Pulsed Electron-electron Double Resonance Experiments Research Articles

Relaxation processes and high-field coherent spin manipulation in color center ensembles in 6 H -SiC

Coherent spin manipulations of spin-$\frac{3}{2}$ color center ensembles in 6H-SiC crystal have been studied in high magnetic fields using methods of pulsed electron paramagnetic resonance, Rabi oscillations, and pulsed electron-electron double resonance under optical alignment conditions of the spin level populations. Rabi oscillation experiments show room temperature coherent control of these spin-$\frac{3}{2}$ color center ensembles in strong magnetic fields. A sharp decrease of the spin-lattice relaxation time ${T}_{1}$, \ensuremath{\sim}40 times, was observed in 6H-SiC at magnetic field of \ensuremath{\sim}3.5 T with increasing temperature from 100 to 300 K, while the spin-spin relaxation time ${T}_{2}$ is only shortened by \ensuremath{\sim}1.3 times. With an increase in the magnetic field, the times ${T}_{1}$ and ${T}_{2}$ were shown to decrease. The relaxation time ${T}_{1}$ in the case of magnetic field directed along the axis of the spin-$\frac{3}{2}$ center is \ensuremath{\sim}2 times longer than ${T}_{1}$ in magnetic field perpendicular to this axis. Relaxation times of the spin center in crystal grown with a reduced concentration of an isotope $^{29}\mathrm{Si}$ are significantly longer than crystal, with the natural content of isotopes. With a decrease in the $^{29}\mathrm{Si}$ content in our experiments by a factor of \ensuremath{\sim}5, the effective nuclear spin bath in SiC is reduced by a factor of \ensuremath{\sim}2. In a zero magnetic field resonance, transitions are allowed as magnetic dipole transitions with frequency ${\ensuremath{\omega}}_{0}$ which correspond to the zero-field splitting. In zero magnetic field and in fixed magnetic fields, the Rabi frequency was shown, using so-called ``Feynman-Vernon-Hellwarth transformation,'' to be ${\ensuremath{\omega}}_{R}=|\ensuremath{\gamma}|{B}_{1}$. In pulsed electron-electron double resonance experiments, a change in the intensity of the electron spin echo signal corresponding to one of the spin-allowed fine structure transitions is recorded depending on the sweep of the second frequency. The experiments show the possibility to coherently detect the optical spin alignment between ${M}_{S}=\ifmmode\pm\else\textpm\fi{}\frac{3}{2}$ via optically pumped silent ${M}_{S}=\ifmmode\pm\else\textpm\fi{}\frac{1}{2}$ sublevels of the spin-$\frac{3}{2}$ color centers, including a detection of Rabi oscillations.

“End-to-end” stacking of small dsRNA

PELDOR (pulsed electron–electron double resonance) is an established method to study intramolecular distances and can give evidence for conformational changes and flexibilities. However, it can also be used to study intermolecular interactions as for example oligerimization. Here, we used PELDOR to study the “end-to-end” stacking of small double-stranded (ds) RNAs. For this study, the dsRNA molecules were only singly labeled with the spin label TPA to avoid multispin effects and to measure only the intermolecular stacking interactions. It can be shown that small dsRNAs tend to assemble to rod-like structures due to π–π interactions between the base pairs at the end of the strands. On the one hand, these interactions can influence or complicate measurements aimed at the determining of the structure and dynamics of the dsRNA molecule itself. On the other hand, it can be interesting to study such intermolecular stacking interactions in more detail, as for example their dependence on ion concentration. We quantitatively determined the stacking probability as a function of the monovalent NaCl salt and the dsRNA concentration. From these data, the dissociation constant Kd was deduced and found to depend on the ratio between the NaCl salt and dsRNA concentrations. Additionally, the distances and distance distributions obtained predict a model for the stacking geometry of dsRNAs. Introducing a nucleotide overhangs at one end of the dsRNA molecule restricts the stacking to the other end, leading only to dimer formations. Introducing such an overhang at both ends of the dsRNA molecule fully suppresses stacking, as we demonstrate by PELDOR experiments quantitatively.

Alamethicin self-assembling in lipid membranes: concentration dependence from pulsed EPR of spin labels.

The antimicrobial action of the peptide antibiotic alamethicin (Alm) is commonly related to peptide self-assembling resulting in the formation of voltage-dependent channels in bacterial membranes, which induces ion permeation. To obtain a deeper insight into the mechanism of channel formation, it is useful to know the dependence of self-assembling on peptide concentration. With this aim, we studied Alm F50/5 spin-labeled analogs in a model 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) membrane, for peptide-to-lipid (P/L) ratios varying between 1/1500 and 1/100. Pulsed electron-electron double resonance (PELDOR) spectroscopy reveals that even at the lowest concentration investigated, the Alm molecules assemble into dimers. Moreover, under these conditions, electron spin echo envelope modulation (ESEEM) spectroscopy of D2O-hydrated membranes shows an abrupt change from the in-plane to the trans-membrane orientation of the peptide. Therefore, we hypothesize that dimer formation and peptide reorientation are concurrent processes and represent the initial step of peptide self-assembling. By increasing peptide concentration, higher oligomers are formed. A simple kinetic model of equilibrium among monomers, dimers, and pentamers allows for satisfactorily describing the experimental PELDOR data. The inter-label distances in the oligomers obtained from PELDOR experiments become better resolved with increasing P/L ratio, thus suggesting that the supramolecular organization of the higher-order oligomers becomes more defined.

De Novo Design of an Artificial Bis[4Fe-4S] Binding Protein

In nature, protein subunits containing multiple iron-sulfur clusters often mediate the delivery of reducing equivalents from metabolic pathways to the active site of redox proteins. The de novo design of redox active proteins should include the engineering of a conduit for the delivery of electrons to and from the active site, in which multiple redox active centers are arranged in a controlled manner. Here, we describe a designed three-helix protein, DSD-bis[4Fe-4S], that coordinates two iron-sulfur clusters within its hydrophobic core. The design exploits the pseudo two-fold symmetry of the protein scaffold, DSD, which is a homodimeric three-helix bundle. Starting from the sequence of the parent peptide, we mutated eight leucine residues per dimer in the hydrophobic core to cysteine to provide the first coordination sphere for cubane-type iron-sulfur clusters. Incorporation of two clusters per dimer is readily achieved by in situ reconstitution and imparts increased stability to thermal denaturation compared to that of the apo form of the peptide as assessed by circular dichroism-monitored thermal denaturation. The presence of [4Fe-4S] clusters in intact proteins is confirmed by UV-vis spectroscopy, gel filtration, analytical ultracentrifugation, and electron paramagnetic resonance spectroscopy. Pulsed electron-electron double-resonance experiments have detected a magnetic dipole interaction between the two clusters ~0.7 MHz, which is consistent with the expected intercluster distance of 29-34 Å. Taken together, our data demonstrate the successful design of an artificial multi-iron-sulfur cluster protein with evidence of cluster-cluster interaction. The design principles implemented here can be extended to the design of multicluster molecular wires.

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.

Conformational Flexibility of DNA

Pulsed Electron-Electron Double Resonance (PELDOR) on double-stranded DNA (ds-DNA) was used to investigate the conformational flexibility of helical DNA. Stretching, twisting, and bending flexibility of ds-DNA was determined by incorporation of two rigid nitroxide spin labels into a series of 20 base pair (bp) DNA duplexes. Orientation-selective PELDOR experiments performed at both X-band (9 GHz/0.3 T) and G-band (180 GHz/6.4 T) with spin label distances in the range of 2-4 nm allowed us to differentiate between different simple models of DNA dynamics existing in the literature. All of our experimental results are in full agreement with a dynamic model for ds-DNA molecules, where stretching of the molecule leads to a slightly reduced radius of the helix induced by a cooperative twist-stretch coupling.

Pulsed electron–electron double resonance (PELDOR) distance measurements in detergent micelles

Pulsed electron−electron double resonance (PELDOR) spectroscopy is a powerful tool for measuring nanometer distances in spin-labeled systems. A common approach is doubly covalent spin-labeling of a macromolecule and measurement of the inter-spin distance, or to use singly-labeled components of a system that forms aggregates or oligomers. This situation has been described as a spin-cluster. The PELDOR signal, however, does not only contain the desired dipolar coupling between the spin-labels of the molecule or cluster under study. In samples of finite concentration the dipolar coupling between the spin-labels of the randomly distributed molecules or spin-clusters also contributes significantly. In homogeneous frozen solutions or lipid vesicle membranes this second contribution can be considered to be an exponential or stretched exponential decay, respectively. In this study, we show that this assumption is not valid in detergent micelles. Spin-labeled fatty acids that are randomly partitioned into different detergent micelles give rise to PELDOR time traces which clearly deviate from stretched exponential decays. The obtained signals can be modeled quantitatively based on the size of the micelles, their aggregation number, the spin-label concentration and the degree of spin-labeling. As a main conclusion a PELDOR signal deviating from a stretched exponential decay does not necessarily prove the observation of specific distance information on the molecule or cluster. These results are important for the interpretation of PELDOR experiments on membrane proteins or lipophilic peptides solubilized in detergent micelles or small vesicles, which often do not show pronounced dipolar oscillations in their time traces.

Electron−Nuclear and Electron−Electron Double Resonance Spectroscopies Show that the Primary Quinone Acceptor QA in Reaction Centers from Photosynthetic Bacteria Rhodobacter sphaeroides Remains in the Same Orientation Upon Light-Induced Reduction

Reaction centers (RCs) from the photosynthetic bacterium Rhodobacter (Rb.) sphaeroides R-26 exhibit changes in the recombination kinetics of the charge-separated radical-pair state, P(·+) Q(A)(·-), composed of the dimeric bacteriochlorophyll donor P and the ubiquinone-10 acceptor Q(A), depending on whether the RCs are cooled to cryogenic temperatures in the dark or under continuous illumination (Kleinfeld et al. Biochemistry 1984, 23, 5780-5786). Structural changes near redox-active cofactors have been postulated to be responsible for these changes in kinetics and to occur in the course of light-induced oxidation and reduction of the cofactors thereby assuring a high quantum yield. Here we investigated such potential light-induced structural changes, associated with the formation of P(·+) Q(A)(·-), via pulsed electron-nuclear double resonance (ENDOR) at Q-band (34 GHz) and pulsed electron-electron double resonance (PELDOR) at W-band (95 GHz). Two types of light excitation have been employed for which identical RC samples were prepared: (a) one sample was frozen in the dark and then illuminated to generate transient P(·+) Q(A)(·-), and (b) one was frozen under illumination which resulted in both trapped and transient P(·+) Q(A)(·-) at 80 K. The hyperfine interactions between Q(A)(·-) and the protein were found to be the same in RCs frozen in the dark as in RCs frozen under illumination. Furthermore, these interactions are completely consistent with those observed in RC crystals frozen in the dark. Thus, QA remains in its binding site with the same position and orientation upon reduction. This conclusion is consistent with the result of our orientation-resolving PELDOR experiments on transient P(·+) Q(A)(·-) radical pairs. However, these findings are incompatible with the recently proposed ~60° reorientation of Q(A) upon its photoreduction, as deduced from an analysis of Q-band quantum-beat oscillations (Heinen et al. J. Am. Chem. Soc. 2007, 129, 15935-15946). Such a large reorientation appears improbable, and our objections against this proposition are substantiated here in detail. Our results show that Q(A) is initially in an orientation that is favorable for its light-driven reduction. This diminishes the reorganization requirements for fast electron reduction and high quantum efficiency.

Pulsed Electron−Electron Double-Resonance Determination of Spin-Label Distances and Orientations on the Tetrameric Potassium Ion Channel KcsA

Pulsed electron-electron double-resonance (PELDOR) measurements are presented from the potassium ion channel KcsA both solubilized in detergent and reconstituted in lipids. Site-directed spin-labeling using (1-oxyl-2,2,5,5-tetramethyl-3-pyrrolin-3-yl)methyl methanethiosulfonate was performed with a R64C mutant of the protein. The orientations of the spin-labels in the tetramer were determined by PELDOR experiments performed at two magnetic field strengths (0.3 T/X-band and 1.2 T/Q-band) and variable probe frequency. Quantitative simulation of the PELDOR data supports a strongly restricted nitroxide, oriented at an angle of 65 degrees relative to the central channel axis. In general, poorer quality PELDOR data were obtained from membrane-reconstituted preparations compared to soluble proteins or detergent-solubilized samples. One reason for this is the reduced transverse spin relaxation time T(2) of nitroxides due to crowding of tetramers within the membrane that occurs even at low protein to lipid ratios. This reduced T(2) can be overcome by reconstituting mixtures of unlabeled and labeled proteins, yielding high-quality PELDOR data. Identical PELDOR oscillation frequencies and their dependencies on the probe frequency were observed in the detergent and membrane-reconstituted preparations, indicating that the position and orientation of the spin-labels are the same in both environments.

Molecular orientation studies by pulsed electron-electron double resonance experiments

Pulsed electron-electron double resonance (PELDOR) has proven to be a valuable tool to measure the distribution of long range distances in noncrystalline macromolecules. These experiments commonly use nitroxide spin labels as paramagnetic markers that are covalently attached to the macromolecule at specific positions. Unless these spin labels are flexible in such a manner that they exhibit an almost random orientation, the PELDOR signals will-apart from the interspin distance-also depend on the orientation of the spin labels. This effect needs to be considered in the analysis of PELDOR signals and can, moreover, be used to obtain additional information on the structure of the molecule under investigation. In this work, we demonstrate that the PELDOR signal can be represented as a convolution of a kernel function containing the distance distribution function and an orientation intensity function. The following strategy is proposed to obtain both functions from the experimental data. In a first step, the distance distribution function is estimated by the Tikhonov regularization, using the average over all PELDOR time traces with different frequency offsets and neglecting angular correlations of the spin labels. Second, the convolution relation is employed to determine the orientation intensity function, using again the Tikhonov regularization. Adopting small nitroxide biradical molecules as simple examples, it is shown that the approach works well and is internally consistent. Furthermore, independent molecular dynamics simulations are performed and used to calculate PELDOR signals, distance distributions, and orientational intensity functions. The calculated and experimental results are found to be in excellent overall agreement.

Conformational flexibility of nitroxide biradicals determined by X-band PELDOR experiments

PELDOR (pulsed electron–electron double resonance) experiments have been performed at X-band (9 GHz) frequencies on a linear and a bent nitroxide biradical. All PELDOR time traces were recorded with the pump frequency νB set at the center of the nitroxide spectra to achieve maximum pumping efficiency, while the probe frequency νA was stepped between a frequency offset ΔνAB = νA − νB of +40 to +80 MHz. The modulation frequencies and the damping of the oscillations change as a function ΔνAB, whereas the modulation depth λ for our investigated systems was only very slightly altered. This can be explained by the selection of different orientations of nitroxide radicals with respect to the external magnetic field as a function of frequency offset. Quantitative simulations of the PELDOR time traces could be achieved for both molecules and for all offset frequencies using a simple geometric model, described by a free rotation of the nitroxide radical around its acetylene bond and a single bending mode of the interconnecting molecular bridge. The results show that the distribution function for the relative orientations of the nitroxides with respect to each other and with respect to the dipolar vector R deviates from a random distribution and thus has to be taken into account to quantitatively simulate the PELDOR traces. Vice versa, a quantitative simulation of PELDOR time traces with variable offset frequencies allows the determination of the conformational freedom of such molecules.

Submicrosecond field-jump device for pulsed high-field ELDOR

A field-jump device for fast stepping the electron paramagnetic resonance magnetic field around 3.4 T during pulsed electron-electron double resonance experiments at W-band (95 GHz) is described. Field jumps up to ±160 G and submicrosecond times for the full field-jump cycle allow precession frequency transfer experiments to be made for the determination of the nanometer distance and the orientation of nitroxide spin-label pairs in disordered samples.