Matrix line in pulsed electron-nuclear double resonance spectra

Determining electron-nucleus distances and Fermi contact couplings from ENDOR spectra

The hyperfine coupling between an electron spin and a nuclear spin depends on the Fermi contact coupling a_iso and, through dipolar coupling, the distance r between the electron and the nucleus. It is measured with electron-nuclear double resonance (ENDOR) spectroscopy and provides insight into the electronic and spatial structure of paramagnetic centers. The analysis and interpretation of ENDOR spectra is commonly done by ordinary least-squares fitting. As this is an ill-posed, inverse mathematical problem, this is challenging, in particular for spectra that show features from several nuclei or where the hyperfine coupling parameters are distributed. We introduce a novel Tikhonov-type regularization approach that analyzes an experimental ENDOR spectrum in terms of a complete non-parametric distribution over r and a_iso. The approach uses a penalty function similar to the cross entropy between the fitted distribution and a Bayesian prior distribution that is derived from density functional theory calculations. Additionally, we show that smoothness regularization, commonly used for a similar purpose in double electron-electron resonance (DEER) spectroscopy, is not suited for ENDOR. We demonstrate that the novel approach is able to identify and quantitate ligand protons with electron-nucleus distances between 4 and 9 Å in a series of vanadyl porphyrin compounds.

Radical transfer in E. coli ribonucleotide reductase: a NH2Y731/R411A-α mutant unmasks a new conformation of the pathway residue 731

Ribonucleotide reductases (RNRs) catalyze the conversion of ribonucleotides to deoxyribonucleotides in all living organisms. The catalytic cycle of E. coli RNR involves a long-range proton-coupled electron transfer (PCET) from a tyrosyl radical (Y122˙) in subunit β2 to a cysteine (C439) in the active site of subunit α2, which subsequently initiates nucleotide reduction. This oxidation occurs over 35 Å and involves a specific pathway of redox active amino acids (Y122 ↔ [W48?] ↔ Y356 in β2 to Y731 ↔ Y730 ↔ C439 in α2). The mechanisms of the PCET steps at the interface of the α2β2 complex remain puzzling due to a lack of structural information for this region. Recently, DFT calculations on the 3-aminotyrosyl radical (NH2Y731˙)-α2 trapped by incubation of NH2Y731-α2/β2/CDP(substrate)/ATP(allosteric effector) suggested that R411-α2, a residue close to the α2β2 interface, interacts with NH2Y731˙ and accounts in part for its perturbed EPR parameters. To examine its role, we further modified NH2Y731-α2 with a R411A substitution. NH2Y731˙/R411A generated upon incubation of NH2Y731/R411A-α2/β2/CDP/ATP was investigated using multi-frequency (34, 94 and 263 GHz) EPR, 34 GHz pulsed electron-electron double resonance (PELDOR) and electron-nuclear double resonance (ENDOR) spectroscopies. The data indicate a large conformational change in NH2Y731˙/R411A relative to the NH2Y731˙ single mutant. Particularly, the inter-spin distance from NH2Y731˙/R411A in one αβ pair to Y122˙ in a second αβ pair decreases by 3 Å in the presence of the R411A mutation. This is the first experimental evidence for the flexibility of pathway residue Y731-α2 in an α2β2 complex and suggests a role for R411 in the stacked Y731/Y730 conformation involved in collinear PCET. Furthermore, NH2Y731˙/R411A serves as a probe of the PCET process across the subunit interface.

Hyperfine interactions of narrow-line trityl radical with solvent molecules

The electron nuclear dipolar interactions responsible for some dynamic nuclear polarization (DNP) mechanisms also are responsible for the presence formally in CW EPR spectra of forbidden satellite lines in which both the electron spin and a nuclear spin flip. Such lines arising from (1)H nuclei are easily resolved in CW EPR measurements of trityl radicals, a popular family of DNP reagents. The satellite lines overlap some of the hyperfine features from (13)C in natural abundance in the trityl radical, but their intensity can be easily determined by simple simulations of the EPR spectra using the hyperfine parameters of the trityl radical. Isotopic substitution of (2)H for (1)H among the hydrogens of the trityl radical and/or the solvent allows the dipolar interactions from the (1)H on the trityl radical and from the solvent to be determined. The intensity of the dipolar interactions, integrated over all the (1)H in the system, is characterized by the traditional parameter called reff. For the so-called Finland trityl in methanol, the reff values indicate that collectively the (1)H in the unlabeled solvent have a stronger integrated dipolar interaction with the unpaired electron spin of the Finland trityl than do the (1)H in the radical and consequently will be a more important DNP route. Although reff has the dimensions of distance, it does not correspond to any simple physical dimension in the trityl radical because the details of the unpaired electron spin distribution and the hydrogen distribution are important in the case of trityls.

Pulsed ENDOR determination of relative orientation of g-frame and molecular frame of imidazole-coordinated heme center of iNOS

Mammalian nitric oxide synthase (NOS) is a flavo-hemoprotein that catalyzes the oxidation of L-arginine to nitric oxide. Information about the relative alignment of the heme and FMN domains of NOS is important for understanding the electron transfer between the heme and FMN centers, but no crystal structure data for NOS holoenzyme are available. In our previous work [Astashkin, A. V.; Elmore, B. O.; Fan, W.; Guillemette, J. G.; Feng, C. J. Am. Chem. Soc. 2010, 132, 12059-12067], the distance between the imidazole-coordinated low-spin Fe(III) heme and FMN semiquinone in a human inducible NOS (iNOS) oxygenase/FMN construct has been determined by pulsed electron paramagnetic resonance (EPR). The orientation of the Fe-FMN radius vector, R(Fe-FMN), with respect to the heme g-frame was also determined. In the present study, pulsed electron-nuclear double resonance (ENDOR) investigation of the deuterons at carbons C2 and C5 in the deuterated coordinated imidazole was used to determine the relative orientation of the heme g-frame and molecular frame, from which R(Fe-FMN) can be referenced to the heme molecular frame. Numerical simulations of the ENDOR spectra showed that the g-factor axis corresponding to the low-field EPR turning point is perpendicular to the heme plane, whereas the axis corresponding to the high-field turning point is in the heme plane and makes an angle of about 80° with the coordinated imidazole plane. The FMN-heme domain docking model obtained in the previous work was found to be in qualitative agreement with the combined experimental results of the two pulsed EPR works.

Solvation of small disulfonate anions in water/methanol mixtures characterized by high-field pulse electron nuclear double resonance and molecular dynamics simulations

The solvation of Fremy's salt, the paramagnetic nitrosodisulfonate anion ON(SO(3)(-))(2), in binary solvent mixtures was investigated by means of pulse (Mims- and Davies-type) electron nuclear double resonance (ENDOR) spectroscopy and molecular dynamics (MD) simulations. (1)H and (2)H pulse ENDOR measurements were performed on small Fremy's salt radicals in isotope-substituted solvent mixtures of methanol and water in frozen solution. We were able to obtain well-resolved, orientation-selective, high-field/high-frequency pulse ENDOR spectra of methyl protons from the alcohol moiety and exchangeable protons from the alcohol-hydroxyl group and water. In the studied solvent systems (volume ratio v/v = 30:70, 50:50, 70:30), the solvation of 2.5 mM Fremy's salt by methyl protons was found to be almost identical. From the analysis of the dependence of pulse ENDOR spectra on the observer field position and spectral simulations, we obtained the principal components of the hyperfine coupling (hfc) tensor for each class of protons. The combination of Mims- and Davies-type pulse ENDOR measurements was necessary to obtain blind spot free information on hfc that spans a broad range of 0.25-6 MHz. Using the point-dipole approximation, the dipolar hfc component yields a prominent electron-nuclear distance of 3.5 A between Fremy's salt and methyl protons, which was found along the molecular z-axis (perpendicular to the approximate plane spanned by ON(S)(2)) of the probe molecule. Exchangeable protons were found to be distributed nearly isotropically, forming a hydrogen-bonded network around the sulfonate groups. The distribution of exchangeable and methyl protons found in MD simulations is in very good agreement with the pulse ENDOR results, and we find that solvation is dominated by an interplay of H-bond (electrostatic) interactions and steric properties. The elucidation of the microscopic solvation of a small probe molecule in binary solvent mixtures represents the first step for understanding the interactions in more complex biochemical systems. In particular, this includes the potential perturbation of the H-bond network due to the presence of a spin probe or other polar molecules.

Phylloquinone and related radical anions studied by pulse electron nuclear double resonance spectroscopy at 34 GHz and density functional theory

1H hyperfine (hf) coupling constants of semiquinone radical anions of 1,4-naphthoquinone, 2-methyl-1,4-naphthoquinone, and 2-methyl-3-phytyl-1,4-naphthoquinone in frozen alcoholic solutions were measured using pulse Q-band electron nuclear double resonance spectroscopy. The resolved signals of the quinone protons as well as from hydrogen bond and solvent shell protons were analyzed and assigned. Both in-plane and out-of-plane hydrogen bonding with respect to the pi-plane of the radical is observed. Interactions with nonexchangeable protons from the surrounding matrix are detected and assigned to solvent protons above and below the quinone plane. Density functional theory was used to calculate spin Hamiltonian parameters of the radical anions. Solvent molecules of the first solvent shell that provide hydrogen bonds to the quinones were included in the geometry optimization. The conductor-like screening model was employed to introduce additional effects of the solvent cage. From a comparison of the experimental and calculated hf tensors it is concluded that four solvent molecules are coordinated via hydrogen bonds to the quinone oxygens. For all radicals very good agreement between experimental and calculated data is observed. The influence of different substituents on the spin density distribution and hydrogen bond geometries is discussed.

Protons bound to the Mn cluster in photosystem II oxygen evolving complex detected by proton matrix ENDOR

Protons in the vicinity of the oxygen-evolving manganese cluster in photosystem II were studied by proton matrix ENDOR. Six pairs of proton ENDOR signals were detected in both the S(0) and S(2) states of the Mn-cluster. Two pairs of signals that show hyperfine constants of 2.3/2.2 and 4.0 MHz, respectively, disappeared after D(2)O incubation in both states. The signals with 2.3/2.2 MHz hyperfine constants in S(0) and S(2) state multiline disappeared after 3 h of D(2)O incubation in the S(0) and S(1) states, respectively. The signal with 4.0 MHz hyperfine constants in S(0) state multiline disappeared after 3 h of D(2)O incubation in the S(0) state, while the similar signal in S(2) state multiline disappeared only after 24 h of D(2)O incubation in the S(1) state. The different proton exchange rates seem to be ascribable to the change in affinities of water molecules to the variation in oxidation state of the Mn cluster during the water oxidation cycle. Based on the point dipole approximation, the distances between the center of electronic spin of the Mn cluster and the exchangeable protons were estimated to be 3.3/3.2 and 2.7 A, respectively. These short distances suggest the protons belong to the water molecules ligated to the manganese cluster. We propose a model for the binding of water to the manganese cluster based on these results.

Probing the water coordination of protein-targeted MRI contrast agents by pulsed ENDOR spectroscopy

A novel methodology based on electron-nuclear double resonance (ENDOR) spectroscopy is used for the direct determination of the water coordination number (q) of gadolinium-based magnetic resonance imaging (MRI) contrast agents. Proton ENDOR spectra can be obtained at approximately physiological concentrations for metal complexes in frozen aqueous solutions either in the presence or absence of protein targets. It is shown that, depending on the structure of the co-ligand, the water hydration number of a complex in aqueous solution can be significantly different to when the complex is noncovalently bound to a protein. From the ENDOR spectra of the exchangeable protons, precise information on the metal-proton distance can be derived as well. These essential parameters directly correlate with the efficacy of MRI contrast agents and should therefore aid the development of novel, highly efficient compounds targeted to various proteins.

Distance measurements between paramagnetic centers and a planar object by matrix Mims electron nuclear double resonance

Frequency-domain electron nuclear double resonance (ENDOR), two time-domain electron nuclear double resonance techniques, and electron spin echo envelope modulation spectroscopy are compared with respect to their merit in measurements of small hyperfine couplings to nuclei with intermediate gyromagnetic ratio such as 31P. The frequency-domain Mims ENDOR experiment is found to provide the most faithful line shapes. In the limit of long electron-nuclear distances of more than 0.5 nm, sensitivity of this experiment is optimized by matching the first interpulse delay to the transverse relaxation time of the electron spins. In the same limit, Mims ENDOR efficiency scales inversely with the sixth power of distance. Hyperfine splittings as small as 33 kHz can be detected, corresponding to an electron-31P distance of 1 nm. In systems, where a certain kind of nuclei is distributed in a plane, measurements of intermolecular hyperfine couplings can be analyzed in terms of a distance of closest approach of a paramagnetic center to that plane. By applying this technique to spin-labeled lipids in a fully hydrated lipid bilayer it is found that for a fraction of lipids, chain tilt angles can be 25 degrees larger than the mean tilt angle of the lipid chains. This model of all-trans hydrocarbon chains with a broad distribution of tilt angles is also consistent with orientation selection effects in high-field ENDOR spectra.