Electron spin echo envelope modulation spectroscopy in photosystem I

HDX-guided EPR spectroscopy to interrogate membrane protein dynamics

Solvent accessibilities of and distances between protein residues measured by pulsed-EPR approaches provide high-resolution information on dynamic protein motions. We describe protocols for the purification and site-directed spin labeling of integral membrane proteins. In our protocol, peptide-level HDX-MS is used as a precursor to guide single-residue resolution ESEEM accessibility measurements and spin labeling strategies for EPR applications. Exploiting the pentameric MscL channel as a model, we discuss the use of cwEPR, DEER/PELDOR, and ESEEM spectroscopies to interrogate membrane protein dynamics.

For complete details on the use and execution of this protocol, please refer to Wang et al. (2022).

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Protocols for an integrated EPR-based approach to study membrane protein dynamics

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Instructions for the sample preparation of spin-labeled membrane proteins

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Used HDX-MS as a precursor to guide spin labeling strategies for EPR methods

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Probed solvent accessibility at the single-residue level by ESEEM

Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.

Electron-Nuclear Coherent Coupling and Nuclear Spin Readout through Optically Polarized VB- Spin States in hBN

Coherent coupling of defect spins with surrounding nuclei along with the endowment to read out the latter are basic requirements for an application in quantum technologies. We show that negatively charged boron vacancies (V_B^-) in hexagonal boron nitride (hBN) meet these prerequisites. We demonstrate Hahn-echo coherence of the V_B^- spin with a characteristic decay time T_coh = 15 μs, close to the theoretically predicted limit of 18 μs for defects in hBN. Elongation of the coherence time up to 36 μs is demonstrated by means of the Carr-Purcell-Meiboom-Gill decoupling technique. Modulation of the Hahn-echo decay is shown to be induced by coherent coupling of the V_B^- spin with the three nearest ¹⁴N nuclei via a nuclear quadrupole interaction of 2.11 MHz. DFT calculation confirms that the electron-nuclear coupling is confined to the defective layer and stays almost unchanged with a transition from the bulk to the single layer.

Shedding Light on Primary Donors in Photosynthetic Reaction Centers

Chlorophylls (Chl)s exist in a variety of flavors and are ubiquitous in both the energy and electron transfer processes of photosynthesis. The functions they perform often occur on the ultrafast (fs-ns) time scale and until recently, these have been difficult to measure in real time. Further, the complexity of the binding pockets and the resulting protein-matrix effects that alter the respective electronic properties have rendered theoretical modeling of these states difficult. Recent advances in experimental methodology, computational modeling, and emergence of new reaction center (RC) structures have renewed interest in these processes and allowed researchers to elucidate previously ambiguous functions of Chls and related pheophytins. This is complemented by a wealth of experimental data obtained from decades of prior research. Studying the electronic properties of Chl molecules has advanced our understanding of both the nature of the primary charge separation and subsequent electron transfer processes of RCs. In this review, we examine the structures of primary electron donors in Type I and Type II RCs in relation to the vast body of spectroscopic research that has been performed on them to date. Further, we present density functional theory calculations on each oxidized primary donor to study both their electronic properties and our ability to model experimental spectroscopic data. This allows us to directly compare the electronic properties of hetero- and homodimeric RCs.

A dimeric chlorophyll electron acceptor differentiates type I from type II photosynthetic reaction centers

This research addresses one of the most compelling issues in the field of photosynthesis, namely, the role of the accessory chlorophyll molecules in primary charge separation. Using a combination of empirical and computational methods, we demonstrate that the primary acceptor of photosystem (PS) I is a dimer of accessory and secondary chlorophyll molecules, Chl_2A and Chl_3A, with an asymmetric electron charge density distribution. The incorporation of highly coupled donors and acceptors in PS I allows for extensive delocalization that prolongs the lifetime of the charge-separated state, providing for high quantum efficiency. The discovery of this motif has widespread implications ranging from the evolution of naturally occurring reaction centers to the development of a new generation of highly efficient artificial photosynthetic systems.

Video abstract

Two-dimensional HYSCORE spectroscopy reveals a histidine imidazole as the axial ligand to Chl3A in the M688HPsaA genetic variant of Photosystem I

Recent studies on Photosystem I (PS I) have shown that the six core chlorophyll a molecules are highly coupled, allowing for efficient creation and stabilization of the charge-separated state. One area of particular interest is the identity and function of the primary acceptor, A₀, as the factors that influence its ultrafast processes and redox properties are not yet fully elucidated. It was recently shown that A₀ exists as a dimer of the closely-spaced Chl₂/Chl₃ molecules wherein the reduced A₀^- state has an asymmetric distribution of electron spin density that favors Chl₃. Previous experimental work in which this ligand was changed to a hard base (histidine, M688H_PsaA) revealed severely impacted electron transfer processes at both the A₀ and A₁ acceptors; molecular dynamics simulations further suggested two distinct conformations of PS I in which the His residue coordinates and forms a hydrogen bond to the A₀ and A₁ cofactors, respectively. In this study, we have applied 2D HYSCORE spectroscopy in conjunction with molecular dynamics simulations and density functional theory calculations to the study of the M688H_PsaA variant. Analysis of the hyperfine parameters demonstrates that the His imidazole serves as the axial ligand to the central Mg²⁺ ion in Chl_3A in the M688H_PsaA variant. Although the change in ligand identity does not alter delocalization of electron density over the Chl₂/Chl₃ dimer, a small shift in the asymmetry of delocalization, coupled with the electron withdrawing properties of the ligand, most likely accounts for the inhibition of forward electron transfer in the His-ligated conformation.

In-Lipid Structure of Pressure-Sensitive Domains Hints Mechanosensitive Channel Functional Diversity

The mechanosensitive channel of large conductance (MscL) from Mycobacterium tuberculosis has been used as a structural model for rationalizing functional observations in multiple MscL orthologs. Although these orthologs adopt similar structural architectures, they reportedly present significant functional differences. Subtle structural discrepancies on mechanosensitive channel nanopockets are known to affect mechanical gating and may be linked to large variability in tension sensitivity among these membrane channels. Here, we modify the nanopocket regions of MscL from Escherichia coli and M. tuberculosis and employ PELDOR/DEER distance and 3pESEEM deuterium accessibility measurements to interrogate channel structure within lipids, in which both channels adopt a closed conformation. Significant in-lipid structural differences between the two constructs suggest a more compact E. coli MscL at the membrane inner-leaflet, as a consequence of a rotated TM2 helix. Observed differences within lipids could explain E. coli MscL’s higher tension sensitivity and should be taken into account in extrapolated models used for MscL gating rationalization.

Two-dimensional 67Zn HYSCORE spectroscopy reveals that a Zn-bacteriochlorophyll aP′ dimer is the primary donor (P840) in the type-1 reaction centers of Chloracidobacterium thermophilum

Using pulsed EPR spectroscopy and isotopic labeling we demonstrate that reaction centers of Chloracidobacterium thermophilum have an unusual primary donor that is a dimer of Zn-bacteriochlorophyll a_P′ molecules.

15N photo-CIDNP MAS NMR on both photosystems and magnetic field-dependent 13C photo-CIDNP MAS NMR in photosystem II of the diatom Phaeodactylum tricornutum

Diatoms contribute about 20-25% to the global marine productivity and are successful autotrophic players in all aquatic ecosystems, which raises the question whether this performance is caused by differences in their photosynthetic apparatus. Photo-CIDNP MAS NMR presents a unique tool to obtain insights into the reaction centres of photosystems (PS), by selective enhancement of NMR signals from both, the electron donor and the primary electron acceptor molecules. Here, we present the first observation of the solid-state photo-CIDNP effect in the pennate diatoms. In comparison to plant PSs, similar spectral patterns have been observed for PS I at 9.4 T and PS II at 4.7 T in the PSs of Phaeodactylum tricornutum. Studies at different magnetic fields reveal a surprising sign change of the ¹³C photo-CIDNP MAS NMR signals indicating an alternative arrangement of cofactors which allows to quench the Chl a donor triplet state in contrast to the situation in plant PS II. This unusual quenching mechanism is related to a carotenoid molecule in close vicinity to the Chl a donor. In addition to the photo-CIDNP MAS NMR signals arising from the donor and the primary electron acceptor cofactors, a complete set of signals of the imidazole ring ligating to the magnesium of Chl a can be observed.

Ion Channel Conformation and Oligomerization Assessment by Site-Directed Spin Labeling and Pulsed-EPR

Mechanosensitive (MS) ion channels are multimeric integral membrane proteins that respond to increased lipid bilayer tension by opening their nonselective pores to release solutes and relieve increased cytoplasmic pressure. These systems undergo major conformational changes during gating and the elucidation of their mechanism requires a deep understanding of the interplay between lipids and proteins. Lipids are responsible for transmitting lateral tension to MS channels and therefore play a key role in obtaining a molecular-detail model for mechanosensation. Site-directed spin labeling combined with electron paramagnetic resonance (EPR) spectroscopy is a powerful spectroscopic tool in the study of proteins. The main bottleneck for its use relates to challenges associated with successful isolation of the protein of interest, introduction of paramagnetic labels on desired sites, and access to specialized instrumentation and expertise. The design of sophisticated experiments, which combine a variety of existing EPR methodologies to address a diversity of specific questions, require knowledge of the limitations and strengths, characteristic of each particular EPR method. This chapter is using the MS ion channels as paradigms and focuses on the application of different EPR techniques to ion channels, in order to investigate oligomerization, conformation, and the effect of lipids on their regulation. The methodology we followed, from the initial strategic selection of mutants and sample preparation, including protein purification, spin labeling, reconstitution into lipid mimics to the complete set-up of the pulsed-EPR experiments, is described in detail.

Advanced Magnetic Resonance Techniques for the Structural Characterization of Aminoxyl Radicals and Their Inorganic-Organic Nanocomposite Systems

Electron and nuclear spins are extremely sensitive probes of their local structural and dynamic surroundings. Their Zeeman energy levels are modified by different types of local magnetic and electric fields created by their structural environment, which influence their magnetic resonance condition. For this reason, electron spin resonance (ESR) and nuclear magnetic resonance (NMR) spectroscopies have become extremely powerful tools of structural analysis, which are being widely used for the structural characterization of complex solids. Following a brief introduction into the basic theoretical foundations the most commonly used techniques and their application towards the structural characterization of paramagnetic solids based on aminoxyl radicals and their inorganic-organic nanocomposites will be described. Both ESR and NMR observables are useful for monitoring intermolecular interactions between unpaired electron spins, which are particularly important for the design of organically based ferromagnetic systems. ESR and NMR methods based on this effect can be used for monitoring the synthesis of polynitroxides and for evaluating the catalytic function of aminoxyl intercalation compounds. Finally, the sensitivity of ESR signals to motional dynamics can be exploited for characterizing molecule-surface interactions in nanocomposite systems. In the context of the latter work recently developed signal enhancement strategies are described, using polarization transfer from electron spins to nuclear spins for NMR spectroscopic detection.

Rare-earth doped fluoride phosphate glasses: structural foundations of their luminescence properties

We report a detailed structural investigation of a series of fluoride–phosphate glasses with different phosphate/fluoride ratios in the system xSr(PO₃)₂–(100 − x)[AlF₃–CaF₂–SrF₂–MgF₂] with x = 5, 10, 20, 40.

Photo-CIDNP in the Reaction Center of the Diatom Cyclotella meneghiniana Observed by 13C MAS NMR

Photo-CIDNP MAS NMR presents a unique tool to obtain insight into the photosynthetic reaction centers (RCs) of bacteria and plants. Using the dramatic enhancement of sensitivity and selectivity of the solid-state photo-CIDNP effect, structural as well as functional information can be obtained from the cofactor molecules forming a light-induced spin-correlated radical pair (SCRP) in a given reaction center. Here we demonstrate that the effect can be observed in a further species, which belongs neither to the plant nor the bacteria kingdom. Cyclotella (C.) meneghiniana is a member of the diatom phylum and, therefore, belongs to the kingdom of chromista. Chromista are some of the most productive organisms in nature, even in comparison to trees and terrestrial grasses. The observation of the effect in chromista indicates that the effect occurs in all photosynthetic organisms and completes the list with the last phototrophic kingdoms. Our data also demonstrate that the photo- and spin-chemical machineries of photosystem I of plants and chromista are very similar with respect to structure as well as function.

Aminoxyl Radicals of B/P Frustrated Lewis Pairs: Refinement of the Spin-Hamiltonian Parameters by Field- and Temperature-Dependent Pulsed EPR Spectroscopy

Q-band and X-band pulsed electron paramagnetic resonance spectroscopic methods (EPR) in the solid state were employed to refine the parameters characterizing the anisotropic interactions present in six nitroxide radicals prepared by N,N addition of NO to various borane-phosphane frustrated Lewis pairs (FLPs). The EPR spectra are characterized by the g-anisotropy as well as by nuclear hyperfine coupling between the unpaired electron and the 11B/10B, 14N and 31P nuclear magnetic moments. It was previously shown that continuous-wave spectra measured at X-band frequency (9.5 GHz) are dominated by the magnetic hyperfine coupling to 14N and 31P, whereas the g-tensor values and the 11B hyperfine coupling parameters cannot be refined with high precision from lineshape fitting. On the other hand, the X-band electron spin echo envelope modulation (ESEEM) and hyperfine sublevel correlation (HYSCORE) spectra are completely dominated by the nuclear hyperfine coupling to the 11B nuclei, allowing a selective determination of their interaction parameters. In the present work this analysis has been further validated by temperature dependent ESEEM measurements. In addition, pulsed EPR data measured in the Q-band (34 GHz) are reported, which present an entirely different situation: the g-tensor components can be measured with much higher precision, and the ESEEM and HYSCORE spectra contain information about all of the 10B, 11B, 14N and 31P hyperfine interaction parameters. Based on these new results, we report here high-accuracy and precision data of the EPR spin Hamiltonian parameters measured on six FLP-NO radical species embedded in their corresponding hydroxylamine host structures. While the ESEEM spectra at Q-band frequency turn out to be very complex (due to the multinuclear contribution to the overall signal) in the HYSCORE experiment the extension over two dimensions renders a better discrimination between the different nuclear species, and the signals arising from hyperfine coupling to 10B, 11B, 14N and 31P nuclei can be individually analyzed.

Determining the Secondary Structure of Membrane Proteins and Peptides Via Electron Spin Echo Envelope Modulation (ESEEM) Spectroscopy

Revealing detailed structural and dynamic information of membrane embedded or associated proteins is challenging due to their hydrophobic nature which makes NMR and X-ray crystallographic studies challenging or impossible. Electron paramagnetic resonance (EPR) has emerged as a powerful technique to provide essential structural and dynamic information for membrane proteins with no size limitations in membrane systems which mimic their natural lipid bilayer environment. Therefore, tremendous efforts have been devoted toward the development and application of EPR spectroscopic techniques to study the structure of biological systems such as membrane proteins and peptides. This chapter introduces a novel approach established and developed in the Lorigan lab to investigate membrane protein and peptide local secondary structures utilizing the pulsed EPR technique electron spin echo envelope modulation (ESEEM) spectroscopy. Detailed sample preparation strategies in model membrane protein systems and the experimental setup are described. Also, the ability of this approach to identify local secondary structure of membrane proteins and peptides with unprecedented efficiency is demonstrated in model systems. Finally, applications and further developments of this ESEEM approach for probing larger size membrane proteins produced by overexpression systems are discussed.

The structure and function of quinones in biological solar energy transduction: a cyclic voltammetry, EPR, and hyperfine sub-level correlation (HYSCORE) spectroscopy study of model naphthoquinones

Quinones function as electron transport cofactors in photosynthesis and cellular respiration. The versatility and functional diversity of quinones is primarily due to the diverse midpoint potentials that are tuned by the substituent effects and interactions with surrounding amino acid residues in the binding site in the protein. In the present study, a library of substituted 1,4-naphthoquinones are analyzed by cyclic voltammetry in both protic and aprotic solvents to determine effects of substituent groups and hydrogen bonds on the midpoint potential. We use continuous-wave electron paramagnetic resonance (EPR) spectroscopy to determine the influence of substituent groups on the electronic properties of the 1,4-naphthoquinone models in an aprotic solvent. The results establish a correlation between the presence of substituent group(s) and the modification of electronic properties and a corresponding shift in the midpoint potential of the naphthoquinone models. Further, we use pulsed EPR spectroscopy to determine the effect of substituent groups on the strength and planarity of the hydrogen bonds of naphthoquinone models in a protic solvent. This study provides support for the tuning of the electronic properties of quinone cofactors by the influence of substituent groups and hydrogen bonding interactions.

Multifrequency pulsed electron paramagnetic resonance on metalloproteins

Metalloproteins often contain metal centers that are paramagnetic in some functional state of the protein; hence electron paramagnetic resonance (EPR) spectroscopy can be a powerful tool for studying protein structure and function. Dipolar spectroscopy allows the determination of the dipole-dipole interactions between metal centers in protein complexes, revealing the structural arrangement of different paramagnetic centers at distances of up to 8 nm. Hyperfine spectroscopy can be used to measure the interaction between an unpaired electron spin and nuclear spins within a distance of 0.8 nm; it therefore permits the characterization of the local structure of the paramagnetic center's ligand sphere with very high precision. In this Account, we review our laboratory's recent applications of both dipolar and hyperfine pulsed EPR methods to metalloproteins. We used pulsed dipolar relaxation methods to investigate the complex of cytochrome c and cytochrome c oxidase, a noncovalent protein-protein complex involved in mitochondrial electron-transfer reactions. Hyperfine sublevel correlation spectroscopy (HYSCORE) was used to study the ligand sphere of iron-sulfur clusters in complex I of the mitochondrial respiratory chain and substrate binding to the molybdenum enzyme polysulfide reductase. These examples demonstrate the potential of the two techniques; however, they also highlight the difficulties of data interpretation when several paramagnetic species with overlapping spectra are present in the protein. In such cases, further approaches and data are very useful to enhance the information content. Relaxation filtered hyperfine spectroscopy (REFINE) can be used to separate the individual components of overlapping paramagnetic species on the basis of differences in their longitudinal relaxation rates; it is applicable to any kind of pulsed hyperfine or dipolar spectroscopy. Here, we show that the spectra of the iron-sulfur clusters in complex I can be separated by this method, allowing us to obtain hyperfine (and dipolar) information from the individual species. Furthermore, performing pulsed EPR experiments at different magnetic fields is another important tool to disentangle the spectral components in such complex systems. Despite the fact that high magnetic fields do not usually lead to better spectral separation for metal centers, they provide additional information about the relative orientation of different paramagnetic centers. Our high-field EPR studies on cytochrome c oxidase reveal essential information regarding the structural arrangement of the binuclear Cu(A) center with respect to both the manganese ion within the enzyme and the cytochrome in the protein-protein complex with cytochrome c.

Kinetics of the interaction of sulfate and hydrogen phosphate radicals with small peptides of glycine, alanine, tyrosine and tryptophan

The kinetics and mechanism of the oxidation of Glycine (Gly), Alanine (Ala), Tyrosine (Tyr), Tryptophan (Trp) and some di-(Gly-Gly, Ala-Ala, Gly-Ala, Gly-Trp, Trp-Gly, Gly-Tyr, Tyr-Gly), tri-(Gly-Gly-Gly, Ala-Gly-Gly) and tetrapeptides (Gly-Gly-Gly-Gly) mediated by sulfate (SO(4) (-)) and hydrogen phosphate (HPO(4) (-)) radicals was studied, employing the flash-photolysis technique. The substrates were found to react with sulfate radicals (SO(4) (-), produced by photolysis of the S(2)O(8)(2-)) faster than with hydrogen phosphate radicals (HPO(4) (-), generated by photolysis of P(2)O(8)(4-) at pH = 7.1). The reactions of the zwitterions of the aliphatic amino acids and peptides with SO(4) (-) radicals take place by electron transfer from the carboxylate moiety to the inorganic radical, whereas those of the HPO(4) (-) proceed by H-abstraction from the alpha carbon atom. The phenoxyl radical of Tyr-Gly and Gly-Tyr are formed as intermediate species of the oxidation of these peptides by the inorganic radicals. The radical cations of Gly-Trp and Trp-Gly (at pH = 4.2) and their corresponding deprotonated forms (at pH = 7) were detected as intermediates species of the oxidation of these peptides with SO(4) (-) and HPO(4) (-). Reaction mechanisms which account for the observed intermediates are proposed.

P700: the primary electron donor of photosystem I

The primary electron donor of photosystem I, P700, is a chlorophyll species that in its excited state has a potential of approximately -1.2 V. The precise chemical composition and electronic structure of P700 is still unknown. Recent evidence indicates that P700 is a dimer of one chlorophyll (Chl) a and one Chl a'. The Chl a' and Chl a are axially coordinated by His residues provided by protein subunits PsaA and PsaB, respectively. The Chl a', but not the Chl a, is also H-bonded to the protein. The H-bonding is likely responsible for selective insertion of Chl a' into the reaction center. EPR studies of P700(+*) in frozen solution and single crystals indicate a large asymmetry in the electron spin and charge distribution towards one Chl of the dimer. Molecular orbital calculations indicate that H-bonding will specifically stabilize the Chl a'-side of the dimer, suggesting that the unpaired electron would predominantly reside on the Chl a. This is supported by results of specific mutagenesis of the PsaA and PsaB axial His residues, which show that only mutations of the PsaB subunit significantly alter the hyperfine coupling constants associated with a single Chl molecule. The PsaB mutants also alter the microwave induced triplet-minus-singlet spectrum indicating that the triplet state is localized on the same Chl. Excitonic coupling between the two Chl a of P700 is weak due to the distance and overlap of the porphyrin planes. Evidence of excitonic coupling is found in PsaB mutants which show a new bleaching band at 665 nm that likely represents an increased intensity of the upper exciton band of P700. Additional properties of P700 that may give rise to its unusually low potential are discussed.