Two-dimensional Electron Spin Echo Envelope Research Articles

The semiquinone at the Qi site of the bc1 complex explored using HYSCORE spectroscopy and specific isotopic labeling of ubiquinone in Rhodobacter sphaeroides via (13)C methionine and construction of a methionine auxotroph.

Specific isotopic labeling at the residue or substituent level extends the scope of different spectroscopic approaches to the atomistic level. Here we describe 13C isotopic labeling of the methyl and methoxy ring substituents of ubiquinone, achieved through construction of a methionine auxotroph in Rhodobacter sphaeroides strain BC17 supplemented with l-methionine with the side chain methyl group 13C-labeled. Two-dimensional electron spin echo envelope modulation (HYSCORE) was applied to study the 13C methyl and methoxy hyperfine couplings in the semiquinone generated in situ at the Qi site of the bc1 complex in its membrane environment. The data were used to characterize the distribution of unpaired spin density and the conformations of the methoxy substituents based on density functional theory calculations of 13C hyperfine tensors in the semiquinone of the geometry-optimized X-ray structure of the bc1 complex (Protein Data Bank entry 1PP9) with the highest available resolution. Comparison with other proteins indicates individual orientations of the methoxy groups in each particular case are always different from the methoxy conformations in the anion radical prepared in a frozen alcohol solution. The protocol used in the generation of the methionine auxotroph is more generally applicable and, because it introduces a gene deletion using a suicide plasmid, can be applied repeatedly.

Modifications of Protein Environment of the [2Fe-2S] Cluster of the bc1 Complex

The rate-determining step in the overall turnover of the bc(1) complex is electron transfer from ubiquinol to the Rieske iron-sulfur protein (ISP) at the Q(o)-site. Structures of the ISP from Rhodobacter sphaeroides show that serine 154 and tyrosine 156 form H-bonds to S-1 of the [2Fe-2S] cluster and to the sulfur atom of the cysteine liganding Fe-1 of the cluster, respectively. These are responsible in part for the high potential (E(m)(,7) approximately 300 mV) and low pK(a) (7.6) of the ISP, which determine the overall reaction rate of the bc(1) complex. We have made site-directed mutations at these residues, measured thermodynamic properties using protein film voltammetry to evaluate the E(m) and pK(a) values of ISPs, explored the local proton environment through two-dimensional electron spin echo envelope modulation, and characterized function in strains S154T, S154C, S154A, Y156F, and Y156W. Alterations in reaction rate were investigated under conditions in which concentration of one substrate (ubiquinol or ISP(ox)) was saturating and the other was varied, allowing calculation of kinetic terms and relative affinities. These studies confirm that H-bonds to the cluster or its ligands are important determinants of the electrochemical characteristics of the ISP, likely through electron affinity of the interacting atom and the geometry of the H-bonding neighborhood. The calculated parameters were used in a detailed Marcus-Brønsted analysis of the dependence of rate on driving force and pH. The proton-first-then-electron model proposed accounts naturally for the effects of mutation on the overall reaction.

Two-dimensional pulsed electron spin resonance characterization of 15N-labeled archaeal Rieske-type ferredoxin

Two-dimensional electron spin-echo envelope modulation (ESEEM) analysis of the uniformly 15N-labeled archaeal Rieske-type [2Fe–2S] ferredoxin (ARF) from Sulfolobus solfataricus P1 has been conducted in comparison with the previously characterized high-potential protein homologs. Major differences among these proteins were found in the hyperfine sublevel correlation (HYSCORE) lineshapes and intensities of the signals in the (++) quadrant, which are contributed from weakly coupled (non-coordinated) peptide nitrogens near the reduced clusters. They are less pronounced in the HYSCORE spectra of ARF than those of the high-potential protein homologs, and may account for the tuning of Rieske-type clusters in various redox systems.

Identification of Hydrogen Bonds to the Rieske Cluster through the Weakly Coupled Nitrogens Detected by Electron Spin Echo Envelope Modulation Spectroscopy

The interaction of the reduced[2Fe-2S] cluster of isolated Rieske fragment from the bc1 complex of Rhodobacter sphaeroides with nitrogens (14N and 15N) from the local protein environment has been studied by X- and S-band pulsed EPR spectroscopy. The two-dimensional electron spin echo envelope modulation spectra of uniformly 15N-labeled protein show two well resolved cross-peaks with weak couplings of approximately 0.3-0.4 and 1.1 MHz in addition to couplings in the range of 6-8 MHz from two coordinating Ndelta of histidine ligands. The quadrupole coupling constants for weakly coupled nitrogens determined from S-band electron spin echo envelope modulation spectra identify them as Nepsilon of histidine ligands and peptide nitrogen (Np), respectively. Analysis of the line intensities in orientation-selected S-band spectra indicated that Np is the backbone N-atom of Leu-132 residue. The hyperfine couplings from Nepsilon and Np demonstrate the predominantly isotropic character resulting from the transfer of unpaired spin density onto the 2s orbitals of the nitrogens. Spectra also show that other peptide nitrogens in the protein environment must carry a 5-10 times smaller amount of spin density than the Np of Leu-132 residue. The appearance of the excess unpaired spin density on the Np of Leu-132 residue indicates its involvement in hydrogen bond formation with the bridging sulfur of the Rieske cluster. The configuration of the hydrogen bond therefore provides a preferred path for spin density transfer. Observation of similar splittings in the 15N spectra of other Rieske-type proteins and [2Fe-2S] ferredoxins suggests that a hydrogen bond between the bridging sulfur and peptide nitrogen is a common structural feature of [2Fe-2S] clusters.

Characterization of the Exchangeable Protons in the Immediate Vicinity of the Semiquinone Radical at the QH Site of the Cytochrome bo3 from Escherichia coli

The cytochrome bo3 ubiquinol oxidase from Escherichia coli resides in the bacterial cytoplasmic membrane and catalyzes the two-electron oxidation of ubiquinol-8 and four-electron reduction of O2 to water. The one-electron reduced semiquinone forms transiently during the reaction, and the enzyme has been demonstrated to stabilize the semiquinone. Two-dimensional electron spin echo envelope modulation has been applied to explore the exchangeable protons involved in hydrogen bonding to the semiquinone by substitution of 1H2O by 2H2O. Three exchangeable protons possessing different isotropic and anisotropic hyperfine couplings were identified. The strength of the hyperfine interaction with one proton suggests a significant covalent O-H binding of carbonyl oxygen O1 that is a characteristic of a neutral radical, an assignment that is also supported by the unusually large hyperfine coupling to the methyl protons. The second proton with a large anisotropic coupling also forms a strong hydrogen bond with a carbonyl oxygen. This second hydrogen bond, which has a significant out-of-plane character, is from an NH2 or NH nitrogen, probably from an arginine (Arg-71) known to be in the quinone binding site. Assignment of the third exchangeable proton with smaller anisotropic coupling is more ambiguous, but it is clearly not involved in a direct hydrogen bond with either of the carbonyl oxygens. The results support a model that the semiquinone is bound to the protein in a very asymmetric manner by two strong hydrogen bonds from Asp-75 and Arg-71 to the O1 carbonyl, while the O4 carbonyl is not hydrogen-bonded to the protein.

Cluster N1 of complex I from Yarrowia lipolytica studied by pulsed EPR spectroscopy

After reduction with nicotinamide adenine dinucleotide (NADH), NADH:ubiquinone oxidoreductase (complex I) of the strictly aerobic yeast Yarrowia lipolytica shows clear signals from five different paramagnetic iron-sulfur (FeS) clusters (N1-N5) which can be detected using electron paramagnetic resonance (EPR) spectroscopy. The ligand environment and the assignment of several FeS clusters to specific binding motifs found in several subunits of the complex are still under debate. In order to characterize the hyperfine interaction of the surrounding nuclei with FeS cluster N1, one- and two-dimensional electron spin echo envelope modulation experiments were performed at a temperature of 30 K. At this temperature only cluster N1 contributes to the overall signal in a pulsed EPR experiment. The hyperfine and quadrupole tensors of a nitrogen nucleus and the isotropic and dipolar hyperfine couplings of two sets of protons could be determined by numerical simulation of the one- and two-dimensional spectra. The values obtained are in perfect agreement with a ferredoxin-like binding structure by four cysteine amino acid residues and allow the assignment of the nitrogen couplings to a backbone nitrogen nucleus and the proton couplings to the beta-protons of the bound cysteine residues.

Mn2+-adenosine nucleotide complexes in the presence of the nitrogenase iron-protein: detection of conformational rearrangements directly at the nucleotide binding site by EPR and 2D-ESEEM (two-dimensional electron spin-echo envelope modulation spectroscopy).

Both ATP and a bivalent nucleotide-bound metal activator, normally Mg2+, are required for nitrogenase activity. EPR and ESEEM (electron spin-echo envelope modulation) measurements have been carried out on adenosine nucleotides in which the Mg2+ ion that is usually bound is replaced by Mn2+ in the presence of Kp2 (nitrogenase Fe-protein from Klebsiella pneumoniae). The Mn2+ zero-field splitting parameters have been determined from the EPR-spectrum to be |D|=0.0125 cm(-1) with a rhombicity lambda=E/D=0.31 by direct diagonalization of the complete spin Hamiltonian. ESEEM spectra of the Fe-protein with MnADP and MnATP both show an ESEEM line pair with one signal component at about 3.6 MHz and a relatively broad resonance at 8 MHz originating from a superhyperfine coupling to a 31P nuclear spin from one or more directly co-ordinated phospho group(s) of the nucleotide. A pronounced resonance overlapping the low-frequency component of the (31)P-signal at about 3.5 MHz is attributed to an interaction of Mn2+ with univalent 23Na nuclei. ESEEM lines at frequencies <3.5 MHz have been ascribed to interactions with 14N nuclei. Differences in the 14N features that depend on the type of nucleotide are consistent with substantial conformational rearrangements at the nucleotide-binding site upon hydrolysis. In addition, four-pulse HYSCORE (hyperfine sublevel correlation spectroscopy) experiments not only confirm the three-pulse ESEEM results, but also achieve significantly better spectral deconvolution, especially of the 31P-couplings, and demonstrate that the nucleotide is at least a unidentate ligand of Mn2+. Moreover it was also possible to identify peaks from an 14N interaction more clearly; these most probably arise from outer-sphere interactions with nitrogen atom(s) of non-co-ordinated residues which are affected by conformational rearrangements upon nucleotide hydrolysis. In addition, different redox states of the [4Fe-4S] cluster of the Fe-protein show disparate conformations of the metal-nucleotide co-ordination environment, demonstrating that also the cluster site communicates with the nucleotide binding site.

Characteristics of ESEEM and HYSCORE spectra of S>1/2 centers in orientationally disordered systems

One- and two-dimensional electron-spin echo envelope modulation (ESEEM) spectra of Kramers’ multiplets in orientationally disordered systems are simulated using a simple mathematical model. A fairly general high-field spin Hamiltonian is considered with a general g-tensor and arbitrary relative orientations between all tensors involving the electron-spin S, the nuclear spin I, and their interaction. The zero field splitting (ZFS) and the nuclear quadrupole interactions are, however, approximated by their respective secular part in a way that retains all orientation dependencies and it is assumed that the nuclear quadrupole interaction is smaller than the hyperfine interaction. These approximations yield an effective sublevel nuclear Hamiltonian for each EPR transition and are sufficient to account for the most important characteristics of the ESEEM spectra of high electronic multiplets in orientationally disordered systems. Moreover, they allow to obtain some analytical expressions that for I=1/2 illuminate important aspects of 2D hyperfine sublevel correlation (HYSCORE) experiments in S=3/2, 5/2 systems. The pulses are considered as ideal and selective with respect to the different EPR transitions. The contributions of the latter to the echo intensity are weighed according to their different nutation angles and equilibrium Boltzmann populations. For simple axial cases with I=1/2, analytical expressions, analogous to the S=1/2 case, were derived for: (i) the modulation depth, (ii) the lineshapes of the HYSCORE cross-correlation ridges, and (iii) ENDOR powder pattern. Experimental results obtained from Mn(D 2O) 6 2+ and VO(D 2O) 5 2+ in frozen solutions are presented, compared, and analyzed in light of the theoretical part.

Numerical Simulation of One- and Two-Dimensional ESEEM Experiments

Numerical simulation has become an indispensable tool for the interpretation of pulse EPR experiments. In this work it is shown how automatic orientation selection, grouping of operator factors, and direct selection and elimination of coherences can be used to improve the efficiency of time-domain simulations of one- and two-dimensional electron spin echo envelope modulation (ESEEM) spectra. The program allows for the computation of magnetic interactions of any symmetry and can be used to simulate spin systems with an arbitrary number of nuclei with any spin quantum number. Experimental restrictions due to finite microwave pulse lengths are addressed and the enhancement of forbidden coherences by microwave pulse matching is illustrated. A comparison of simulated and experimental HYSCORE (hyperfine sublevel correlation) spectra of ordered and disordered systems with varying complexity shows good qualitative agreement.

Multiple quantum coherence in HYSCORE spectra

The implementation of matched pulses in two-dimensional electron spin echo envelope modulation experiments results in a drastic increase in intensity of peaks representing nuclear multiple quantum coherence. For a spin system consisting of one electron spin S=12 and two nuclei with spin I=12 the nuclear coherence created by the sequence (π/2)−τ−(π/2) is calculated. The transfer amplitudes between different kinds of nuclear coherences of a microwave π pulse are given. A new matched HYSCORE pulse sequence, called SMART HYSCORE, is introduced with only one microwave pulse for the generation and detection of nuclear coherence, which does not suffer from blind spots. This sequence is applied to a single crystal and a disordered system, and it is demonstrated how the resolution of weakly coupled nuclei can be increased. Furthermore we show that information about the relative sign of hyperfine couplings and about the relative orientation of the hyperfine tensors can be derived from the ridge patterns in a HYSCORE experiment. The numerical simulations are confirmed experimentally.

QH•- Ubisemiquinone Radical in the bo3-Type Ubiquinol Oxidase Studied by Pulsed Electron Paramagnetic Resonance and Hyperfine Sublevel Correlation Spectroscopy

The high-affinity QH ubiquinone-binding site in the bo(3) ubiquinol oxidase from Escherichia coli has been characterized by an investigation of the native ubiquinone radical anion QH(*-) by pulsed electron paramagnetic resonance (EPR) spectroscopy. One- and two-dimensional electron spin-echo envelope modulation (ESEEM) spectra reveal strong interactions of the unpaired electron of QH(*-) with a nitrogen nucleus from the surrounding protein matrix. From analysis of the experimental data, the (14)N nuclear quadrupolar parameters have been determined: kappa = e(2)qQ/4h = 0.93 MHz and eta = 0.50. This assignment is confirmed by hyperfine sublevel correlation (HYSCORE) spectroscopy. On the basis of a comparison of these data with those obtained previously for other membrane-protein bound semiquinone radicals and model systems, this nucleus is assigned to a protein backbone nitrogen. This result is discussed with regard to the location and potential function of QH in the enzyme.

Two-Dimensional Nuclear-Zeeman-Resolved Electron Spin Echo Envelope Modulation (NZ-ESEEM) Spectroscopy

A two-dimensional electron spin echo envelope modulation (ESEEM) experiment, called nuclear-Zeeman-resolved ESEEM (NZ-ESEEM), that correlates nuclear transition frequencies with nuclear Zeeman frequencies is introduced. NZ-ESEEM is basically a three-pulse ESEEM experiment complemented by a magnetic-field pulse applied during part of the free evolution period between the second and third microwave pulse. The inner working of the new approach is explained and the instrumentation is discussed. The capacity of the method is illustrated by two examples of applications.

Sensitivity Enhancement by Matched Microwave Pulses in One- and Two-Dimensional Electron Spin Echo Envelope Modulation Spectroscopy

The concept of microwave pulse matching is applied to three-pulse electron spin echo envelope modulation and sublevel correlation (HYSCORE) spectroscopy. Matched pulses enhance the efficiency of forbidden transfers and may drastically increase the signal intensity of basic frequency and combination frequency transitions in these conventional pulse EPR experiments. The theory of matched pulses is extended to the case of strong and largely isotropic hyperfine interactions, and numerical simulations are presented to gain a deeper insight into the inner working of the matched-pulse approach. It is shown that the enhancement of combination frequencies in matched HYSCORE can be used to determine the relative sign of hyperfine coupling constants as well as the number of equivalent nuclei. The enormous capacity of the approach is demonstrated on ordered and disordered systems. In particular, it is shown that in HYSCORE experiments the signal-to-noise ratio improvement for strongly coupled nitrogens and for proton combination peaks may be considerably larger than one order of magnitude, corresponding to a reduction in measuring time of more than a factor of 100.

A two-dimensional sum combination frequency pulse EPR experiment

A two-dimensional electron-spin echo envelope modulation method for measuring sum combination frequencies is introduced. The approach is free of blind spots and is distinguished by diagonal- and cross-peaks in the two-dimensional spectrum that correlate basic frequencies and combination frequencies of nuclear spin transitions. Analytical formulae for the description of the experiments are derived and the features predicted by theory are confirmed by experiments on ordered and disordered spin systems.

Indications of proton tunneling in the proton glass (betainetphosphate)0.15(betainetphosphite)0.85from ENDOR and pulsed ESR studies

The local proton order in the proton glass (betaine phosphate${)}_{0.15}$ (betaine phosphite${)}_{0.85}$ is studied by means of electron nuclear double-resonance and two-dimensional electron spin-echo envelope modulation (ESEEM) techniques. The experimental results allow very detailed comparisons with theoretical models such as the one-, and three-dimensional random-bond random-field (RBRF) Ising glass model. The attempt to describe the experimental behavior within the framework of the random-bond random-field (RBRF) Ising glass, which was worked out for deuteron glasses, suffers in conspicuous insufficiency at least at lower temperatures. Taking the influence of proton tunneling into account by using the stochastic model of a quantum RBRF Ising glass, the experimental results can fully be described. Furthermore, ESEEM experiments on a partially deuterated ${\mathrm{BP}}_{0.15}$${\mathrm{BPI}}_{0.85}$ crystal confirm the different local polarization behavior in the protonated and deuterated hydrogen bonds in agreement with the model expectation.

Coordination of the Rieske-type [2Fe-2S] cluster of the terminal iron-sulfur protein of Pseudomonas putida benzene 1,2-dioxygenase, studied by one- and two-dimensional electron spin-echo envelope modulation spectroscopy.

One- and two-dimensional (1D and 2D) electron spin-echo envelope modulation (ESEEM) spectroscopy has been used to investigate the ligand environment of the [2Fe-2S] cluster from the terminal dioxygenase (ISPBED) of the Pseudomonas putida benzene dioxygenase complex. The modulation frequencies observed in the 0.5-8.5 MHz region of the Fourier transforms of 1D and 2D ESEEM spectra measured across the electron paramagnetic resonance (EPR) absorbance envelope (from gz through to gx) are consistent with their assignment to two 14N nuclei. Using hyperfine sublevel correlation spectroscopy (HYSCORE), two sets of correlated double quantum transitions sharing the same hyperfine coupling were observed and were identified as being due to the same two 14N nuclei. On the basis of the isotropic hyperfine and quadrupolar couplings estimated for these 14N nuclei [N(1), Aiso = 3.6 MHz and e2qQ = 2.2-2.8 MHz; N(2), Aiso = 4.8 MHz and e2qQ = 2.2-2.4 MHz], the ESEEM pattern of ISPBED is assigned to two histidine nitrogens which are directly coordinated to the reduced iron-sulfur cluster. Bonding parameters of the two [14N]histidine ligands were calculated from these hyperfine couplings. The primary covalent contributions to the hyperfine interaction arise from 14N-to-Fe2+ sigma bonds. For N(1), our analysis of the percentage of unpaired 2s and 2p electrons gave f2s approximately 1.3% and f2p approximately 0.2%, while values of f2s approximately 1.7% and f2p approximately 1.4% were estimated for N(2). Comparison of these values with those determined from electron nuclear double resonance (ENDOR) data of the Rieske-type [2Fe-2S] center of Pseudomonas cepacia phthalate dioxygenase [Gurbiel, R. J., Batie, C. J., Sivaraja, M., True, A. E., Fee, J. A., Hoffman, B. M., & Ballou, D. P. (1989) Biochemistry 28, 4861-4871] indicates an apparent reduction in unpaired electron spin density residing on the two 14N ligands of ISPBED. Analysis of slices of the HYSCORE spectrum has provided evidence for another 14N nucleus (A approximately 1.1 MHz, e2qQ = 3.3 MHz), which we have attributed to a weakly coupled peptide nitrogen, similar to those observed for ferredoxin-type [2Fe-2S] clusters. This type of weak interaction has not been previously described by the detailed ENDOR and ESEEM studies of Rieske-type centers. The resolution of the spectra demonstrates the effectiveness of 2D ESEEM for the disentanglement of multiple hyperfine interactions to metalloprotein centers.

A new six-pulse two-dimensional electron spin echo envelope modulation (ESEEM) correlation spectroscopy

A new six-pulse two-dimensional electron spin echo envelope modulation (2D ESEEM) method is introduced. It is based on augmenting the five-pulse sequence proposed by Gemperle, Schweiger and Ernst with an additional π pulse. It is shown that the intensity ratio of cross peaks to diagonal peaks is significantly enhanced compared with the four-pulse 2D ESEEM method of Höfer, Grupp, Nebenführ and Mehring. A single crystal of KCl doped with Fe(CN) 6 3− is used to demonstrate this new 2D ESEEM spectroscopy together with an effective phase cycling scheme.