We demonstrate a series of multitrityl radical compounds where accurate spin-counting by pulsed electron paramagnetic resonance (EPR) can be achieved at X-band (9 GHz) frequencies, even for molecules with very short and flexible linkers. Multiquantum filter experiments, well-known from NMR, were used to count the number of coupled electron spins in these compounds. The six pulse double quantum filter sequence used in EPR for distance determinations in biradicals was used. Precise phase settings to separate higher quantum coherences were achieved by an arbitrary waveform generator. The trityl radicals have narrow spectral width so that homogeneous excitation of all spins by the pulses is possible. The transversal relaxation times of higher quantum coherences of trityl radicals are sufficiently long to allow their detection. Our results on model compounds show the potential of this approach to determine oligomeric states in protein complexes in their native environment using functionalized trityl spin labels.

Ubiquitination is the most versatile posttranslational modification. The information is encoded by linkage type as well as chain length, which are translated by ubiquitin binding domains into specific signaling events. Chain topology determines the conformational space of a ubiquitin chain and adds an additional regulatory layer to this ubiquitin code. In particular, processes that modify chain length will be affected by chain conformations as they require access to the elongation or cleavage sites. We investigated conformational distributions in the context of chain elongation and disassembly using pulsed electron-electron double resonance spectroscopy in combination with molecular modeling. Analysis of the conformational space of diubiquitin revealed conformational selection or remodeling as mechanisms for chain recognition during elongation or hydrolysis, respectively. Chain elongation to tetraubiquitin increases the sampled conformational space, suggesting that a high intrinsic flexibility of K48-linked chains may contribute to efficient proteasomal degradation.

Pulsed Electron-Electron Double Resonance spectroscopy (PELDOR or DEER) has been used to investigate structure and dynamics of nucleic acid (NA) molecules which are double-labeled by a paramagnetic cytidine analogue [1,2]. This new type of spin-label, rigidly incorporated into double stranded NA motives, allows measuring the distance R and the mutual orientation between both two spin-labeled cytidine rings. Performing the experiment with several distinct probe frequencies and at different magnetic field strengths allows obtaining unambiguous information on the structure and conformational flexibility from a small set of double-labeled NA molecules [3,4]. Extending the PELDOR measurements to room temperature gives access to the time scale of the conformational dynamics. Quantitative comparison with MD studies will be given [5] and newly designed pulse sequences with superior performance discussed. [1] N. Barhate, P. Cekan, A. P. Massey, S. T. Sigurdsson, Angew. Chem., Int. Ed., 2007, 46, 2655-2658. [2] O. Schiemann, P. Cekan, D. Margraf, T. F. Prisner, S. T. Sigurdsson, Angew. Chem., Int. Ed., 2009, 48, 3292-3295 [3] A. Marko, V. Denysenkov, D. Margraft, P. Cekan, O. Schiemann, S. T. Sigurdsson, T. F. Prisner, J. Am. Chem. Soc. 2011, 133, 13375-13379. [4] C. M. Grytz, A. Marko, P. Cekan, S. T. Sigurdsson and T. F. Prisner, Phys. Chem. Chem. Phys., 2016, 18, 2993-3002. [5] L. S. Stelzl, N. Erlenbach, M. Heinz, T. F. Prisner, G. Hummer, J. Am. Chem. Soc., 2017, 139, 11674-11677.

The investigation of the structure and conformational dynamics of biomolecules under physiological conditions is challenging for structural biology. Although pulsed electron paramagnetic resonance (like PELDOR) techniques provide long-range distance and orientation information with high accuracy, such studies are usually performed at cryogenic temperatures. At room temperature (RT) PELDOR studies are seemingly impossible due to short electronic relaxation times and loss of dipolar interactions through rotational averaging. We incorporated the rigid nitroxide spin label Ç into a DNA duplex and immobilized the sample on a solid support to overcome this limitation. This enabled orientation-selective PELDOR measurements at RT. A comparison with data recorded at 50 K revealed averaging of internal dynamics, which occur on the ns time range at RT. Thus, our approach adds a new method to study structural and dynamical processes at physiological temperature in the <10 μs time range with atomistic resolution.

Fundamentally, the stability of coordination complexes and of templated (bio)macromolecular assemblies depends on the thermodynamic and kinetic properties of the intermediates and final complexes formed. Here, we used pulse EPR (electron paramagnetic resonance) spectroscopy to determine the stabilities of nanoscopic assemblies formed between one or two nitroxide spin-labelled tridentate 2,2':6',2''-terpyridine (tpy) ligands and divalent metal ions (FeII, ZnII, CoII and CuII). In three distinct approaches we exploited (a) the modulation depth of pulsed electron-electron double resonance (PELDOR) experiments in samples with increasing metal-to-ligand ratios, (b) the frequencies of PELDOR under broadband excitation using shaped pulses and (c) the distances recovered from well-resolved PELDOR data in fully deuterated solvents measured at 34 GHz. The results demonstrate that PELDOR is highly sensitive to resolving the stability of templated dimers and allows to readily distinguish anti-cooperative binding (for CuII ions) from cooperative binding (for CoII or FeII ions). In the case of paramagnetic ions (CoII and CuII) the use of broadband PELDOR allowed to identify the cooperativity of binding from the time domain and distance data. By using a second labelled tpy ligand and by mixing two homoleptic complexes of the same metal centre we could probe the kinetic stability on a timescale of tens of seconds. Here, tpy complexes of CuII and ZnII were found to be substitutionally labile, CoII showed very slow exchange and FeII was inert under our conditions. Not only do our chemical models allow studying metal-ligand interactions via PELDOR spectroscopy, the design of our study is directly transferable to (bio)macromolecular systems for determining the kinetic and thermodynamic stabilities underpinning (templated) multimerisation. Considering the limited methods available to obtain direct information on the composition and stability of complex assemblies we believe our approach to be a valuable addition to the armoury of methods currently used to study these systems.

ATP-binding cassette (ABC) exporters actively move chemically diverse substrates across biological membranes. Their malfunction leads to human diseases. Many ABC exporters encompass asymmetric nucleotide-binding sites (NBSs), and some of them are inhibited by the transported substrate. The functional relevance of the catalytic asymmetry or the mechanism for trans-inhibition remains elusive. Here, we investigated TmrAB, a functional homologue of the human antigen translocation complex TAP using advanced electron-electron double resonance spectroscopy. In the presence of ATP, the heterodimeric ABC exporter exists in a tunable equilibrium between inward- and outward-facing conformations. The two NBSs exhibit pronounced asymmetry in the open-to-close equilibrium. The closed conformation is more favored at the degenerate NBS, and closure of either of the NBS is sufficient to open the extracellular gate. We define the mechanistic basis for trans-inhibition, which operates by a reverse transition from the outward-facing state through an occluded conformation. These novel findings uncover the central role of reversible conformational equilibrium in the function and regulation of an ABC exporter and establish a mechanistic framework for future investigations on other medically important transporters with imprinted asymmetry. Also, this study demonstrates for the first-time the feasibility to resolve equilibrium populations at multiple domains and their interdependence for global conformational changes in a large membrane protein complex.

Dynamic nuclear polarization (DNP) is a methodology to increase the sensitivity of nuclear magnetic resonance (NMR) spectroscopy. It relies on the transfer of the electron spin polarization from a radical to coupled nuclear spins, driven by microwave excitation resonant with the electron spin transitions. In this work we explore the potential of pulsed multi-frequency microwave excitation in liquids. Here, the relevant DNP mechanism is the Overhauser effect. The experiments were performed with TEMPOL radicals in aqueous solution at room temperature using a Q-band frequency (1.2 T) electron paramagnetic resonance (EPR) spectrometer combined with a Minispec NMR spectrometer. A fast arbitrary waveform generator (AWG) enabled the generation of multi-frequency pulses used to either sequentially or simultaneously excite all three N-14-hyperfine lines of the nitroxide radical. The multi-frequency excitation resulted in a doubling of the observed DNP enhancements compared to single-frequency microwave excitation. Q-band free induction decay (FID) signals of TEMPOL were measured as a function of the excitation pulse length allowing the efficiency of the electron spin manipulation by the microwave pulses to be extracted. Based on this knowledge we could quantitatively model our pulsed DNP enhancements at 1.2 T by numerical solution of the Bloch equations, including electron spin relaxation and experimental parameters. Our results are in good agreement with theoretical predictions. Whereas for a narrow and homogeneous single EPR line continuous wave excitation leads to more efficient DNP enhancements compared to pulsed excitation for the same amount of averaged microwave power. The situation is different for radicals with several hyperfine lines or in the presence of inhomogeneous line broadening. In such cases pulsed single/multi-frequency excitation can lead to larger DNP enhancements.

This article describes current uses of shaped pulses, generated by an arbitrary waveform generator, in the field of EPR spectroscopy. We show applications of sech/tanh and WURST pulses to dipolar spectroscopy, including new pulse schemes and procedures, and discuss the more general concept of optimum-control-based pulses for applications in EPR spectroscopy. The article also describes a procedure to correct for experimental imperfections, mostly introduced by the microwave resonator, and discusses further potential applications and limitations of such pulses.

Carbon-centered radicals are interesting alternatives to otherwise commonly used nitroxide spin labels for dipolar spectroscopy techniques because of their narrow ESR linewidth. Herein, we present a novel BDPA biradical, where two BDPA (α,α,γ,γ-bisdiphenylene-β-phenylallyl) radicals are covalently tethered by a saturated biphenyl acetylene linker. The inter-spin distance between the two spin carrier fragments was measured using double quantum coherence (DQC) ESR methodology. The DQC experiment revealed a mean distance of only 1.8 nm between the two unpaired electron spins. This distance is shorter than the predictions based on a simple modelling of the biradical geometry with the electron spins located at the central carbon atoms. Therefore, DFT (density functional theory) calculations were performed to obtain a picture of the spin delocalization, which may give rise to a modified dipolar interaction tensor, and to find those conformations that correspond best to the experimentally observed inter-spin distance. Quantum chemical calculations showed that the attachment of the biphenyl acetylene linker at the second position of the fluorenyl ring of BDPA did not affect the spin population or geometry of the BDPA radical. Therefore, spin delocalization and geometry optimization of each BDPA moiety could be performed on the monomeric unit alone. The allylic dihedral angle θ1 between the fluorenyl rings in the monomer subunit was determined to be 30° or 150° using quantum chemical calculations. The proton hyperfine coupling constant calculated from both energy minima was in very good agreement with literature values. Based on the optimal monomer geometries and spin density distributions, the dipolar coupling interaction between both BDPA units could be calculated for several dimer geometries. It was shown that the rotation of the BDPA units around the linker axis (θ2) does not significantly influence the dipolar coupling strength when compared to the allylic dihedral angle θ1. A good agreement between the experimental and calculated dipolar coupling was found for θ1 = 30°.

In this article, we describe the implementation and advantages of shaped pulses in EPR spectroscopy. Phase/amplitude-modulated pulses on a nanosecond timescale allow improved excitation bandwidth and profile, and compensation of spatial field variations. The application of shaped pulses in magnetic resonance is briefly reviewed in the introduction, the frequency responses of some of the most frequently used shaped pulses are outlined in the theoretical part, the implementation of such pulses with EPR spectrometers is described, and finally some recent applications highlighting the potential to improve the performance of pulsed EPR experiments are illustrated.

Pulsed electron paramagnetic resonance (EPR) spectroscopy allows the determination of distances, in the range of 1.5-8 nm, between two spin-labels attached to macromolecules containing protons. Unfortunately, for hydrophobic lipid-bound or detergent-solubilized membrane proteins, the maximum distance accessible is much lower, because of a strongly reduced coherence time of the electron spins. Here we introduce a pulse sequence, based on a Carr-Purcell decoupling scheme on the observer spin, where each π-pulse is accompanied by a shaped sech/tanh inversion pulse applied to the second spin, to overcome this limitation. This pump/probe excitation scheme efficiently recouples the dipolar interaction, allowing a substantially longer observation time window to be achieved. This increases the upper limit and accuracy of distances that can be determined in membrane protein complexes. We validated the method on a bis-nitroxide model compound and applied this technique to the trimeric betaine transporter BetP. Interprotomer distances as long as 6 nm could be reliably determined, which is impossible with the existing methods.

Applications of broadband pulses for EPR have been reported for FID, echo detection and inversion pulses recently. Here we present a broadband Hahn, stimulated and refocused echo sequence derived from adiabatic pulses. The formation of echoes is accomplished by using variable chirp rates and pulse lengths. In all three broadband echo experiments the complete spectral shape of a nitroxide (about 70 Gauss at X-band frequency) could be recovered by Fourier transformation of the quadrature detected echo signals. Such broadband echoes provide an exciting opportunity to optimize pulse sequences where a full excitation of the spectrum is mandatory for an optimum performance. We applied our pulses to the SIFTER (single frequency technique for refocusing dipolar couplings) experiment, a solid echo based pulse sequence to measure the dipolar coupling between two unpaired electron spins. By employing our broadband Hahn echo sequence on a nitroxide biradical we could achieve an artifact free dipolar evolution time trace in the SIFTER experiment with 95% modulation depth at X-band frequency and of 10% modulation depth at Q-band frequency.

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.

A 1 ns resolution pulse shaping unit has been developed for pulsed EPR spectroscopy to enable 14-bit amplitude and phase modulation. Shaped broadband excitation pulses designed using optimal control theory (OCT) have been tested with this device at X-band frequency (9 GHz). FT-EPR experiments on organic radicals in solution have been performed with the new pulses, designed for uniform excitation over a significantly increased bandwidth compared to a classical rectangular π/2 pulse of the same B1 amplitude. The concept of a dead-time compensated prefocused pulse has been introduced to EPR with a self-refocusing of 200 ns after the end of the pulse. Echo-like refocused signals have been recorded and compared to the performance of a classical Hahn-echo sequence. The impulse response function of the microwave setup has been measured and incorporated into the algorithm for designing OCT pulses, resulting in further significant improvements in performance. Experimental limitations and potential new applications of OCT pulses in EPR spectroscopy will be discussed.