The pulsed electron–electron double resonance and “2+1” electron spin echo study of the oriented oxygen-evolving and Mn-depleted preparations of photosystem II

Efficient sampling of molecular orientations for Cu(II)-based DEER on protein labels

Combining rigid Cu(II) labels and pulsed-EPR techniques enables distance constraint measurements that are incisive probes of protein structure and dynamics. However, the labels can lead to a dipolar signal that is biased by the relative orientation of the two spins, which is typically unknown a priori in a bilabeled protein. This effect, dubbed orientational selectivity, becomes a bottleneck in measuring distances. This phenomenon also applies to other pulsed-EPR techniques that probe electron-nucleus interactions. In this work, we dissect orientational selectivity by generating an in silico sample of Cu(II)-labeled proteins to evaluate pulse excitation in the context of double electron-electron resonance (DEER) at Q-band frequencies. This approach enables the observation of the contribution of each protein orientation to the dipolar signal, which provides direct insights into optimizing acquisition schemes to mitigate orientational effects. Furthermore, we incorporate the excitation profile of realistic pulses to identify the excited spins. With this method, we show that rectangular pulses, despite their imperfect inversion capability, can sample similar spin orientations as other sophisticated pulses with the same bandwidth. Additionally, we reveal that the efficiency of exciting spin-pairs in DEER depends on the frequency offset of two pulses used in the experiment and the relative orientation of the two spins. Therefore, we systematically examine the frequency offset of the two pulses used in this double resonance experiment to determine the optimal frequency offset for optimal distance measurements. This procedure leads to a protocol where two measurements are sufficient to acquire orientational-independent DEER at Q-band. Notably, this procedure is feasible with any commercial pulsed-EPR spectrometer. Furthermore, we experimentally validate the computational results using DEER experiments on two different proteins. Finally, we show that increasing the amplitude of the rectangular pulse can increase the efficiency of DEER experiments by almost threefold. Overall, this work provides an attractive new approach for analyzing pulsed-EPR spectroscopy to obtain microscopic nuances that cannot be easily discerned from analytical or numerical calculations.

Orientation-Selective and Frequency-Correlated Light-Induced Pulsed Dipolar Spectroscopy

We explore the potential of orientation-resolved pulsed dipolar spectroscopy (PDS) in light-induced versions of the experiment. The use of triplets as spin-active moieties for PDS offers an attractive tool for studying biochemical systems containing optically active cofactors. Cofactors are often rigidly bound within the protein structure, providing an accurate positional marker. The rigidity leads to orientation selection effects in PDS, which can be analyzed to give both distance and mutual orientation information. Herein we present a comprehensive analysis of the orientation selection of a full set of light-induced PDS experiments. We exploit the complementary information provided by the different light-induced techniques to yield atomic-level structural information. For the first time, we measure a 2D frequency-correlated laser-induced magnetic dipolar spectrum, and we are able to monitor the complete orientation dependence of the system in a single experiment. Alternatively, the summed spectrum enables an orientation-independent analysis to determine the distance distribution.

Studies of transmembrane peptides by pulse dipolar spectroscopy with semi-rigid TOPP spin labels

Electron paramagnetic resonance (EPR)-based pulsed dipolar spectroscopy measures the dipolar interaction between paramagnetic centers that are separated by distances in the range of about 1.5-10 nm. Its application to transmembrane (TM) peptides in combination with modern spin labelling techniques provides a valuable tool to study peptide-to-lipid interactions at a molecular level, which permits access to key parameters characterizing the structural adaptation of model peptides incorporated in natural membranes. In this mini-review, we summarize our approach for distance and orientation measurements in lipid environment using novel semi-rigid TOPP [4-(3,3,5,5-tetramethyl-2,6-dioxo-4-oxylpiperazin-1-yl)-L-phenylglycine] labels specifically designed for incorporation in TM peptides. TOPP labels can report single peak distance distributions with sub-angstrom resolution, thus offering new capabilities for a variety of TM peptide investigations, such as monitoring of various helix conformations or measuring of tilt angles in membranes.

DEER distance measurements on trityl/trityl and Gd(iii)/trityl labelled proteins

Trityl–trityl and trityl–Gd(iii) DEER distance measurements in proteins are performed using a new trityl spin label affording thioether–protein conjugation.

Performance of PELDOR, RIDME, SIFTER, and DQC in measuring distances in trityl based bi- and triradicals: exchange coupling, pseudosecular coupling and multi-spin effects

The performance of pulsed EPR methods for distance measurements is evaluated on three different trityl model systems.

Single and double nitroxide labeled bis(terpyridine)-copper(ii): influence of orientation selectivity and multispin effects on PELDOR and RIDME

The structure of Jahn–Teller distorted copper–nitroxide complexes in neutral and acidic solutions is investigated using EPR distance measurements taking into account the influence of orientation selectivity and multispin effects.

DEER distance measurements on proteins

Distance distributions between paramagnetic centers in the range of 1.8 to 6 nm in membrane proteins and up to 10 nm in deuterated soluble proteins can be measured by the DEER technique. The number of paramagnetic centers and their relative orientation can be characterized. DEER does not require crystallization and is not limited with respect to the size of the protein or protein complex. Diamagnetic proteins are accessible by site-directed spin labeling. To characterize structure or structural changes, experimental protocols were optimized and techniques for artifact suppression were introduced. Data analysis programs were developed, and it was realized that interpretation of the distance distributions must take into account the conformational distribution of spin labels. First methods have appeared for deriving structural models from a small number of distance constraints. The present scope and limitations of the technique are illustrated.

Cytochrome b₅₅₉ and cyclic electron transfer within photosystem II

Cytochrome b₅₅₉ (Cyt b₅₅₉), β-carotene (Car), and chlorophyll (Chl) cofactors participate in the secondary electron-transfer pathways in photosystem II (PSII), which are believed to protect PSII from photodamage under conditions in which the primary electron-donation pathway leading to water oxidation is inhibited. Among these cofactors, Cyt b₅₅₉ is preferentially photooxidized under conditions in which the primary electron-donation pathway is blocked. When Cyt b₅₅₉ is preoxidized, the photooxidation of several of the 11 Car and 35 Chl molecules present per PSII is observed. In this review, the discovery of the secondary electron donors, their structures and electron-transfer properties, and progress in the characterization of the secondary electron-transfer pathways are discussed. This article is part of a Special Issue entitled: Photosystem II.

Pulsed electron-electron double resonance: beyond nanometre distance measurements on biomacromolecules

PELDOR (or DEER; pulsed electron-electron double resonance) is an EPR (electron paramagnetic resonance) method that measures via the dipolar electron-electron coupling distances in the nanometre range, currently 1.5-8 nm, with high precision and reliability. Depending on the quality of the data, the error can be as small as 0.1 nm. Beyond mere mean distances, PELDOR yields distance distributions, which provide access to conformational distributions and dynamics. It can also be used to count the number of monomers in a complex and allows determination of the orientations of spin centres with respect to each other. If, in addition to the dipolar through-space coupling, a through-bond exchange coupling mechanism contributes to the overall coupling both mechanisms can be separated and quantified. Over the last 10 years PELDOR has emerged as a powerful new biophysical method without size restriction to the biomolecule to be studied, and has been applied to a large variety of nucleic acids as well as proteins and protein complexes in solution or within membranes. Small nitroxide spin labels, paramagnetic metal ions, amino acid radicals or intrinsic clusters and cofactor radicals have been used as spin centres.

Long-range distance determinations in biomacromolecules by EPR spectroscopy

Electron paramagnetic resonance (EPR) spectroscopy provides a variety of tools to study structures and structural changes of large biomolecules or complexes thereof. In order to unravel secondary structure elements, domain arrangements or complex formation, continuous wave and pulsed EPR methods capable of measuring the magnetic dipole coupling between two unpaired electrons can be used to obtain long-range distance constraints on the nanometer scale. Such methods yield reliably and precisely distances of up to 80 A, can be applied to biomolecules in aqueous buffer solutions or membranes, and are not size limited. They can be applied either at cryogenic or physiological temperatures and down to amounts of a few nanomoles. Spin centers may be metal ions, metal clusters, cofactor radicals, amino acid radicals, or spin labels. In this review, we discuss the advantages and limitations of the different EPR spectroscopic methods, briefly describe their theoretical background, and summarize important biological applications. The main focus of this article will be on pulsed EPR methods like pulsed electron-electron double resonance (PELDOR) and their applications to spin-labeled biosystems.

The functional sites of chlorophylls in D1 and D2 subunits of photosystem II identified by pulsed EPR

The functional site of ChlZ, an auxiliary electron donor to P680+, was determined by pulsed ELDOR applied to a radical pair of YD * and Chlz+ in oriented PS II membranes from spinach. The radical-radical distance was determined to be 29.5 A and its direction was 50 degrees from the membrane normal, indicating that a chlorophyll on the D2 protein is responsible for the EPR Chlz+ signal. Spin polarized ESEEM (Electronin Spin Echo Envelop Modulation) of a 3Chl and QA - radical pair induced by a laser flash was observed in reaction center D1D2Cytb559 complex, in which QA was functionally reconstituted with DBMIB and reduced chemically. QA -ESEEM showed a characteristic oscillating time profile due to dipolar coupling with 3Chl. By fitting with the dipolar interaction parameters, the distance between 3Chl and QA - was determined to be 25.9 A, indicating that the accessory chlorophyll on the D1 protein is responsible for the 3Chl signal.

Electron dipole-dipole ESEEM in field-step ELDOR of nitroxide biradicals

The use of a rapid stepping of the magnetic field for investigation of electron dipole-dipole ESEEM in pulsed X-band ELDOR is described. The magnetic field jump, synchronized with a microwave pumping pulse, is positioned between the second and the third pulses of the stimulated echo pulse sequence. This echo is measured as a function of the delay between the first and the second pulses. The data are analyzed for a Fourier transform resulting in a Pake resonance pattern. To remove the electron-nuclear contributions to ESEEM, time traces with pumping were divided by those without. This resulted in complete elimination of electron-nuclear contributions, which is seen from the absence of peaks at nuclear frequencies and the similarity of results for protonated and deuterated solvents. For increasing the electron-electron modulation depth, a scanning of the magnetic field during the microwave pumping is proposed. The interspin distances and their distribution are determined for two long-chained (ca. 2 nm) nitroxide biradicals in glassy toluene and in frozen nematic liquid crystal 4-cyano-4'-pentyl-biphenyl. For the latter solvent, the alignment of the axis connecting two nitroxides in biradicals is quantitatively analyzed.

Pulsed EPR spectroscopy: biological applications

Pulsed electron paramagnetic resonance (EPR) methods such as ESEEM, PELDOR, relaxation time measurements, transient EPR, high-field/high-frequency EPR, and pulsed ENDOR, have been used successfully to investigate the local structure and dynamics of paramagnetic centers in biological samples. These methods allow different contributions to the EPR spectra to be distinguished and can help unravel complicated EPR spectra consisting of overlapping resonance lines, as are often found in disordered protein samples. The basic principles, specific potentials, technical requirements, and limitations of these advanced EPR techniques will be reviewed together with recent applications to metal centers, organic radicals, and spin labels in proteins.

Probing the Mn oxidation states in the OEC. Insights from spectroscopic, computational and kinetic data

Results from a variety of experimental techniques which have been used to define the oxidation levels of Mn and other components in the S states of the water oxidising complex in Photosystem II are reviewed. A self-consistent interpretation of Mn X-ray absorption near edge spectroscopy, UV-visible and near infrared spectroscopic data suggests that Mn oxidation occurs only on the S0-->S1 transition, and that all four Mn centres have formal oxidation state III thereafter. Ligand oxidation occurs on the transitions to S2 and S3. This is supported by high level quantum chemical calculations and an analysis of the kinetics of substrate water exchange, as recently determined by Wydrzynski et al. (this journal). One type of model for the catalytic site structure and water oxidation mechanism, consistent with these conclusions, is discussed. This model invokes magnetically separate oxo bridged dimers with water oxidation occurring by a concerted 2H+/2e- transfer mechanism, with one H transfer to a bridge oxygen on each dimer.

The position of cytochrome b(559) relative to Q(A) in photosystem II studied by electron-electron double resonance (ELDOR)

The electron-electron double resonance (ELDOR) method was applied to measure the dipole interaction between cytochrome (Cyt) b(+)(559) and the primary acceptor quinone (Q(-)(A)), observed at g=2.0045 with the peak to peak width of about 9 G, in Photosystem II (PS II) in which the non-heme Fe(2+) was substituted by Zn(2+). The paramagnetic centers of Cyt b(+)(559)Y(D)Q(-)(A) were trapped by illumination at 273 K for 8 min, followed by dark adaptation for 3 min and freezing into 77 K. The distance between the pair Cyt b(+)(559)-Q(-)(A) was estimated from the dipole interaction constant fitted to the observed ELDOR time profile to be 40+/-1 A. In the membrane oriented PS II particles the angle between the vector from Q(A) to Cyt b(559) and the membrane normal was determined to be 80+/-5 degrees. The position of Cyt b(559) relative to Q(A) suggests that the heme plane is located on the stromal side of the thylakoid membrane. ELDOR was not observed for Cyt b(+)(559) Y(D) spin pair, suggesting the distance between them is more than 50 A.