Pulsed Electron-electron Double Resonance Research Articles

A high-frequency electron paramagnetic resonance spectrometer for multi-dimensional, multi-frequency, and multi-phase pulsed measurements.

We describe instrumentation for a high-frequency electron paramagnetic resonance (EPR) and pulsed electron-electron double resonance (PELDOR) spectroscopy. The instrumentation is operated in the frequency range of 107-120 GHz and 215-240 GHz and in the magnetic field range of 0-12.1 T. The spectrometer consisting of a high-frequency high-power solid-state source, a quasioptical system, a phase-sensitive detection system, a cryogenic-free superconducting magnet, and a (4)He cryostat enables multi-frequency continuous-wave EPR spectroscopy as well as pulsed EPR measurements with a few hundred nanosecond pulses. Here we discuss the details of the design and the pulsed EPR sensitivity of the instrumentation. We also present performance of the instrumentation in unique experiments including PELDOR spectroscopy to probe correlations in an insulating electronic spin system and application of dynamical decoupling techniques to extend spin coherence of electron spins in an insulating solid-state system.

The Role of Select Subtype Polymorphisms on HIV-1 Protease Conformational Sampling and Dynamics

HIV-1 protease is an essential enzyme for viral particle maturation and is a target in the fight against HIV-1 infection worldwide. Several natural polymorphisms are also associated with drug resistance. Here, we utilized both pulsed electron double resonance, also called double electron-electron resonance, and NMR (15)N relaxation measurements to characterize equilibrium conformational sampling and backbone dynamics of an HIV-1 protease construct containing four specific natural polymorphisms commonly found in subtypes A, F, and CRF_01 A/E. Results show enhanced backbone dynamics, particularly in the flap region, and the persistence of a novel conformational ensemble that we hypothesize is an alternative flap orientation of a curled open state or an asymmetric configuration when interacting with inhibitors.

Porphyrin triplet state as a potential spin label for nanometer distance measurements by PELDOR spectroscopy.

This work demonstrates, for the first time, the feasibility of applying pulsed electron-electron double resonance (PELDOR/DEER) to determine the interspin distance between a photoexcited porphyrin triplet state (S = 1) and a nitroxide spin label chemically incorporated into a small helical peptide. The PELDOR trace shows deep envelope modulation induced by electron-electron dipole interaction between the partners in the pair, providing an accurate distance measurement. This new labeling approach has a high potential for measuring nanometer distances in more complex biological systems due to the sensitivity acquired from the spin polarization of the photoexcited triplet state spectrum.

Energy Landscapes and Catalysis in Nitric-oxide Synthase

Nitric oxide (NO) plays diverse roles in mammalian physiology. It is involved in blood pressure regulation, neurotransmission, and immune response, and is generated through complex electron transfer reactions catalyzed by NO synthases (NOS). In neuronal NOS (nNOS), protein domain dynamics and calmodulin binding are implicated in regulating electron flow from NADPH, through the FAD and FMN cofactors, to the heme oxygenase domain, the site of NO generation. Simple models based on crystal structures of nNOS reductase have invoked a role for large scale motions of the FMN-binding domain in shuttling electrons from the FAD-binding domain to the heme oxygenase domain. However, molecular level insight of the dynamic structural transitions in NOS enzymes during enzyme catalysis is lacking. We use pulsed electron-electron double resonance spectroscopy to derive inter-domain distance relationships in multiple conformational states of nNOS. These distance relationships are correlated with enzymatic activity through variable pressure kinetic studies of electron transfer and turnover. The binding of NADPH and calmodulin are shown to influence interdomain distance relationships as well as reaction chemistry. An important effect of calmodulin binding is to suppress adventitious electron transfer from nNOS to molecular oxygen and thereby preventing accumulation of reactive oxygen species. A complex landscape of conformations is required for nNOS catalysis beyond the simple models derived from static crystal structures of nNOS reductase. Detailed understanding of this landscape advances our understanding of nNOS catalysis/electron transfer, and could provide new opportunities for the discovery of small molecule inhibitors that bind at dynamic protein interfaces of this multidimensional energy landscape.

The histone chaperones Vps75 and Nap1 form ring-like, tetrameric structures in solution

NAP-1 fold histone chaperones play an important role in escorting histones to and from sites of nucleosome assembly and disassembly. The two NAP-1 fold histone chaperones in budding yeast, Vps75 and Nap1, have previously been crystalized in a characteristic homodimeric conformation. In this study, a combination of small angle X-ray scattering, multi angle light scattering and pulsed electron–electron double resonance approaches were used to show that both Vps75 and Nap1 adopt ring-shaped tetrameric conformations in solution. This suggests that the formation of homotetramers is a common feature of NAP-1 fold histone chaperones. The tetramerisation of NAP-1 fold histone chaperones may act to shield acidic surfaces in the absence of histone cargo thus providing a ‘self-chaperoning’ type mechanism.

Probing the Structure of the Mechanosensitive Channel of Small Conductance in Lipid Bilayers with Pulsed Electron-Electron Double Resonance

Mechanosensitive channel proteins are important safety valves against osmotic shock in bacteria, and are involved in sensing touch and sound waves in higher organisms. The mechanosensitive channel of small conductance (MscS) has been extensively studied. Pulsed electron-electron double resonance (PELDOR or DEER) of detergent-solubilized protein confirms that as seen in the crystal structure, the outer ring of transmembrane helices do not pack against the pore-forming helices, creating an apparent void. The relevance of this void to the functional form of MscS in the bilayer is the subject of debate. Here, we report PELDOR measurements of MscS reconstituted into two lipid bilayer systems: nanodiscs and bicelles. The distance measurements from multiple mutants derived from the PELDOR data are consistent with the detergent-solution arrangement of the protein. We conclude, therefore, that the relative positioning of the transmembrane helices is preserved in mimics of the cell bilayer, and that the apparent voids are not an artifact of detergent solution but a property of the protein that will have to be accounted for in any molecular mechanism of gating.

Site-Directed Spin Labelling of Sulfite Oxidase using Non Natural Amino Acids

Site-directed spin labeling (SDSL) in combination with EPR spectroscopy has proven to be a valuable tool to investigate structure and dynamics of proteins. Commonly, spin labels are introduced into proteins using cysteine residues. However, this strategy fails if proteins contain functionally important cysteines. A recent proof-of-principle study using T4 Lysozyme as a model system has shown that non-natural p-acetylphenylalanine binding the spin label through a ketoxime ligation can be used for SDSL [1]. While T4 Lysozyme does not contain essential amino acids and is a rather stable protein, the current contribution will present a study on sulfite oxidase, a molybdo-enzyme, which carries an essential cysteine residue binding the Moco-cofactor, using the same spin labeling strategy as in [1].Within this contribution we will discuss challenges involved in the labeling of a more fragile protein using the less reactive ketoxime ligation in comparison to the disulfide linkage and will explore the information gained from the EPR line shapes of these spin labels in terms of structure determination, using mutations along a helical turn as an exploratory example. In addition, doubly spin labeled proteins were created to determine distances between the spin labels using pulsed electron-electron double resonance (pELDOR/DEER) experiments. The distance distributions extracted from these measurements will be discussed in light of expectations based on simple geometric considerations and will be compared to results of cysteine based distance determinations.[1] M. R. Fleissner, E. M. Brustad, T. S. Kalai, C. Altenbach, D. Cascio, F. B. Peters, K. L. N. Hideg, S. Parker, et al., Site-directed spin labeling of a genetically encoded unnatural amino acid, Proc. Nat. Acad. Sci. 2009, 106, 21637.

Synthesis and conformational properties of a TOAC doubly spin‐labeled analog of the medium‐length, membrane active peptaibiotic ampullosporin a as revealed by cd, fluorescence, and EPR spectroscopies

We describe the challenging solid-phase synthesis of the medium-length (14 amino-acid residues) peptaibiotic ampullosporin A, originally extracted from the fungus Sepedonium ampullosporum, and an analog doubly spin labeled (at positions 3 and 13) with the stable nitroxyl free-radical 4-amino-1-oxyl-2,2,6,6-tetramethylpiperidine-4-carboxylic acid (TOAC). The results of a circular dichrosim investigation in methanol strongly support the view that both peptides are essentially right-handed helical, in particular endowed with a large population of α-helical conformers. We also observed a significant quenching effect from the TOAC(3) nitroxyl radical on the fluorescence of Trp(1), compatible with that expected when both residues are closely located on the same helix segment. Combined continuous wave and pulsed electron-electron double resonance electron paramagnetic resonance methodologies converge on the conclusion obtained from the other aforementioned spectroscopies, namely, that the [TOAC(3,13)] ampullosporin A analog is mostly folded in the α-helical conformation. A liposome leakage assay demonstrated that the membrane-modifying properties of this bis-labeled analog are remarkable and even slightly superior to those of the natural peptaibiotic itself.

A versatile approach for site-directed spin labeling and structural EPR studies of RNAs

Site-directed spin labeling (SDSL) is widely applied for structural studies of biopolymers by electron paramagnetic resonance (EPR). However, SDSL of long RNA sequences still remains a challenging task. Here, we propose a novel SDSL approach potentially suitable for long natural RNAs, which is based on the attachment of a linker containing an aliphatic amino group to the target nucleotide residue followed by selective coupling of a spin label to this amino group. Such a linker can be attached to the desired RNA residue via a sequence-specific reaction with the derivatives of oligodeoxyribonucleotides. To verify this approach, we applied it to model RNA duplex with known structure and expected distance between corresponding residues. A new 2,5-bis(spirocyclohexane)-substituted spin label with advanced stability and relaxation properties has been used, and the distance distribution measured using Q-band (34 GHz) pulsed double electron-electron resonance corresponds well to the expected one. We have additionally validated the obtained results by studying a similar RNA duplex, where the linker with the aliphatic amino group was introduced via solid-phase synthesis. Although this novel SDSL approach does not provide an advantage in precision of molecular distance measurements, we believe that its applicability to long RNAs is a crucial benefit for future structural studies using pulse EPR.

4,4′-{Diazenediylbis[(1,4-phenylene)bis(carbonyloxy)]}bis(2,2,6,6-tetramethylpiperidinyloxidanyl): the first crystal structure determination from powder data of a nitroxide radical

The title compound, C32H42N4O6, is a novel nitroxide radical used for pulsed electron-electron double resonance (PELDOR) spectroscopy. Its crystal structure was determined from laboratory X-ray powder diffraction data. The attractive forces between the molecules in the crystal structure are mainly of dispersive nature. A special interaction of the nitroxide radicals was not observed.

Nitroxyls and PELDOR: Nitroxyl radicals in pulsed electron-electron double resonance spectroscopy

The review considers the main propositions of PELDOR theory. It is shown how from the analysis of PELDOR time traces it is possible to find the parameters of a spin system such as the distance and the distance distribution (spectrum), number of spins in aggregates and complexes, exchange integral and how to separate for the following analysis the inter- and intramolecular contributions to the general dipole interaction. Examples of PELDOR application in the studies of the spatial distribution of nitroxyl radicals, the charge effect of dipolar interacting nitroxyls on their spatial distribution are given and the results of the determination of distances and the spectrum of distances for nitroxyl bi-, tri-, and tetraradicals are presented. The works on nitroxyl radicals in which the orientation selectivity effect, spin exchange, and conformational properties of the radicals are examined by the PELDOR method are analyzed. The studies of the structure of paramagnetic ion-nitroxyl radical pairs and the PELDOR data on nitroxyls at high frequencies (high fields) are considered. The last section of the review is devoted to the works examining the properties such as the molecular flexibility of oligomers and supramolecules contains nitroxyl radicals.

Out-of-phase PELDOR

Pulsed electron–electron double resonance (PELDOR) is a method frequently used to determine the structure of bio-macromolecule on a nanometre scale. Usually PELDOR experiments are carried out in the high-temperature limit, when the Boltzmann population of spins oriented parallel and antiparallel to the external magnetic field are almost equal. Also the well-developed theories describing PELDOR apply to this case. However, the high-temperature conditions are no more fulfilled for experiments done in a high magnetic field (above 6 T) and at low temperatures (below 5 K), when the Zeeman interaction energy of an electron spin becomes comparable with thermal energy . In this work we demonstrate that PELDOR signals measured at these conditions differ from the usual PELDOR signals. Additional to the standard in-phase component the PELDOR signal at low temperature and high magnetic field also contains an out-of-phase component that disappears in the high-temperature limit. This means that we observe not only the modulation of the refocused transverse magnetisation along a single axis in the rotating coordinate system but rather its precession in the x-y plane with a dipolar frequency. Here, we provide a quantitative explanation as well as a detailed analysis of the spin magnetisation dynamics under such conditions based on density matrix formalism. Understanding the PELDOR phenomena in high field and at low temperatures offers a tool to separate intra from intermolecular interactions, which might be extremely helpful and important for applications to biomolecules with a high degree of conformational flexibility.

PELDOR in rotationally symmetric homo-oligomers

Nanometre distance measurements by pulsed electron−electron double resonance (PELDOR) spectroscopy have become an increasingly important tool in structural biology. The theoretical underpinning of the experiment is well defined for systems containing two nitroxide spin-labels (spin pairs); however, recently experiments have been reported on homo-oligomeric membrane proteins consisting of up to eight spin-labelled monomers. We have explored the theory behind these systems by examining model systems based on multiple spins arranged in rotationally symmetric polygons. The results demonstrate that with a rising number of spins within the test molecule, increasingly strong distortions appear in distance distributions obtained from an analysis based on the simple spin pair approach. These distortions are significant over a range of system sizes and remain so even when random errors are introduced into the symmetry of the model. We present an alternative approach to the extraction of distances on such systems based on a minimisation that properly treats multi-spin correlations. We demonstrate the utility of this approach on a spin-labelled mutant of the heptameric Mechanosensitive Channel of Small Conductance of E. coli.

Orientation Resolving Dipolar High-Field EPR Spectroscopy on Disordered Solids: II. Structure of Spin-Correlated Radical Pairs in Photosystem I

The distance and relative orientation of functional groups within protein domains and their changes during chemical reactions determine the efficiency of biological processes. In this work on electron transfer proteins, we report the results of orientation resolving dipolar high-field EPR spectroscopy on the charge-separated state P700•+ A1•– (P700, primary electron donor; A1, phylloquinone electron acceptor) in Photosystem I (PS I). Pulsed high-field EPR spectroscopy at W-band (95 GHz, 3.4 T) with extensions to PELDOR (pulsed electron–electron double resonance) and RIDME (relaxation-induced dipolar modulation enhancement) was utilized to obtain the parameters describing the three-dimensional structure of the laser-flash-induced transient radical pair P700•+ A1•– in a frozen solution of deuterated PS I from the cyanobacterium Synechocystis sp. PCC 6803, which is performing oxygenic photosynthesis. The measured distances and relative orientations of the weakly coupled radical ions in the radical pair P700•+ A1•– are compared with previously reported geometries and with those of the precursor cofactors P700 and A1 known from X-ray crystallography. Cyclic electron transfer was found to proceed exclusively via the A-branch of the cofactor chain of PS I at cryogenic temperature. The position and orientation of the reduced phylloquinone coincide with those of the precursor, revealing that no substantial orientational changes of the phylloquinone molecule upon charge separation occur. Several distinct orientations of the P700•+ g-tensor axes with respect to the molecular frame of the primary donor were found experimentally, which we explain by several conformational substates of the P700•+ radical structure having slightly different electron spin density distributions.

Spin‐Echo Electron Paramagnetic Resonance (EPR) Spectroscopy of a Pore‐Forming (Lipo)Peptaibol in Model and Bacterial Membranes

This review compiles the unusual structural and dynamic peculiarities of trichogin GA IV and its analogs in lipid bilayers. Different electron spin echo (ESE) spectroscopic techniques were employed to study a set of spin-labeled analogs of trichogin GA IV in model and natural membranes. Pulsed electron-electron double resonance (PELDOR) method enabled the elucidation of the peptide conformation, while the ESE envelope modulation (ESEEM) technique was applied to study the insertion of the site-specifically spin-labeled peptide into the core of the membrane. The latter technique was also used to examine the water accessibility for peptide-attached spin labels at different levels of membrane depth. Finally, it will be shown that measurement of the ESE decays at different temperatures reveals molecular information on the mobility of the transmembrane lipopeptide aggregate. The experimental results are discussed in terms of the antibiotic and toxic activities of trichogin GA IV.

Structure and Nature of Manganese(II) Imidazole Complexes in Frozen Aqueous Solutions

A common feature of a large majority of the manganese metalloenzymes, as well as many synthetic biomimetic complexes, is the bonding between the manganese ion and imidazoles. This interaction was studied by examining the nature and structure of manganese(II) imidazole complexes in frozen aqueous solutions using 285 GHz high magnet-field continuous-wave electron paramagnetic resonance (cw-HFEPR) and 95 GHz pulsed electron-nuclear double resonance (ENDOR) and pulsed electron-double resonance detected nuclear magnetic resonance (PELDOR-NMR). The (55)Mn hyperfine coupling and isotropic g values of Mn(II) in frozen imidazole solutions continuously decreased with increasing imidazole concentration. ENDOR and PELDOR-NMR measurements demonstrated that the structural basis for this behavior arose from the imidazole concentration-dependent distribution of three six-coordinate and two four-coordinate species: [Mn(H2O)6](2+), [Mn(imidazole)(H2O)5](2+), [Mn(imidazole)2(H2O)4](2+), [Mn(imidazole)3(H2O)](2+), and [Mn(imidazole)4](2+). The hyperfine and g values of manganese proteins were also fully consistent with this imidazole effect. Density functional theory methods were used to calculate the structures, spin and charge densities, and hyperfine couplings of a number of different manganese imidazole complexes. The use of density functional theory with large exact-exchange admixture calculations gave isotropic (55)Mn hyperfine couplings that were semiquantitative and of predictive value. The results show that the covalency of the Mn-N bonds play an important role in determining not only magnetic spin parameters but also the structure of the metal binding site. The relationship between the isotropic (55)Mn hyperfine value and the number of imidazole ligands provides a quick and easy test for determining whether a protein binds an Mn(II) ion using histidine residues and, if so, how many are involved. Application of this method shows that as much as 40% of the Mn(II) ions in Deinococcus radiodurans are ligated to two histidines (Tabares, L. C.; Un, S. J. Biol. Chem 2013, in press).

Pulsed Electron Double Resonance in Structural Studies of Spin-Labeled Nucleic Acids

This review deals with the application of the pulsed electron double resonance (PELDOR) method to studies of spin-labeled DNA and RNA with complicated spatial structures, such as tetramers, aptamers, riboswitches, and three- and four-way junctions. The use of this method for studying DNA damage sites is also described.

Broadband Inversion PELDOR Spectroscopy with Partially Adiabatic Shaped Pulses

Distance and spins: A new broadband, frequency-selective inversion pulse has been devised for pulsed electron–electron double resonance (PELDOR) spectroscopy, a unique method used to determine distance distributions between two or more paramagnetic centers 2–10 nm apart. The PELDOR modulation depth can be increased by substituting the rectangular pump pulse by a shaped pulse. As a service to our authors and readers, this journal provides supporting information supplied by the authors. Such materials are peer reviewed and may be re-organized for online delivery, but are not copy-edited or typeset. Technical support issues arising from supporting information (other than missing files) should be addressed to the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.

Electronic structure of S2 state of the oxygen-evolving complex of photosystem II studied by PELDOR

Photosynthetic water splitting is catalyzed by a Mn4CaO5 cluster in photosystem II, whose structure was recently determined at a resolution of 1.9Å [Umena, Y. et al. 2011, Nature, 473:55–60]. To determine the electronic structure of the Mn4CaO5 cluster, pulsed electron–electron double resonance (PELDOR) measurements were performed for the tyrosine residue YD and S2 state signals with non-oriented and oriented photosystem II (PS II) samples. Based on these measurements, the spin density distributions were calculated by comparing with the experimental results. The best fitting parameters were obtained with a model in which Mn1 has a large positive projection, Mn3 has a small positive projection, and Mn2 and Mn4 have negative projections (the numbering of Mni (i=1–4) is based on the crystal structure at a 1.9Å resolution), which yielded spin projections of 1.97, −1.20, 1.19 and −0.96 for Mn1–4 ions. The results show that the Mn1 ion, which is coordinated by H332, D342 and E189, has a valence of Mn(III) in the S2 state. The sign of the exchange interactions J13 is positive, and the other signs are negative.

Refined Distances Between Paramagnetic Centers of a Multi‐Copper Nitrite Reductase Determined by Pulsed EPR (iDEER) Spectroscopy

Refined Distances Between Paramagnetic Centers of a Multi‐Copper Nitrite Reductase Determined by Pulsed EPR (<i>i</i>DEER) Spectroscopy