A Q-band pulse EPR/ENDOR spectrometer and the implementation of advanced one- and two-dimensional pulse EPR methodology

Ti-Doping in Silica-Supported PtZn Propane Dehydrogenation Catalysts: From Improved Stability to the Nature of the Pt-Ti Interaction

Propane dehydrogenation is an important industrial reaction to access propene, the world's second most used polymer precursor. Catalysts for this transformation are required to be long living at high temperature and robust toward harsh oxidative regeneration conditions. In this work, combining surface organometallic chemistry and thermolytic molecular precursor approach, we prepared well-defined silica-supported Pt and alloyed PtZn materials to investigate the effect of Ti-doping on catalytic performances. Chemisorption experiments and density functional calculations reveal a significant change in the electronic structure of the nanoparticles (NPs) due to the Ti-doping. Evaluation of the resulting materials PtZn/SiO₂ and PtZnTi/SiO₂ during long deactivation phases reveal a stabilizing effect of Ti in PtZnTi/SiO₂ with a k_d of 0.015 h^-1 compared to PtZn/SiO₂ with a k_d of 0.022 h^-1 over 108 h on stream. Such a stabilizing effect is also present during a second deactivation phase after applying a regeneration protocol to the materials under O₂ and H₂ at high temperatures. A combined scanning transmission electron microscopy, in situ X-ray absorption spectroscopy, electron paramagnetic resonance, and density functional theory study reveals that this effect is related to a sintering prevention of the alloyed PtZn NPs in PtZnTi/SiO₂ due to a strong interaction of the NPs with Ti sites. However, in contrast to classical strong metal-support interaction, we show that the coverage of the Pt NPs with TiO_x species is not needed to explain the changes in adsorption and reactivity properties. Indeed, the interaction of the Pt NPs with Ti^III sites is enough to decrease CO adsorption and to induce a red-shift of the CO band because of electron transfer from the Ti^III sites to Pt⁰.

Interaction of barley β-glucan with food dye molecules - An insight from pulse dipolar EPR spectroscopy

The interactions between dietary fibers (DFs) and small molecules are of great interest to food chemistry and nutrition science. However, the corresponding interaction mechanisms and structural rearrangements of DFs at the molecular level are still opaque due to the usually weak binding and the lack of appropriate techniques to determine details of conformational distributions in such weakly organized systems. By combining our previously established methodology on stochastic spin-labelling of DFs with the appropriately revised set of pulse electron paramagnetic resonance techniques, we present here a toolkit to determine the interactions between DFs and small molecules, using barley β-glucan as an example for neutral DF and a selection of food dye molecules as examples for small molecules. The proposed here methodology allowed us to observe subtle conformational changes of β-glucan by detecting multiple details of the local environment of the spin labels. Substantial variations of binding propensities were detected for different food dyes.

Pulsed Electron-Nuclear Double Resonance in the Fourier Regime

Nuclear magnetic resonance (NMR) spectroscopy provides atomic-level molecular structural information. However, in molecules containing unpaired electron spins, NMR signals are difficult to measure directly. In such cases, data is obtained using the electron-nuclear double resonance (ENDOR) method, where nuclei are detected through their interaction with nearby unpaired electron spins. Unfortunately, electron spins spread the ENDOR signals, which challenges current acquisition techniques, often resulting in low spectral resolution that provides limited structural details. Here, we show that by using miniature microwave resonators to detect a small number of electron spins, integrated with miniature NMR coils, one can excite and detect a wide bandwidth of ENDOR data in a single pulse. This facilitates the measurement of ENDOR spectra with narrow lines spread over a large frequency range at much better spectral resolution than conventional approaches, which helps reveal details of the paramagnetic molecules' chemical structure that were not accessible before.

Efficient Dynamic Nuclear Polarization up to 230 K with Hybrid BDPA-Nitroxide Radicals at a High Magnetic Field

Pairing the spectral resolution provided by high magnetic fields at ambient temperature with the enhanced sensitivity offered by dynamic nuclear polarization (DNP) is a major goal of modern solid-state NMR spectroscopy, which will allow one to unlock ever-challenging applications. This study demonstrates that, by combining HyTEK2, a hybrid BDPA-nitroxide biradical polarizing agent, with ortho-terphenyl (OTP), a rigid DNP matrix, enhancement factors as high as 65 can be obtained at 230 K, 40 kHz magic angle spinning (MAS), and 18.8 T. The temperature dependence of the DNP enhancement and its behavior around the glass transition temperature (T_g) of the matrix is investigated by variable-temperature EPR measurements of the electron relaxation properties and numerical simulations. A correlation is suggested between the decrease in enhancement at the passage of the T_g and the concomitant drop of both transverse electron relaxation times in the biradical.

Resolving distance variations by single-molecule FRET and EPR spectroscopy using rotamer libraries

Förster resonance energy transfer (FRET) and electron paramagnetic resonance (EPR) spectroscopy are complementary techniques for quantifying distances in the nanometer range. Both approaches are commonly employed for probing the conformations and conformational changes of biological macromolecules based on site-directed fluorescent or paramagnetic labeling. FRET can be applied in solution at ambient temperature and thus provides direct access to dynamics, especially if used at the single-molecule level, whereas EPR requires immobilization or work at cryogenic temperatures but provides data that can be more reliably used to extract distance distributions. However, a combined analysis of the complementary data from the two techniques has been complicated by the lack of a common modeling framework. Here, we demonstrate a systematic analysis approach based on rotamer libraries for both FRET and EPR labels to predict distance distributions between two labels from a structural model. Dynamics of the fluorophores within these distance distributions are taken into account by diffusional averaging, which improves the agreement with experiment. Benchmarking this methodology with a series of surface-exposed pairs of sites in a structured protein domain reveals that the lowest resolved distance differences can be as small as ∼0.25 nm for both techniques, with quantitative agreement between experimental and simulated transfer efficiencies within a range of ±0.045. Rotamer library analysis thus establishes a coherent way of treating experimental data from EPR and FRET and provides a basis for integrative structural modeling, including studies of conformational distributions and dynamics of biological macromolecules using both techniques.

NMR and EPR reveal a compaction of the RNA-binding protein FUS upon droplet formation

Many RNA-binding proteins undergo liquid-liquid phase separation, which underlies the formation of membraneless organelles, such as stress granules and P-bodies. Studies of the molecular mechanism of phase separation in vitro are hampered by the coalescence and sedimentation of organelle-sized droplets interacting with glass surfaces. Here, we demonstrate that liquid droplets of fused in sarcoma (FUS)-a protein found in cytoplasmic aggregates of amyotrophic lateral sclerosis and frontotemporal dementia patients-can be stabilized in vitro using an agarose hydrogel that acts as a cytoskeleton mimic. This allows their spectroscopic characterization by liquid-phase NMR and electron paramagnetic resonance spectroscopy. Protein signals from both dispersed and condensed phases can be observed simultaneously, and their respective proportions can be quantified precisely. Furthermore, the agarose hydrogel acts as a cryoprotectant during shock-freezing, which facilitates pulsed electron paramagnetic resonance measurements at cryogenic temperatures. Surprisingly, double electron-electron resonance measurements revealed a compaction of FUS in the condensed phase.

Integrin α6β4 Recognition of a Linear Motif of Bullous Pemphigoid Antigen BP230 Controls Its Recruitment to Hemidesmosomes

Mechanical stability of epithelia requires firm attachment to the basement membrane via hemidesmosomes. Dysfunction of hemidesmosomal proteins causes severe skin-blistering diseases. Two plakins, plectin and BP230 (BPAG1e), link the integrin α6β4 to intermediate filaments in epidermal hemidesmosomes. Here, we show that a linear sequence within the isoform-specific N-terminal region of BP230 binds to the third and fourth FnIII domains of β4. The crystal structure of the complex and mutagenesis analysis revealed that BP230 binds between the two domains of β4. BP230 induces closing of the two FnIII domains that are locked in place by an interdomain ionic clasp required for binding. Disruption of BP230-β4 binding prevents recruitment of BP230 to hemidesmosomes in human keratinocytes, revealing a key role of this interaction for hemidesmosome assembly. Phosphomimetic substitutions in β4 and BP230 destabilize the complex. Thus, our study provides insights into the architecture of hemidesmosomes and potential mechanisms of regulation.

Quantitative analysis of zero-field splitting parameter distributions in Gd(iii) complexes

The magnetic properties of paramagnetic species with spin S > 1/2 are parameterized by the familiar g tensor as well as "zero-field splitting" (ZFS) terms that break the degeneracy between spin states even in the absence of a magnetic field. In this work, we determine the mean values and distributions of the ZFS parameters D and E for six Gd(iii) complexes (S = 7/2) and critically discuss the accuracy of such determination. EPR spectra of the Gd(iii) complexes were recorded in glassy frozen solutions at 10 K or below at Q-band (∼34 GHz), W-band (∼94 GHz) and G-band (240 GHz) frequencies, and simulated with two widely used models for the form of the distributions of the ZFS parameters D and E. We find that the form of the distribution of the ZFS parameter D is bimodal, consisting roughly of two Gaussians centered at D and -D with unequal amplitudes. The extracted values of D (σD) for the six complexes are, in MHz: Gd-NO3Pic, 485 ± 20 (155 ± 37); Gd-DOTA/Gd-maleimide-DOTA, -714 ± 43 (328 ± 99); iodo-(Gd-PyMTA)/MOMethynyl-(Gd-PyMTA), 1213 ± 60 (418 ± 141); Gd-TAHA, 1361 ± 69 (457 ± 178); iodo-Gd-PCTA-[12], 1861 ± 135 (467 ± 292); and Gd-PyDTTA, 1830 ± 105 (390 ± 242). The sign of D was adjusted based on the Gaussian component with larger amplitude. We relate the extracted P(D) distributions to the structure of the individual Gd(iii) complexes by fitting them to a model that superposes the contribution to the D tensor from each coordinating atom of the ligand. Using this model, we predict D, σD, and E values for several additional Gd(iii) complexes that were not measured in this work. The results of this paper may be useful as benchmarks for the verification of quantum chemical calculations of ZFS parameters, and point the way to designing Gd(iii) complexes for particular applications and estimating their magnetic properties a priori.

A Q-band low noise GaAs pHEMT MMIC power amplifier for pulse electron spin resonance spectrometer

We present the design and development of a single stage pulse power amplifier working in the frequency range 32-38 GHz based on a monolithic microwave integrated circuit (MMIC). We have designed the MMIC power amplifier by using the commercially available packaged GaAs pseudomorphic high electron mobility transistor. The circuit fabrication and assembly process includes the elaboration of the matching networks for the MMIC power amplifier and their assembling as well as the topology outline and fabrication of the printed circuit board of the waveguide-microstrip line transitions. At room ambient temperature, the measured peak output power from the prototype amplifier is 35.5 dBm for 16.6 dBm input driving power, corresponding to 19 dB gain. The measured rise/fall time of the output microwave signal modulated by a high-speed PIN diode was obtained as 5-6 ns at 20-250 ns pulse width with 100 kHz pulse repetition rate frequency.

Water accessibility in a membrane-inserting peptide comparing Overhauser DNP and pulse EPR methods

Water accessibility is a key parameter for the understanding of the structure of biomolecules, especially membrane proteins. Several experimental techniques based on the combination of electron paramagnetic resonance (EPR) spectroscopy with site-directed spin labeling are currently available. Among those, we compare relaxation time measurements and electron spin echo envelope modulation (ESEEM) experiments using pulse EPR with Overhauser dynamic nuclear polarization (DNP) at X-band frequency and a magnetic field of 0.33 T. Overhauser DNP transfers the electron spin polarization to nuclear spins via cross-relaxation. The change in the intensity of the (1)H NMR spectrum of H2O at a Larmor frequency of 14 MHz under a continuous-wave microwave irradiation of the nitroxide spin label contains information on the water accessibility of the labeled site. As a model system for a membrane protein, we use the hydrophobic α-helical peptide WALP23 in unilamellar liposomes of DOPC. Water accessibility measurements with all techniques are conducted for eight peptides with different spin label positions and low radical concentrations (10-20 μM). Consistently in all experiments, the water accessibility appears to be very low, even for labels positioned near the end of the helix. The best profile is obtained by Overhauser DNP, which is the only technique that succeeds in discriminating neighboring positions in WALP23. Since the concentration of the spin-labeled peptides varied, we normalized the DNP parameter ϵ, being the relative change of the NMR intensity, by the electron spin concentration, which was determined from a continuous-wave EPR spectrum.

Model-free extraction of spin label position distributions from pseudocontact shift data

Not a point, but a cloud: advanced PCS data analysis using 3D probability density reconstruction provides more information.

A significant problem with paramagnetic tags attached to proteins and nucleic acids is their conformational mobility. Each tag is statistically distributed within a volume between 5 and 10 Angstroms across; structural biology conclusions from NMR and EPR work are necessarily diluted by this uncertainty. The problem is solved in electron spin resonance, but remains open in the other major branch of paramagnetic resonance – pseudocontact shift (PCS) NMR spectroscopy, where structural biologists have so far been reluctantly using the point paramagnetic centre approximation. Here we describe a new method for extracting probability densities of lanthanide tags from PCS data. The method relies on Tikhonov-regularised 3D reconstruction and opens a new window into biomolecular structure and dynamics because it explores a very different range of conditions from those accessible to double electron resonance work on paramagnetic tags: a room-temperature solution rather than a glass at cryogenic temperatures. The method is illustrated using four different Tm³⁺ DOTA-M8 tagged mutants of human carbonic anhydrase II; the results are in good agreement with rotamer library and DEER data. The wealth of high-quality pseudocontact shift data accumulated by the biological magnetic resonance community over the last 30 years, and so far only processed using point models, could now become a major source of useful information on conformational distributions of paramagnetic tags in biomolecules.

Early folding events during light harvesting complex II assembly in vitro monitored by pulsed electron paramagnetic resonance

Efficient energy transfer in the major light harvesting complex II (LHCII) of green plants is facilitated by the precise alignment of pigments due to the protein matrix they are bound to. Much is known about the import of the LHCII apoprotein into the chloroplast via the TOC/TIC system and its targeting to the thylakoid membrane but information is sparse about when and where the pigments are bound and how this is coordinated with protein folding. In vitro, the LHCII apoprotein spontaneously folds and binds its pigments if the detergent-solubilized protein is combined with a mixture of chlorophylls a and b and carotenoids. In the present work, we employed this approach to study apoprotein folding and pigment binding in a time-resolved manner by using pulsed electron paramagnetic resonance (EPR). Intra-molecular distances were measured before folding, after 255 ms and 40 s folding time in the absence of cryoprotectant, and in the fully folded and assembled LHCII. In accordance with earlier results, the most of the folding of the three membrane-spanning alpha helices precedes their apposition into the final tertiary structure. However, their formation follows different kinetics, partially extending into the final phase of LHCII formation during which much of the condensation of the pigment-protein structure occurs, presumably governed by the binding of chlorophyll b. A rough timetable is proposed to sort partial events into the LHCII formation process.

Gd(III) complexes for electron-electron dipolar spectroscopy: Effects of deuteration, pH and zero field splitting

Spectral parameters of Gd(III) complexes are intimately linked to the performance of the Gd(III)-nitroxide or Gd(III)-Gd(III) double electron-electron resonance (DEER or PELDOR) techniques, as well as to that of relaxation induced dipolar modulation enhancement (RIDME) spectroscopy with Gd(III) ions. These techniques are of interest for applications in structural biology, since they can selectively detect site-to-site distances in biomolecules or biomolecular complexes in the nanometer range. Here we report relaxation properties, echo detected EPR spectra, as well as the magnitude of the echo reduction effect in Gd(III)-nitroxide DEER for a series of Gadolinium(III) complexes with chelating agents derived from tetraazacyclododecane. We observed that solvent deuteration does not only lengthen the relaxation times of Gd(III) centers but also weakens the DEER echo reduction effect. Both of these phenomena lead to an improved signal-to-noise ratios or, alternatively, longer accessible distance range in pulse EPR measurements. The presented data enrich the knowledge on paramagnetic Gd(III) chelate complexes in frozen solutions, and can help optimize the experimental conditions for most types of the pulse measurements of the electron-electron dipolar interactions.

Spin trapping combined with quantitative mass spectrometry defines free radical redistribution within the oxidized hemoglobin:haptoglobin complex

Extracellular or free hemoglobin (Hb) accumulates during hemolysis, tissue damage, and inflammation. Heme-triggered oxidative reactions can lead to diverse structural modifications of lipids and proteins, which contribute to the propagation of tissue damage. One important target of Hb׳s peroxidase reactivity is its own globin structure. Amino acid oxidation and crosslinking events destabilize the protein and ultimately cause accumulation of proinflammatory and cytotoxic Hb degradation products. The Hb scavenger haptoglobin (Hp) attenuates oxidation-induced Hb degradation. In this study we show that in the presence of hydrogen peroxide (H2O2), Hb and the Hb:Hp complex share comparable peroxidative reactivity and free radical generation. While oxidation of both free Hb and Hb:Hp complex generates a common tyrosine-based free radical, the spin-trapping reaction with 5,5-dimethyl-1-pyrroline N-oxide (DMPO) yields dissimilar paramagnetic products in Hb and Hb:Hp, suggesting that radicals are differently redistributed within the complex before reacting with the spin trap. With LC-MS(2) mass spectrometry we assigned multiple known and novel DMPO adduct sites. Quantification of these adducts suggested that the Hb:Hp complex formation causes extensive delocalization of accessible free radicals with drastic reduction of the major tryptophan and cysteine modifications in the β-globin chain of the Hb:Hp complex, including decreased βCys93 DMPO adduction. In contrast, the quantitative changes in DMPO adduct formation on Hb:Hp complex formation were less pronounced in the Hb α-globin chain. In contrast to earlier speculations, we found no evidence that free Hb radicals are delocalized to the Hp chain of the complex. The observation that Hb:Hp complex formation alters free radical distribution in Hb may help to better understand the structural basis for Hp as an antioxidant protein.

Advanced EPR Methods for Studying Conformational Dynamics of Nucleic Acids

Pulsed electron paramagnetic resonance (EPR) spectroscopy has become an important tool for structural characterization of biomolecules allowing measurement of the distances between two paramagnetic spin labels attached to a biomolecule in the 2-8 nm range. In this chapter, we will focus on applications of this approach to investigate tertiary structure elements as well as conformational dynamics of nucleic acid molecules. Both aspects take advantage of using specific spin labels that are rigidly attached to the nucleobases, as they allow obtaining not only the distance but also the relative orientation between both nitroxide moieties with high accuracy. Thus, not only the distance but additionally the three Euler angles between both the nitroxide axis systems and the two polar angles of the interconnecting vector with respect to the nitroxide axis systems can be extracted from a single pair of spin labels. To extract all these parameters independently and unambiguously, a set of multifrequency/multifield pulsed EPR experiments have to be performed. We will describe the experimental procedure as well as newly developed spin labels, which are helpful to disentangle all these parameters, and tools which we have developed to analyze such data sets. The procedures and analyses will be illustrated by examples from our laboratory.

Shape Persistence of Polyproline II Helical Oligoprolines

Oligoprolines are commonly used as molecular scaffolds. Past studies on the persistence length of their secondary structure, the polyproline II (PPII) helix, and on the fraction of backbone cis amide bonds have provided conflicting results. We resolved this debate by studying a series of spin-labeled proline octadecamers with EPR spectroscopy. Distance distributions between an N-terminal Gd(III) -DOTA (DOTA=1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid) label and a nitroxide label at one of five evenly spaced backbone sites allowed us to discriminate between the flexibility of the PPII helix and the cis amide contributions. An upper limit of 2 % cis amide bonds per residue was found in a 7:3 (v/v) water/glycerol mixture, whereas cis amides were not observed in trifluoroethanol. Extrapolation of Monte Carlo models from the glass transition to ambient temperature predicts a persistence length of ≈3-3.5 nm in both solvents. The method is generally applicable to any type of oligomer for which the persistence length is of interest.

Combination of X-ray crystallography, SAXS and DEER to obtain the structure of the FnIII-3,4 domains of integrin α6β4

Integrin α6β4 is a major component of hemidesmosomes that mediate the stable anchorage of epithelial cells to the underlying basement membrane. Integrin α6β4 has also been implicated in cell proliferation and migration and in carcinoma progression. The third and fourth fibronectin type III domains (FnIII-3,4) of integrin β4 mediate binding to the hemidesmosomal proteins BPAG1e and BPAG2, and participate in signalling. Here, it is demonstrated that X-ray crystallography, small-angle X-ray scattering and double electron-electron resonance (DEER) complement each other to solve the structure of the FnIII-3,4 region. The crystal structures of the individual FnIII-3 and FnIII-4 domains were solved and the relative arrangement of the FnIII domains was elucidated by combining DEER with site-directed spin labelling. Multiple structures of the interdomain linker were modelled by Monte Carlo methods complying with DEER constraints, and the final structures were selected against experimental scattering data. FnIII-3,4 has a compact and cambered flat structure with an evolutionary conserved surface that is likely to correspond to a protein-interaction site. Finally, this hybrid method is of general application for the study of other macromolecules and complexes.

EPR-aided approach for solution structure determination of large RNAs or protein-RNA complexes

High-resolution structural information on RNA and its functionally important complexes with proteins is dramatically underrepresented compared with proteins but is urgently needed for understanding cellular processes at the molecular and atomic level. Here we present an EPR-based protocol to help solving large RNA and protein-RNA complex structures in solution by providing long-range distance constraints between rigid fragments. Using enzymatic ligation of smaller RNA fragments, large doubly spin-labelled RNAs can be obtained permitting the acquisition of long distance distributions (>80 Å) within a large protein-RNA complex. Using a simple and fast calculation in torsion angle space of the spin-label distributions with the program CYANA, we can derive simple distance constraints between the spin labels and use them together with short-range distance restraints derived from NMR to determine the structure of a 70 kDa protein-RNA complex composed of three subcomplexes.

High-field EPR on membrane proteins - crossing the gap to NMR

In this review on advanced EPR spectroscopy, which addresses both the EPR and NMR communities, considerable emphasis is put on delineating the complementarity of NMR and EPR concerning the measurement of molecular interactions in large biomolecules. From these interactions, detailed information can be revealed on structure and dynamics of macromolecules embedded in solution- or solid-state environments. New developments in pulsed microwave and sweepable cryomagnet technology as well as ultrafast electronics for signal data handling and processing have pushed to new horizons the limits of EPR spectroscopy and its multifrequency extensions concerning the sensitivity of detection, the selectivity with respect to interactions, and the resolution in frequency and time domains. One of the most important advances has been the extension of EPR to high magnetic fields and microwave frequencies, very much in analogy to what happens in NMR. This is exemplified by referring to ongoing efforts for signal enhancement in both NMR and EPR double-resonance techniques by exploiting dynamic nuclear or electron spin polarization via unpaired electron spins and their electron-nuclear or electron-electron interactions. Signal and resolution enhancements are particularly spectacular for double-resonance techniques such as ENDOR and PELDOR at high magnetic fields. They provide greatly improved orientational selection for disordered samples that approaches single-crystal resolution at canonical g-tensor orientations - even for molecules with small g-anisotropies. Exchange of experience between the EPR and NMR communities allows for handling polarization and resolution improvement strategies in an optimal manner. Consequently, a dramatic improvement of EPR detection sensitivity could be achieved, even for short-lived paramagnetic reaction intermediates. Unique structural and dynamic information is thus revealed that can hardly be obtained by any other analytical techniques. Micromolar quantities of sample molecules have become sufficient to characterize stable and transient reaction intermediates of complex molecular systems - offering highly interesting applications for chemists, biochemists and molecular biologists. In three case studies, representative examples of advanced EPR spectroscopy are reviewed: (I) High-field PELDOR and ENDOR structure determination of cation-anion radical pairs in reaction centers from photosynthetic purple bacteria and cyanobacteria (Photosystem I); (II) High-field ENDOR and ELDOR-detected NMR spectroscopy on the oxygen-evolving complex of Photosystem II; and (III) High-field electron dipolar spectroscopy on nitroxide spin-labelled bacteriorhodopsin for structure-function studies. An extended conclusion with an outlook to further developments and applications is also presented.

Can copper(II) mediate Hoogsteen base-pairing in a left-handed DNA duplex? A pulse EPR study

Pulse EPR spectroscopy is used to investigate possible structural features of the copper(II) ion coordinated to poly(dG-dC).poly(dG-dC) in a frozen aqueous solution, and the structural changes of the polynucleotide induced by the presence of the metal ion. Two different copper species were identified and their geometry explained by a molecular model. According to this model, one species is exclusively coordinated to a single guanine with the N7 nitrogen atom forming a coordinative bond with the copper. In the other species, a guanine and a cytosine form a ternary complex together with the copper ion. A copper crosslink between the N7 of guanine and N3 of cytosine is proposed as the most probable coordination site. Moreover, no evidence was found for an interaction of either copper species with a phosphate group or equatorial water molecules. In addition, circular dichroism (CD) spectroscopy showed that the DNA of the Cu(II)-poly(dG-dC).poly(dG-dC) adducts resembles the left-handed Z-form. These results suggest that metal-mediated Hoogsteen base pairing, as previously proposed for a right-handed DNA duplex, can also occur in a double-stranded left-handed DNA.

Binding of coenzyme B induces a major conformational change in the active site of methyl-coenzyme M reductase

Methyl-coenzyme M reductase (MCR) is the key enzyme in methane formation by methanogenic Archaea. It converts the thioether methyl-coenzyme M and the thiol coenzyme B into methane and the heterodisulfide of coenzyme M and coenzyme B. The catalytic mechanism of MCR and the role of its prosthetic group, the nickel hydrocorphin coenzyme F(430), is still disputed, and no intermediates have been observed so far by fast spectroscopic techniques when the enzyme was incubated with the natural substrates. In the presence of the competitive inhibitor coenzyme M instead of methyl-coenzyme M, addition of coenzyme B to the active Ni(I) state MCR(red1) induces two new species called MCR(red2a) and MCR(red2r) which have been characterized by pulse EPR spectroscopy. Here we show that the two MCR(red2) signals can also be induced by the S-methyl- and the S-trifluoromethyl analogs of coenzyme B. (19)F-ENDOR data for MCR(red2a) and MCR(red2r) induced by S-CF(3)-coenzyme B show that, upon binding of the coenzyme B analog, the end of the 7-thioheptanoyl chain of coenzyme B moves closer to the nickel center of F(430) by more than 2 A as compared to its position in both, the Ni(I) MCR(red1) form and the X-ray structure of the inactive Ni(II) MCR(ox1-silent) form. The finding that the protein is able to undergo a conformational change upon binding of the second substrate helps to explain the dramatic change in the coordination environment induced in the transition from MCR(red1) to MCR(red2) forms and opens the possibility that nickel coordination geometries other than square planar, tetragonal pyramidal, or elongated octahedral might occur in intermediates of the catalytic cycle.

Cryogenic 35GHz pulse ENDOR probehead accommodating large sample sizes: Performance and applications

The construction and performance of a cryogenic 35GHz pulse electron nuclear double resonance (ENDOR) probehead for large samples is presented. The resonator is based on a rectangular TE(102) cavity in which the radio frequency (rf) B(2)-field is generated by a two turn saddle ENDOR coil crossing the resonator along the sample axis with minimal distance to the sample tube. An rf power efficiency factor is used to define the B(2)-field strength per square-root of the transmitted rf power over the frequency range 2-180MHz. The distributions of the microwave B(1)- and E(1)-field, and the rf B(2)-field are investigated by electromagnetic field calculations. All dielectrics, the sample tube, and coupling elements are included in the calculations. The application range of the probehead and the advantages of using large sample sizes are demonstrated and discussed on a number of paramagnetic samples containing transition metal ions.

Structural basis for VO2+ inhibition of nitrogenase activity (A): 31P and 23Na interactions with the metal at the nucleotide binding site of the nitrogenase Fe protein identified by ENDOR spectroscopy

We previously reported the vanadyl hyperfine couplings of VO(2+)-ATP and VO(2+)-ADP complexes in the presence of the nitrogenase Fe protein from Klebsiella pneumoniae (Petersen et al. in Biochemistry 41:13253-13263, 2002). It was demonstrated that different VO(2+)-nucleotide coordination environments coexist and are distinguishable by electron paramagnetic resonance (EPR) spectroscopy. Here orientation-selective continuous-wave electron-nuclear double resonance (ENDOR) spectra have been investigated especially in the low-radio-frequency range in order to identify superhyperfine interactions with nuclei other than protons. Some of these resonances have been attributed to the presence of a strong interaction with a 31P nucleus although no resolvable superhyperfine structure due to 31P or other nuclei was detected in the EPR spectra. The superhyperfine coupling component is determined to be about 25 MHz. Such a 31P coupling is consistent with an interaction of the metal with phosphorus from a directly, equatorially coordinated nucleotide phosphate group(s). Additionally, novel more prominent 31P ENDOR signals are detected in the low-frequency region. Some of these correspond to a relatively weak 31P coupling. This coupling is present with ATP for all pH forms but is absent with ADP. The ENDOR resonances of these weakly coupled 31P are likely to originate from an interaction of the metal with a nucleotide phosphate group of the nucleoside triphosphate and are attributed to a phosphorus with axial characteristics. Another set of resonances, split about the nuclear Zeeman frequency of 23Na, was detected, suggesting that a monovalent Na+ ion is closely associated with the divalent metal-nucleotide binding site. Na+ replacement by K+ unambiguously confirmed that ENDORs at radio frequencies between 3.0 and 4.5 MHz arise from an interaction with Na+ ions. In contrast to the low-frequency 31P signal, these resonances are present in spectra with both ADP and ATP, and for both low- and neutral-pH forms, although slight differences are detected, showing that these are sensitive to the nucleotide and pH.

HYSCORE and DEER with an upgraded 95GHz pulse EPR spectrometer

The set-up of a new microwave bridge for a 95 GHz pulse EPR spectrometer is described. The virtues of the bridge are its simple and flexible design and its relatively high output power (0.7 W) that generates pi pulses of 25 ns and a microwave field, B(1)=0.71 mT. Such a high B(1) enhances considerably the sensitivity of high field double electron-electron resonance (DEER) measurements for distance determination, as we demonstrate on a nitroxide biradical with an interspin distance of 3.6 nm. Moreover, it allowed us to carry out HYSCORE (hyperfine sublevel-correlation) experiments at 95 GHz, observing nuclear modulation frequencies of 14N and 17O as high as 40 MHz. This opens a new window for the observation of relatively large hyperfine couplings, yet not resolved in the EPR spectrum, that are difficult to observe with HYSCORE carried out at conventional X-band frequencies. The correlations provided by the HYSCORE spectra are most important for signal assignment, and the improved resolution due to the two dimensional character of the experiment provides 14N quadrupolar splittings.

Coordination and binding geometry of methyl-coenzyme M in the red1m state of methyl-coenzyme M reductase

Methane formation in methanogenic Archaea is catalyzed by methyl-coenzyme M reductase (MCR) and takes place via the reduction of methyl-coenzyme M (CH3-S-CoM) with coenzyme B (HS-CoB) to methane and the heterodisulfide CoM-S-S-CoB. MCR harbors the nickel porphyrinoid coenzyme F430 as a prosthetic group, which has to be in the Ni(I) oxidation state for the enzyme to be active. To date no intermediates in the catalytic cycle of MCRred1 (red for reduced Ni) have been identified. Here, we report a detailed characterization of MCRred1m ("m" for methyl-coenzyme M), which is the complex of MCRred1a ("a" for absence of substrate) with CH3-S-CoM. Using continuous-wave and pulse electron paramagnetic resonance spectroscopy in combination with selective isotope labeling (13C and 2H) of CH3-S-CoM, it is shown that CH3-S-CoM binds in the active site of MCR such that its thioether sulfur is weakly coordinated to the Ni(I) of F430. The complex is stable until the addition of the second substrate, HS-CoB. Results from EPR spectroscopy, along with quantum mechanical calculations, are used to characterize the electronic and geometric structure of this complex, which can be regarded as the first intermediate in the catalytic mechanism.

A multi-frequency pulse EPR and ENDOR approach to study strongly coupled nuclei in frozen solutions of high-spin ferric heme proteins

In spite of the tremendous progress in the field of pulse electron paramagnetic resonance (EPR) in recent years, these techniques have been scarcely used to investigate high-spin (HS) ferric heme proteins. Several technical and spin-system-specific reasons can be identified for this. Additional problems arise when no single crystals of the heme protein are available. In this work, we use the example of a frozen solution of aquometmyoglobin (metMb) to show how a multi-frequency pulse EPR approach can overcome these problems. In particular, the performance of the following pulse EPR techniques are tested: Davies electron nuclear double resonance (ENDOR), hyperfine correlated ENDOR (HYEND), electron-electron double resonance (ELDOR)-detected NMR, and several variants of hyperfine sublevel correlation (HYSCORE) spectroscopy including matched and SMART HYSCORE. The pulse EPR experiments are performed at X-, Q- and W-band microwave frequencies. The advantages and drawbacks of the different methods are discussed in relation to the nuclear interaction that they intend to reveal. The analysis of the spectra is supported by several simulation procedures, which are discussed. This work focuses on the analysis of the hyperfine and nuclear-quadrupole tensors of the strongly coupled nuclei of the first coordination sphere, namely, the directly coordinating heme and histidine nitrogens and the 17O nucleus of the distal water ligand. For the latter, 17O-isotope labeling was used. The accuracy of our results and the spectral resolution are compared in detail to an earlier single-crystal continuous-wave ENDOR study on metMb, and it will be shown how additional information can be obtained from the multi-frequency approach. The current work is therefore prone to become a template for future EPR/ENDOR investigations of HS ferric heme proteins for which no single crystals are available.

A new pulse width reduction technique for pulsed electron paramagnetic resonance spectroscopy

We present a new technique for a microwave pulse modulator that generates a short microwave pulse of approximately 1ns for use in an electron paramagnetic resonance (EPR) spectrometer. A quadruple-frequency multiplier that generates a signal of 16-20GHz from an input of 4-5GHz was employed to reduce the rise and fall times of the pulse prepared by a PIN diode switch. We examined the transient response characteristics of a commercial frequency multiplier and found that the device can function as a multiplier for pulsed signal even though it was designed for continuous wave operation. We applied the technique to a Ku band pulsed EPR spectrometer and successfully observed a spin echo signal with a broad excitation bandwidth of approximately 1.6mT using 80 degrees pulses of 1.5ns.

Cryogenic Q-band (35GHz) probehead featuring large excitation microwave fields for pulse and continuous wave electron paramagnetic resonance spectroscopy: performance and applications

The construction and performance of a Q-band (35GHz) cryogenic probehead for pulse electron paramagnetic resonance and continuous wave electron paramagnetic resonance measurements with down-scaled loop gap resonators (LGRs) is presented. The advantage of the LGR in comparison to TE(012) resonators lies in the large B(1) microwave (mw) fields that can be generated with moderate input mw power. We demonstrated with several examples that this allows optimal performance for double-quantum electron coherence, HYSCORE, and hyperfine decoupling experiments employing matched and high turning angle mw pulses with high B(1)-fields. It is also demonstrated that with very low excitation power (i.e. 10-40 mW), B(1)-fields in LGRs are still sufficient to allow short mw pulses and thus experiments such as HYSCORE with high-spin systems to be performed with good sensitivity. A sensitivity factor Lambda(rs) of LGRs with different diameters and lengths is introduced in order to compare the sensitivity of different resonant structures. The electromagnetic field distribution, the B(1)-field homogeneity, the E(1)-field strength, and the microwave coupling between wave guide and LGRs are investigated by electromagnetic field calculations. The advantage and application range using LGRs for small sample diameters is discussed.

Thermally induced spin transitions in nitroxide-copper(II)-nitroxide spin triads studied by EPR

Thermally induced spin transitions in a family of heterospin polymer chain complexes of Cu2+ hexafluoroacetylacetonate with two pyrazole-substituted nitronyl nitroxides are studied using electron paramagnetic resonance (EPR) spectroscopy. The structural rearrangements at low temperatures induce spin transitions in exchange-coupled spin triads of nitroxide-copper(II)-nitroxide. The values of exchange interactions in spin triads of studied systems are typically on the order of tens to hundreds of inverse centimeters. The large magnitude of exchange interaction determines the specific and very informative peculiarities in EPR spectra due to the predominant population of the ground state of a spin triad and spin exchange processes. The variety of these manifestations depending on structure and magnetic properties of spin triads are described. EPR is demonstrated as an efficient tool for the characterization of spin transitions and for obtaining information on the temperature-dependent sign and value of the exchange interaction in strongly coupled spin triads.

Electron Spin Exchange Processes in Strongly Coupled Spin Triads

The complexes of Cu2+ hexafluoroacetylacetonate with two pyrazol-substituted nitronyl nitroxides are the choice systems to study the spin dynamics of strongly exchange-coupled spin triads. The large values of exchange coupling (ca. 100 cm-1) and high-resolution electron paramagnetic resonance (EPR) at Q- and W-bands (35 and 94 GHz) allowed us to observe and interpret specific characteristics of these systems. An electron spin exchange process has been found between different multiplets of the spin triad, which manifests itself as a significant shift of the EPR line position with temperature. We propose that the spin exchange process is caused by the modulation of exchange interaction between copper and nitroxides by lattice vibrations. The estimations of the rate of exchange process and model calculations essentially support the observed phenomena. The studied characteristics of strongly coupled spin triads explain previously obtained results, agree with literature, and should be accounted for in future investigations of similar spin systems.

Continuous-Wave and Pulse EPR Study of the Copper(II) Complex of N-Confused Tetraphenylporphyrin: Direct Observation of a σ Metal−Carbon Bond

N-confused or inverted porphyrins, a family of porphyrin isomers that contain a confused pyrrole ring connected through its alpha and beta' positions in the macrocycle, exhibit unique physical and chemical properties, like, for instance, the ability to stabilize unusual oxidation states of metals due to the reactivity of the inverted pyrrole. In this Article, a combined multifrequency continuous-wave and pulse electron paramagnetic resonance (EPR) study of the copper(II) complex of N-confused tetraphenylporphyrin (TPP) is presented. By use of pulse EPR methods like ENDOR and HYSCORE, the magnetic interactions between the unpaired electron of the compound and the surrounding nitrogen nuclei were revealed. Through 13C labeling of the macrocycle, a detailed study of the carbon hyperfine interaction became possible and provided further insight into the character of the metal-carbon bond. The observed hyperfine couplings of the ligand atoms in the first coordination sphere showed the presence of a remarkably strong sigma Cu-C bond and allowed for a detailed analysis of the spin delocalization over the porphyrin macrocycle. Interestingly, it was found that the observed delocalization is approximately 11% larger than the corresponding one for CuTPP.

EPR and HYSCORE investigation of the electronic structure of the model complex Mn(imidazole)6: exploring Mn(II)-imidazole binding using single crystals

The electronic structure of the Mn(II)-imidazole binding was studied by EPR spectroscopy using the model complex Mn(Im)(6) diluted in a single crystal of Zn(Im)(6)Cl(2).4(H(2)O). The second rank zero-field splitting (ZFS) tensor (D tensor) of the two sites, a and b, present in the crystal was determined by measuring the orientation patterns of the echo-detected EPR spectra in three different planes at 10K (D(a)=-106, D(b)=-118, E(a)=-17, E(b)=-22x10(-4)cm(-1). Euler angles with respect to the crystal habitus: alpha(a)=13 degrees , beta(a)=76 degrees , gamma(a)=108.5 degrees , alpha(b)=14 degrees , beta(b)=73.5 degrees , gamma(b)=103.5 degrees ). The contribution of cubic ZFS terms to the spectrum allowed us to determine the orientation of the N-Mn-N directions of the complex as well (Euler angles in the D tensor reference frame alpha=100 degrees , beta=23 degrees , gamma=0 degrees , both centers having the same orientation). The hyperfine interactions with (14)N were explored by HYSCORE spectroscopy. The correlation patterns and modulation amplitudes in the 2D experiments were studied for different electron spin transitions and orientations of the crystal. Signals of three different pairs of nitrogens were found. The results were analyzed considering that the N-Mn binding directions are principal directions of the hyperfine and nuclear quadrupole tensor of (14)N. All three pairs of nitrogens were found to be almost equivalent with an isotropic contribution of A(iso) approximately 3.2MHz and an almost axial anisotropic coupling of 2T approximately 1.1MHz along the N-Mn bonding direction. The nuclear quadrupole principal values are 1.5MHz along the bonding direction, -0.6MHz in the direction perpendicular to the imidazole plane, and -0.9MHz in the direction perpendicular to both.

Matrix effects on copper(II)phthalocyanine complexes. A combined continuous wave and pulse EPR and DFT study

The effect of the electron withdrawing or donating character of groups located at the periphery of the phthalocyanine ligand, as well as the influence of polar and nonpolar solvents are of importance for the redox chemistry of metal phthalocyanines. Continuous wave and pulse electron paramagnetic resonance and pulse electron nuclear double resonance spectroscopy at X- and Q-band are applied to investigate the electronic structure of the complexes Cu(II)phthalocyanine (CuPc), copper(II) 2,9,16,23-tetra-tert-butyl-29H,31H-phthalocyanine (CuPc(t)), and copper(II) 1,2,3,4,8,9,10,11,15,16,17,18,22,23,24,25-hexadecafluoro-29H,31H-phthalocyanine (CuPc(F)) in various matrices. Isotope substitutions are used to determine the g values, the copper hyperfine couplings and the hyperfine interactions with the 14N, 1H and 19F nuclei of the macrocycle and the surrounding matrix molecules. Simulations and interpretations of the spectra are shown and discussed, and a qualitative analysis of the data using previous theoretical models is given. Density functional computations facilitate the interpretation of the EPR parameters. The experimental g, copper and nitrogen hyperfine and nuclear quadrupole values are found to be sensitive to changes of the solvent and the structure of the macrocycle. To elucidate the electronic, structural and bonding properties the changes in the g principal values are related to data from UV/Vis spectroscopy and to density functional theory (DFT) computations. The analysis of the EPR data indicates that the in-plane metal-ligand sigma bonding is more covalent for CuPc(t) in toluene than in sulfuric acid. Furthermore, the out-of-plane pi bonding is found to be less covalent in the case of a polar sulfuric acid environment than with nonpolar toluene or H2Pc environment, whereby the covalency of this bonding is increased upon addition of tert-butyl groups. No contribution from in-plane pi bonding is found.

High field ENDOR as a characterization tool for functional sites in microporous materials

The determination of the details of the spatial and electronic structure of functional sites (centers) in any system, be it in materials chemistry or in biology, is the first step towards understanding their function. When such sites happen to be paramagnetic in any point of their activity cycle, the tool box offered by a variety of high resolution electron paramagnetic resonance (EPR) spectroscopic techniques becomes very attractive for their characterization. This tool box has been considerably expanded by the developments in high field (HF) EPR in general, and HF electron nuclear double resonance (ENDOR), in particular. These have led to numerous new applications in the fields of biology, physics, chemistry and materials sciences. This overview focuses specifically on recent applications of pulsed HF ENDOR spectroscopy to microporous materials, such as zeotype materials, presenting the new opportunities it offers. First, a brief description of the theoretical basis required for the analysis of the HF ENDOR spectrum is given, followed by a description of the pulsed techniques used to record spectra and assign the signals, along with a brief presentation of the required instrumentation. Next, specific applications are given, including transition metal ions and complexes exchanged into zeolite cages, transition metal substitution into frameworks of zeolites, aluminophosphate molecular sieves, and silicious mesoporous materials, the interaction of NO with Lewis sites in zeolite cages and trapped S. We end with a discussion of the advantages and the shortcomings of the method and conclude with a future outlook.

Spin Density and Coenzyme M Coordination Geometry of the ox1 Form of Methyl-Coenzyme M Reductase: A Pulse EPR Study

Methyl-coenzyme M reductase (MCR) catalyses the reduction of methyl-coenzyme M (CH3-S-CoM) with coenzyme B (H-S-CoB) to CH4 and CoM-S-S-CoB in methanogenic archaea. Here we present a pulse EPR study of the "ready" form MCR(ox1), providing a detailed description of the spin density and the coordination of coenzyme M (CoM) to the Ni cofactor F430. To achieve this, MCR was purified from cells grown in a 61Ni enriched medium and samples were prepared in D2O with the substrate analogue CoM either deuterated in the beta-position or with 33S in the thiol group. To obtain the magnetic parameters ENDOR and HYSCORE measurements were done at X- and Q-band, and CW EPR, at X- and W-band. The hyperfine couplings of the beta-protons of CoM indicate that the nickel to beta-proton distances in MCR(ox1) are very similar to those in Ni(II)-MCR(ox1-silent), and thus the position of CoM relative to F430 is very similar in both species. Our thiolate sulfur and nickel EPR data prove a Ni-S coordination, with an unpaired spin density on the sulfur of 7 +/- 3%. These results highlight the redox-active or noninnocent nature of the sulfur ligand on the oxidation state. Assuming that MCR(ox1) is oxidized relative to the Ni(II) species, the complex is formally best described as a Ni(III) (d7) thiolate in resonance with a thiyl radical/high-spin Ni(II) complex, Ni(III)-(-)SR <--> Ni(II)-*SR.

Spin Distribution and the Location of Protons in Paramagnetic Proteins

▪ Abstract  Two current frontiers in EPR research are high-field ([Formula: see text]) electron paramagnetic resonance (EPR) and high-field electron-nuclear double resonance (ENDOR). This review focuses on recent advances in high-field ENDOR and its applications to the study of proteins containing native paramagnetic sites. It concentrates on two aspects; the first concerns the determination of the location of protons and is related to the site geometry, and the second focuses on the spin density distribution within the site, which is inherent to the electronic structure. Both spin density and proton locations can be derived from ligand hyperfine couplings determined by ENDOR measurements. A brief description of the experimental methods is presented along with a discussion of the advantages and disadvantages of high-field ENDOR compared with conventional X-band (∼ 9.5 GHz) experiments. Specific examples of both protein single crystals and frozen solutions are then presented. These include the determination of the coordinates of water ligand protons in the Mn(II) site of concanavalin A, the detection of hydrogen bonds in a quinone radical in the bacterial photosynthetic reaction center as well as in the tyrosyl radical in ribonuclease reductase, and the study of the spin distribution in copper proteins. The copper proteins discussed are the type I copper of azurin and the binuclear CuA center in a number of proteins. The last part of the review presents a brief discussion of the interpretation of hyperfine couplings using quantum chemical calculations, primarily density functional theory (DFT) methods. Such methods are becoming an integral part of the data analysis tools, as they can facilitate signal assignment and provide the ultimate relation between the experimental hyperfine couplings and the electronic wave function.