency pulse directly after the 3-pulse Mims-type microwave sequence, an anomalous ENDOR effect was observed. The observed “positive” and “negative” ENDOR response can be attributed to efficient hole and anti-hole formation in the inhomogeneously broadened EPR spectrum and can be used to determine the sign of hyperfine coupling constants.     

Pulse EPR, ENDOR, and ELDOR Study of Anionic Flavin Radicals in Na+-Translocating NADH:Quinone Oxidoreductase

The Na⁺-translocating nicotinamide adenine dinucleotide (NADH):quinine oxidoreductase (Na⁺–NQR) is a component of respiratory chain of various bacteria and it generates a redox-driven transmembrane electrochemical Na⁺ potential. It contains four different flavin prosthetic groups, including two flavin mononucleotide (FMN) residues covalently bound to the subunits NqrB and NqrC. Na⁺–NQR from Vibrio harveyi was poised at different redox potentials to prepare two samples, containing either both FMN_NqrB and FMN_NqrC or only FMN_NqrB in a paramagnetic state. These two samples were comparatively studied using pulse electron paramagnetic resonance (EPR), electron-nuclear double resonance (ENDOR), and electron-electron double resonance (ELDOR) spectroscopy. The echo-detected EPR spectra and electron spin relaxation properties were very similar for flavin radicals in both samples. The splitting of the outer peaks in the proton ENDOR spectra, assigned to the C(8α) methyl protons, allows to identify both radicals as anionic flavosemiquinones. The mean interspin distance of 20.7 Å between these radicals was determined by pulse ELDOR experiment, which allows to estimate the edge-to-edge distance (r _e) between these flavin centers as: 11.7 Å < r _e < 20.7 Å. The direct electron transfer between FMN_NqrB and FMN_NqrC during the physiological turnover of the Na⁺–NQR complex is suggested.     

1H and31P ENDOR of the isotropic CO2 − signal atg=2.0007 in the EPR spectra of precipitated carbonated apatites

The isotropic EPR signal atg=2.0007 in X-irradiated carbonated apatites, precipitated from aquaeous solutions and dried at 25°C, is investigated with Electron Nuclear Double Resonance (ENDOR). The²³Na,³¹P and¹H ENDOR results indicate that the precursor of this radical is most probably located in an aqueous phase entrapped between the crystallites (the so-called occluded water). Other experimental features, such as the correlation between the appearance of the signal in the EPR spectrum and the presence of some residual (adsorbed and/or occluded) water in the sample seem to strengthen our hypothesis.     

EPR and ENDOR Studies of Shallow Donors in SiC

Recent progress in the investigation of the electronic structure of the shallow nitrogen (N) and phosphorus (P) donors in 3C–, 4H– and 6H–SiC is reviewed with focus on the applications of magnetic resonance including electron paramagnetic resonance (EPR) and other pulsed methods such as electron spin echo, pulsed electron nuclear double resonance (ENDOR), electron spin-echo envelope modulation and two-dimensional EPR. EPR and ENDOR studies of the ²⁹Si and ¹³C hyperfine interactions of the shallow N donors and their spin localization in the lattice are discussed. The use of high-frequency EPR in combination with other pulsed magnetic resonance techniques for identification of low-temperature P-related centers in P-doped 3C–, 4H– and 6H–SiC and for determination of the valley–orbit splitting of the shallow N and P donors are presented and discussed.     

Matrix ENDOR of ion-exchange systems

Electron nuclear double resonance (ENDOR) has been investigated in sulfocation exchangers, containing free radicals stabilized in polymeric matrix or Cu²⁺ and (VO)²⁺ as counterions. It was shown that the ENDOR signal is mainly due to electron-nuclear dipole-dipole interactions between the unpaired electron and nuclei of polymeric matrix or hydrogen atoms of water molecules which hydrate the charge groups. In order to quantitatively describe the ENDOR line shape and intensity, the theory of matrix ENDOR is developed. The correctness of this theory was tested by comparing the temperature dependence of spin-lattice relaxation times calculated from ENDOR line intensities with the corresponding dependence obtained from stationary saturation electron spin resonance spectra. A good agreement was observed in the temperature range from 200 to 350 K. The structural parameters of surroundings of paramagnetic ions Cu²⁺ and (VO)²⁺, which include four coordinated spheres on the distance from 0.3 to 1.2 nm, were calculated. The motional parameters, correlation time and activation energy of mobile protons were also determined. It is concluded that the activation processes of water self-diffusion and proton exchange take place at high temperature, whereas the proton tunneling transfer is possible at low temperature.     

Radio frequencies in EPR: Conventional and advanced use

This mini-review focuses on various aspects of the application of radio frequency (rf) irradiation in electron paramagnetic resonance (EPR). The development of the electron-nuclear double resonance (ENDOR) technique is briefly described, and we highlight the use of circularly polarized rf fields and pulse ENDOR methodology in one- and two-dimensional experiments. The capability of pulse ENDOR at Q-band is illustrated with interesting experimental examples. Electron spin echo envelope modulation effects induced by an rf field in liquid samples demonstrate another role which rf fields can play. Technical achievements in the design of ENDOR resonators are illustrated by the example of a bridged loop-gap resonator. Finally, the influence of longitudinal rf fields on the dynamics of EPR transitions is explained using a dressed spin resonance treatment.     

Structure and conformation of nitroxyl spin-label compounds in frozen solutions by electron nuclear double resonance spectroscopy

The structure and conformation of carboxylic acid, formyl, and propenoic acid derivatives of the nitroxyl spin-label 2,2,5,5-tetramethyl-1-oxypyrroline have been determined by electron nuclear double resonance (ENDOR) spectroscopy. From ENDOR spectra of the spin-label compounds in frozen solutions, we have assigned the resonance absorption features for each class of protons. The ENDOR spectra were analyzed on the basis of their dependence onH ₀. The maximum and minimum ENDOR shifts for each proton were shown to correspond to axially symmetric principal hyperfine coupling (hfc) components, from which the dipolar contributions were estimated to calculate electron-proton separations. Conformational analysis on the basis of torsion angle search calculations constrained by the ENDOR determined electron-proton distances revealed that in all three spin-label compounds the side chains are in a planar conformation with respect to the oxypyrrolinyl ring. In the carboxylic acid and formyl derivatives the C=O group is in as-trans conformation with respect to the vinyl group of the spin-label, while in the spin-labeled propenoic acid the conformation is found to be all planartrans-s-cis.     

Quantitative characterization of the Mn2+ complexes of ADP and ATPγS by W-band ENDOR

W-band (95 GHz) pulsed electron nuclear double resonance (ENDOR) measurements were carried out to determine quantitatively the first coordination shell of Mn²⁺ with ADP and ATPγS. The intensity of the ENDOR effect was used for counting the number of equivalent phosphate oxygens and water ligands. Titration curves for determining the binding constant of Mn²⁺. ADP were obtained using the intensity of the X-band EPR spectrum and the³¹P ENDOR effect. Both curves gave the same binding constant showing that phosphate ligand counting is plausible, provided that an appropriate reference is available. The comparison of the³¹P ENDOR effect of the 1:1 ADP and ATPγS complexes shows that two phosphates are coordinated in both; while in ADP they are equivalent, in ATPγS they are slightly different. The reference system for water ligand counting was Mn(H₂O) ₆ ²⁺ in a H₂O-D₂O mixture. The results show a smaller error for the²H ENDOR effect, compared to the¹H ENDOR effect. Unlike the³¹P ENDOR effect, the¹H ENDOR effect dependence on [ADP] in the titration experiments showed that it is sensitive to variations in the zero-field splitting, which in turn alters the contributions of transitions other than the ‖?1/2>?‖1/2>. This results in a larger error in the determination of the number of water ligands.     

The use of ENDOR to identify the atomic structure of defects in diamond

Although nearly 100 paramagnetic defects have been catalogued in diamond by spin Hamiltonian parameters measured by electron paramagnetic resonance (EPR), very few of these have been unambiguously associated with an atomic model. It has been necessary to use electron nuclear double resonance (ENDOR) to obtain enough information to make proper assignment of such models. The reason for the limitation of EPR, and the way in which ENDOR overcomes these limitations are discussed. The interpretation of hyperfine structure in terms of unpaired electrons in molecular orbitals, and of quadrupole interactions in terms of all electrons, paired and unpaired, as a source of information about molecular structure in diamond, is evaluated by reference to some well documented examples. The measurements so far made by ENDOR on defects in diamond are reviewed, and the salient contribution for the assignment of a model for each defect is explained. The details revealed by ENDOR considerably increase knowledge about defects, particularly those involving substitutional nitrogen atoms. This in turn helps in understanding the complex electron and atom, migration processes which go on under appropriate conditions of temperature and pressure, or optical excitation. The possibilities are discussed for using ENDOR to increase the number of well characterized centres.     

High-field ENDOR and the sign of the hyperfine coupling

Two different approaches for assigning electron nuclear double resonance (ENDOR) signals to their respectiveM _s manifolds by a controlled generation of asymmetric ENDOR spectra, are described and applied to a number of systems. This assignment then allows a straightforward determination of the sign of the hyperfine coupling. Both approaches rely on a high thermal polarization that is easily achieved at high fields and low temperatures. For high-spin systems, such asS = 5/2 the assignment is afforded by the selective inversion of the | ?3/2〉 → | ?1/2〉 electron paramagnetic resonance (EPR) transition which is highly populated as compared to its symmetric counterpart, the |1/2〉 → |3/2〉 EPR transition, and therefore is easily identified. ForS = 1/2 the determination of the sign of the hyperfine coupling becomes possible when the cross- and nuclear-spin relaxation rates are much slower than the electron-spin relaxation rate and variable mixing time pulse ENDOR is used to measure the spectrum. Under these conditions the signals of theM _s = 1/2 (α) manifold become negative when the mixing time is on order of the electron-spin relaxation time, whereas those of theM _s =?1/2 (β) manifold remain positive. Under partial saturation of the nuclear transitions and short mixing time the opposite behavior is observed. Pulse W-band¹H ENDOR experiments demonstrating these approaches were applied and the signs of the hyperfine couplings of the water ligands in Mn(H₂O) ₆ ²⁺ , the H_α and H_β histidine protons in the Cu(histidine)₂ complex, the imidazole protons in Cu(imidazole) ₄ ²⁺ and the cysteine β-protons in nitrous oxide reductase were determined.     

Pulsed EPR and ENDOR on the Peridinin Triplet State Involved in the Photoprotective Mechanism in Peridinin–Chlorophyll a–Proteins

The photoexcited triplet state of the carotenoid peridinin in the peridinin–chlorophyll a–protein (PCP) of the dinoflagellate Heterocapsa pygmaea has been investigated by pulsed electron paramagnetic resonance (EPR) and pulsed electron-nuclear double resonance (ENDOR) spectroscopies. The α- and β-protons hyperfine couplings of the peridinin-conjugated chain have been derived from Davies and Mims ENDOR experiments. The spectroscopic results have been compared to those obtained for the main form of the PCP complex and for the high-salt PCP form from Amphidinium carterae. The EPR features of the peridinin triplet state are very similar in the antenna complexes belonging to the two different dinoflagellate species, proving that the triplet formation pathway and the triplet localization on one specific peridinin per subcluster are common features of different PCP antennas. No significant variation of the hyperfine couplings of the peridinin triplet state has been detected between the main form of the PCP complex from A. carterae and H. pygmaea. The spectroscopic results confirm the close relationship between the Amphidinium PCP and the corresponding Heterocapsa complex at least in terms of mutual arrangement of the chlorophyll a–peridinin pair involved in photoprotection and in terms of conformation of the peridinin-conjugated chain.