The CW-EPR Capabilities of a Dual DNP/EPR Spectrometer Operating at 14 and 7 T.

High-field electron paramagnetic resonance (EPR) measurements are indispensable for a better understanding of dynamic nuclear polarization (DNP), which relies on polarization transfer between electron and nuclear spins. DNP experiments are typically performed at high > 7 T magnetic fields and low ≤ 100 K temperatures, while EPR instrumentation capable of EPR measurements under these conditions is scarce. In this paper, we describe the CW EPR capabilities of a dual DNP/EPR spectrometer that is designed to carry out EPR experiments under "DNP conditions" at 14 and 7 T. In the first part, we present the design of this instrument, highlighting the choices made to allow for both DNP and EPR operations. The spectrometer uses a sweepable cryogen-free magnet with NMR-grade homogeneity, a closed-cycle cooling system, a quasi-optical induction mode bridge, and a superheterodyne receiver system. The probe design is optimized for low heat load and fast sample exchange under cryogenic conditions. The spectrometer can operate in frequency and field sweep modes, including wide field sweeps using the main coil of the magnet. In the second part, we present EPR spectra acquired over a wide range of samples and operating conditions, illustrating the CW EPR capabilities of the instrument.

Nitrogen Substitutions Aggregation and Clustering in Diamonds as Revealed by High-Field Electron Paramagnetic Resonance.

Diamonds have been shown to be an excellent platform for quantum computing and quantum sensing applications. These applications are enabled by the presence of defects in the lattice, which are also known as color centers. The most common nitrogen-based defect in synthetic diamonds is the paramagnetic nitrogen substitution (P1) center. While the majority of quantum applications rely on nitrogen-vacancy (NV) centers, the properties of the latter are heavily influenced by the presence and the spatial distribution of the P1 centers. Hence, understanding the spatial distribution and mutual interactions of P1 centers is crucial for the successful development of diamond-based quantum devices. Unlike NV centers, P1 centers do not have a spin-dependent optical signature, and their spin-related properties, therefore, have to be detected and characterized using magnetic resonance methods. We show that using high-field (6.9 and 13.8 T) pulsed electron paramagnetic resonance (EPR) and dynamic nuclear polarization (DNP) experiments, we can distinguish and quantify three distinct populations of P1 centers: isolated P1 centers, weakly interacting ones, and exchange-coupled ones that are clustered together. While such clustering was suggested before, these clusters were never detected directly and unambiguously. Moreover, by using electron-electron double resonance (ELDOR) pump-probe experiments, we demonstrate that the latter clustered population does not exist in isolation but coexists with the more weakly interacting P1 centers throughout the diamond lattice. Its presence thus strongly affects the quantum properties of the diamond. We also show that the existence of this population can explain recent hyperpolarization results in type Ib high-pressure, high-temperature (HPHT) diamonds. We propose a combination of high-field pulsed EPR, ELDOR, and DNP as a tool for probing the aggregation state and interactions among different populations of nitrogen substitution centers.

Spin state and magnetic coupling in polynuclear Ni(II) complexes from density functional theory: is there an optimal amount of Fock exchange?

Reliable prediction of the ground-state spin and magnetic coupling constants in transition-metal complexes is a well-known challenge for density functional theory (DFT). One popular strategy for addressing this long-standing issue involves the modification of the fraction of Fock exchange in a hybrid functional. Here we explore the viability of this approach using three polynuclear metal-organic complexes based on a Ni4O4 cubane motif, having different ground state spin values (S = 0, 2, 4) owing to the use of different ligands. We systematically search for an optimum fraction of Fock exchange, across various global, range-separated, and double hybrid functionals. We find that for all functionals tested, at best there only exists a very narrow range of Fock exchange fractions which results in a correct prediction of the ground-state spin for all three complexes. The useful range is functional dependent, but general trends can be identified. Typically, at least two similar systems must be used in order to determine both an upper and lower limit of the optimal range. This is likely owing to conflicting demands of minimizing delocalization errors, which typically requires a higher percentage of Fock exchange, and addressing static correlation, which typically requires a lower one. Furthermore, we find that within the optimal range of Fock exchange, the sign and relative magnitude of Ni-Ni magnetic coupling constants are reasonably well reproduced, but there is still room for quantitative improvement in the prediction. Thus, the prediction of spin state and magnetic coupling in polynuclear complexes remains an ongoing challenge for DFT.

DEER experiments reveal fundamental differences between calmodulin complexes with IQ and MARCKS peptides in solution.

Calmodulin (CaM) is a calcium-binding protein that regulates the function of many proteins by indirectly conferring Ca2+ sensitivity, and it undergoes a large conformational change on partners' binding. We compared the solution binding mode of the target peptides MARCKS and IQ by double electron-electron resonance (DEER) distance measurements and paramagnetic NMR. We combined nitroxide and Gd(III) spin labels, including specific substitution of one of the Ca2+ ions in the CaM mutant N60D by a Gd(III) ion. The binding of MARCKS to holo-CaM resulted neither in a closed conformation nor in a unique relative orientation between the two CaM domains, in contrast with the crystal structure. Binding of IQ to holo-CaM did generate a closed conformation. Using elastic network modeling and 12 distance restraints obtained from multiple holo-CaM/IQ DEER data, we derived a model of the solution structure, which is in reasonable agreement with the crystal structure.

Time domain simulation of Gd3+-Gd3+ distance measurements by EPR.

Gd3+-based spin labels are useful as an alternative to nitroxides for intramolecular distance measurements at high fields in biological systems. However, double electron-electron resonance (DEER) measurements using model Gd3+ complexes featured a low modulation depth and an unexpected broadening of the distance distribution for short Gd3+-Gd3+ distances, when analysed using the software designed for S = 1/2 pairs. It appears that these effects result from the different spectroscopic characteristics of Gd3+-the high spin, the zero field splitting (ZFS), and the flip-flop terms in the dipolar Hamiltonian that are often ignored for spin-1/2 systems. An understanding of the factors affecting the modulation frequency and amplitude is essential for the correct analysis of Gd3+-Gd3+ DEER data and for the educated choice of experimental settings, such as Gd3+ spin label type and the pulse parameters. This work uses time-domain simulations of Gd3+-Gd3+ DEER by explicit density matrix propagation to elucidate the factors shaping Gd3+ DEER traces. The simulations show that mixing between the |+½, -½ã€‰ and |-½, +½ã€‰ states of the two spins, caused by the flip-flop term in the dipolar Hamiltonian, leads to dampening of the dipolar modulation. This effect may be mitigated by a large ZFS or by pulse frequency settings allowing for a decreased contribution of the central transition and the one adjacent to it. The simulations reproduce both the experimental line shapes of the Fourier-transforms of the DEER time domain traces and the trends in the behaviour of the modulation depth, thus enabling a more systematic design and analysis of Gd3+ DEER experiments.

Gd(3+) Spin Labels Report the Conformation and Solvent Accessibility of Solution and Vesicle-Bound Melittin.

Although Gd(3+)-based spin labels have been shown to be an alternative to nitroxides for double electron-electron resonance (DEER) distance measurements at high fields, their ability to provide solvent accessibility information, as nitroxides do, has not been explored. In addition, the effect of the label type on the measured distance distribution has not been sufficiently characterized. In this work, we extended the applicability of Gd(3+) spin labels to solvent accessibility measurements on a peptide in model membranes, namely, large unilamellar vesicles (LUVs) using W-band (2)H Mims electron-nuclear double resonance (ENDOR) and electron spin echo envelope modulation (ESEEM) techniques and Gd(3+)-ADO3A-labeled melittin. In addition, we carried out Gd(3+)-Gd(3+) DEER distance measurements to probe the peptide conformation in solution and when bound to LUVs. A comparison with earlier results reported for the same system with nitroxide labels shows that, although in both cases the peptide binds parallel to the membrane surface, the Gd(3+)-ADO3A label tends to protrude from the membrane into the solvent, whereas the nitroxide does the opposite. This can be explained on the basis of the hydrophilicity of the Gd(3+)-ADO3A labels in contrast with the hydrophobicity of nitroxides. The distance distributions obtained from different labels are accordingly different, with the Gd(3+)-ADO3A yielding consistently broader distributions. These discrepancies are most pronounced when the peptide termini are labeled, which implies that such labeling positions may be inadvisible.

W-band orientation selective DEER measurements on a Gd3+/nitroxide mixed-labeled protein dimer with a dual mode cavity.

Double electron-electron resonance (DEER) at W-band (95 GHz) was applied to measure the distance between a pair of nitroxide and Gd(3+) chelate spin labels, about 6 nm apart, in a homodimer of the protein ERp29. While high-field DEER measurements on systems with such mixed labels can be highly attractive in terms of sensitivity and the potential to access long distances, a major difficulty arises from the large frequency spacing (about 700 MHz) between the narrow, intense signal of the Gd(3+) central transition and the nitroxide signal. This is particularly problematic when using standard single-mode cavities. Here we show that a novel dual-mode cavity that matches this large frequency separation dramatically increases the sensitivity of DEER measurements, allowing evolution times as long as 12 µs in a protein. This opens the possibility of accessing distances of 8 nm and longer. In addition, orientation selection can be resolved and analyzed, thus providing additional structural information. In the case of W-band DEER on a Gd(3+)-nitroxide pair, only two angles and their distributions have to be determined, which is a much simpler problem to solve than the five angles and their distributions associated with two nitroxide spin labels.

HIV-1 gp41 transmembrane domain interacts with the fusion peptide: implication in lipid mixing and inhibition of virus-cell fusion.

Fusion of the human immunodeficiency virus (HIV) with target cells is mediated by the gp41 subunit of the envelope protein. Mutation and deletion studies within the transmembrane domain (TMD) of intact gp41 influenced its fusion activity. In addition, current models suggest that the TMD is in proximity with the fusion peptide (FP) at the late fusion stages, but there are no direct experimental data to support this hypothesis. Here, we investigated the TMD focusing on two regions: the N-terminal containing the GxxxG motif and the C-terminal containing the GLRI motif, which is conserved among the TMDs of HIV and the T-cell receptor. Studies utilizing the ToxR expression system combined with synthetic peptides and their fluorescent analogues derived from TMD revealed that the GxxxG motif is important for TMD self-association, whereas the C-terminal region is for its heteroassociation with FP. Functionally, all three TMD peptides induced lipid mixing that was enhanced significantly upon mixing with FP. Furthermore, the TMD peptides inhibited virus-cell fusion apparently through their interaction with their endogenous counterparts. Notably, the R2E mutant (in the GLRI) was significantly less potent than the two others. Overall, our findings provide experimental evidence that HIV-1 TMD contributes to membrane assembly and function of the HIV-1 envelope. Owing to similarities between functional domains within viruses, these findings suggest that the TMDs and FPs may contribute similarly in other viruses as well.