High-field EPR studies of the structure and conformational changes of site-directed spin labeled bacteriorhodopsin

Probing Small-Angle Molecular Motions with EPR Spectroscopy: Dynamical Transition and Molecular Packing in Disordered Solids

Disordered molecular solids present a rather broad class of substances of different origin—amorphous polymers, materials for photonics and optoelectronics, amorphous pharmaceutics, simple molecular glass formers, and others. Frozen biological media in many respects also may be referred to this class. Theoretical description of dynamics and structure of disordered solids still does not exist, and only some phenomenological models can be developed to explain results of particular experiments. Among different experimental approaches, electron paramagnetic resonance (EPR) applied to spin probes and labels also can deliver useful information. EPR allows probing small-angle orientational molecular motions (molecular librations), which intrinsically are inherent to all molecular solids. EPR is employed in its conventional continuous wave (CW) and pulsed—electron spin echo (ESE)—versions. CW EPR spectra are sensitive to dynamical librations of molecules while ESE probes stochastic molecular librations. In this review, different manifestations of small-angle motions in EPR of spin probes and labels are discussed. It is shown that CW-EPR-detected dynamical librations provide information on dynamical transition in these media, similar to that explored with neutron scattering, and ESE-detected stochastic librations allow elucidating some features of nanoscale molecular packing. The possible EPR applications are analyzed for gel-phase lipid bilayers, for biological membranes interacting with proteins, peptides and cryoprotectants, for supercooled ionic liquids (ILs) and supercooled deep eutectic solvents (DESs), for globular proteins and intrinsically disordered proteins (IDPs), and for some other molecular solids.

Electron spin echo detection of stochastic molecular librations: Non-cooperative motions on solid surface

In frozen biological media and molecular glasses only restricted motions exist; because of the weakness and disorder of intermolecular bonds these motions may have stochastic nature. Electron spin echo (ESE) spectroscopy of spin-labeled molecules allows detecting their restricted stochastic rotations (stochastic molecular librations). As in molecular disordered media motions may be highly cooperative, it would be desirable to investigate their spectroscopic manifestation also in the systems where cooperative effects would be certainly ruled out. In this work, ESE of spin-labeled molecules adsorbed on inorganic SiO₂ surface was investigated in a wide temperature range. The rate of motion-induced spin relaxation was found to become measurable above 130 K, increasing with temperature and attaining then a saturating behavior with a well-defined maximum near 250 K. For two types of molecules differing remarkably in their size and polarity (a small highly-polar nitroxide radical and a large spin-labeled peptide), quite similar results were obtained. This saturating behavior was quantitatively reproduced in simulations within a simple model of jump between two close orientations. Comparison with experiment allowed estimate that at 250 K the correlation time of the motion τ_c is of the order of several tens of nanoseconds and the angle α between two orientations is around 0.02 rad. As the found saturating behavior is a property of individual motions, for any other molecular system an excess of the spin relaxation rate above the maximum found here for adsorbed molecules may be ascribed to cooperative motions. Comparison with literature data on molecular systems of different origin has shown that effects of cooperativity indeed are present and, moreover, may be very essential.

EPR Techniques to Probe Insertion and Conformation of Spin-Labeled Proteins in Lipid Bilayers

Electron paramagnetic resonance (EPR) spectroscopy of spin-labeled membrane proteins is a valuable biophysical technique to study structural details and conformational transitions of proteins close to their physiological environment, for example, in liposomes, membrane bilayers, and nanodiscs. Unlike in nuclear magnetic resonance (NMR) spectroscopy, having only one or few specific side chains labeled at a time with paramagnetic probes makes the size of the object under investigation irrelevant in terms of technique sensitivity. As a drawback, extensive site-directed mutagenesis is required in order to analyze the properties of the protein under investigation. EPR can provide detailed information on side chain dynamics of large membrane proteins or protein complexes embedded in membranes with an exquisite sensitivity for flexible regions and on water accessibility profiles across the membrane bilayer. Moreover, distances between the two spin-labeled side chains in membrane proteins can be detected with high precision at cryogenic temperatures. The application of EPR to membrane proteins still presents some challenges in terms of sample preparation, sensitivity and data interpretation, thus it is difficult to give ready-to-go methodological recipes. However, new technological developments (arbitrary waveform generators) and new spin labels spectroscopically orthogonal to nitroxides increased the range of applicability from in vitro toward in-cell EPR experiments. This chapter is an updated version of the one published in the first edition of the book and describes the state of the art in the application of nitroxide-based site-directed spin labeling EPR to membrane proteins, addressing new tools such as arbitrary waveform generators and spectroscopically orthogonal labels, such as Gd(III)-based labels. We will present challenges in sample preparation and data analysis for functional and structural membrane protein studies using site-directed spin labeling techniques and give experimental details on EPR techniques providing information on side chain dynamics and water accessibility using nitroxide probes. An updated optimal Q-band DEER setup for nitroxide probes will be described, and its extension to gadolinium-containing samples will be addressed.

Exploring the pH-Induced Functional Phase Space of Human Serum Albumin by EPR Spectroscopy

A systematic study on the self-assembled solution system of human serum albumin (HSA) and paramagnetic doxyl stearic acid (5-DSA and 16-DSA) ligands is reported covering the broad pH range 0.7–12.9, mainly using electron paramagnetic resonance (EPR) methods. It is tested to which extent the pH-induced conformational isomers of HSA reveal themselves in continuous wave (CW) EPR spectra from this spin probing approach in comparison to an established spin-labeling strategy utilizing 3-maleimido proxyl (5-MSL). Most analyses are conducted on empirical levels with robust strategies that allow for the detection of dynamic changes of ligand, as well as protein. Special emphasis has been placed on the EPR spectroscopic detection of a molten globule (MG) state of HSA that is typically found by the fluorescent probe 8-Anilino- naphthalene-1-sulfonic acid (ANS). Moreover, four-pulse double electron-electron resonance (DEER) experiments are conducted and substantiated with dynamic light scattering (DLS) data to determine changes in the solution shape of HSA with pH. All results are ultimately combined in a detailed scheme that describes the pH-induced functional phase space of HSA.

Jim Hyde and the ENDOR Connection: A Personal Account

In this minireview, we report on our year-long EPR work, such as electron-nuclear double resonance (ENDOR), pulse electron double resonance (PELDOR) and ELDOR-detected NMR (EDNMR) at X-band and W-band microwave frequencies and magnetic fields. This report is dedicated to James S. Hyde and honors his pioneering contributions to the measurement of spin interactions in large (bio)molecules. From these interactions, detailed information is revealed on structure and dynamics of macromolecules embedded in liquid-solution or solid-state environments. New developments in pulsed microwave and sweepable cryomagnet technology as well as ultra-fast electronics for signal data handling and processing have pushed the limits of EPR spectroscopy and its multi-frequency extensions to new horizons concerning sensitivity of detection, selectivity of molecular interactions and time resolution. Among the most important advances is the upgrading of EPR to high magnetic fields, very much in analogy to what happened in NMR. The ongoing progress in EPR spectroscopy is exemplified by reviewing various multi-frequency electron-nuclear double-resonance experiments on organic radicals, light-generated donor-acceptor radical pairs in photosynthesis, and site-specifically nitroxide spin-labeled bacteriorhodopsin, the light-driven proton pump, as well as EDNMR and ENDOR on nitroxides. Signal and resolution enhancements are particularly spectacular for ENDOR, EDNMR and PELDOR on frozen-solution samples at high Zeeman fields. They provide orientation selection for disordered samples approaching single-crystal resolution at canonical g-tensor orientations-even for molecules with small g-anisotropies. Dramatic improvements of EPR detection sensitivity could be achieved, even for short-lived paramagnetic reaction intermediates. Thus, unique structural and dynamic information is revealed that can hardly be obtained by other analytical techniques. Micromolar concentrations of sample molecules have become sufficient to characterize stable and transient reaction intermediates of complex molecular systems-offering exciting applications for physicists, chemists, biochemists and molecular biologists.

Toward increased concentration sensitivity for continuous wave EPR investigations of spin-labeled biological macromolecules at high fields

High-field, high-frequency electron paramagnetic resonance (EPR) spectroscopy at W-(∼94 GHz) and D-band (∼140 GHz) is important for investigating the conformational dynamics of flexible biological macromolecules because this frequency range has increased spectral sensitivity to nitroxide motion over the 100 ps to 2 ns regime. However, low concentration sensitivity remains a roadblock for studying aqueous samples at high magnetic fields. Here, we examine the sensitivity of a non-resonant thin-layer cylindrical sample holder, coupled to a quasi-optical induction-mode W-band EPR spectrometer (HiPER), for continuous wave (CW) EPR analyses of: (i) the aqueous nitroxide standard, TEMPO; (ii) the unstructured to α-helical transition of a model IDP protein; and (iii) the base-stacking transition in a kink-turn motif of a large 232 nt RNA. For sample volumes of ∼50 μL, concentration sensitivities of 2-20 μM were achieved, representing a ∼10-fold enhancement compared to a cylindrical TE011 resonator on a commercial Bruker W-band spectrometer. These results therefore highlight the sensitivity of the thin-layer sample holders employed in HiPER for spin-labeling studies of biological macromolecules at high fields, where applications can extend to other systems that are facilitated by the modest sample volumes and ease of sample loading and geometry.

Site-directed spin labeling of proteins for distance measurements in vitro and in cells

We here review strategies for site-directed spin labeling (SDSL) of proteins and discuss their potential for EPR distance measurements to study protein function in vitro and in cells.

Tunable dynamic hydrophobic attachment of guest molecules in amphiphilic core–shell polymers

In this study, synthesis and dynamic properties of amphiphilic core–shell polymers are reported as monitored through their interaction with small amphiphilic ligands. Our findings point to a most complex self-assembling nature of those host and guest molecules.

Elucidating the design principles of photosynthetic electron-transfer proteins by site-directed spin labeling EPR spectroscopy

Site-directed spin labeling electron paramagnetic resonance (SDSL EPR) spectroscopy is a powerful tool to determine solvent accessibility, side-chain dynamics, and inter-spin distances at specific sites in biological macromolecules. This information provides important insights into the structure and dynamics of both natural and designed proteins and protein complexes. Here, we discuss the application of SDSL EPR spectroscopy in probing the charge-transfer cofactors in photosynthetic reaction centers (RC) such as photosystem I (PSI) and the bacterial reaction center (bRC). Photosynthetic RCs are large multi-subunit proteins (molecular weight≥300 kDa) that perform light-driven charge transfer reactions in photosynthesis. These reactions are carried out by cofactors that are paramagnetic in one of their oxidation states. This renders the RCs unsuitable for conventional nuclear magnetic resonance spectroscopy investigations. However, the presence of native paramagnetic centers and the ability to covalently attach site-directed spin labels in RCs makes them ideally suited for the application of SDSL EPR spectroscopy. The paramagnetic centers serve as probes of conformational changes, dynamics of subunit assembly, and the relative motion of cofactors and peptide subunits. In this review, we describe novel applications of SDSL EPR spectroscopy for elucidating the effects of local structure and dynamics on the electron-transfer cofactors of photosynthetic RCs. Because SDSL EPR Spectroscopy is uniquely suited to provide dynamic information on protein motion, it is a particularly useful method in the engineering and analysis of designed electron transfer proteins and protein networks. This article is part of a Special Issue entitled Biodesign for Bioenergetics--the design and engineering of electronic transfer cofactors, proteins and protein networks, edited by Ronald L. Koder and J.L. Ross Anderson.

Electron spin resonance of spin-labeled lipid assemblies and proteins

Spin-label electron spin resonance (ESR) spectroscopy is a valuable means to study molecular mobility and interactions in biological systems. This paper deals with conventional, continuous wave ESR of nitroxide spin-labels at 9-GHz providing an introduction to the basic principles of the technique and applications to self-assembled lipid aggregates and proteins. Emphasis is given to segmental lipid chain order and rotational dynamics of lipid structures, environmental polarity of membranes and proteins, structure and conformational dynamics of proteins.

High-field ELDOR-detected NMR study of a nitroxide radical in disordered solids: towards characterization of heterogeneity of microenvironments in spin-labeled systems

The combination of high-field EPR with site-directed spin-labeling (SDSL) techniques employing nitroxide radicals has turned out to be particularly powerful in probing the polarity and proticity characteristics of protein/matrix systems. This information is concluded from the principal components of the nitroxide Zeeman (g), nitrogen hyperfine (A) and quadrupole (P) tensors of the spin labels attached to specific sites. Recent multi-frequency high-field EPR studies underlined the complexity of the problem to treat the nitroxide microenvironment in proteins adequately due to inherent heterogeneities which result in several principal x-components of the nitroxide g-tensor. Concomitant, but distinctly different nitrogen hyperfine components could, however, not be determined from high-field cw EPR experiments owing to the large intrinsic EPR linewidth in fully protonated guest/host systems. It is shown in this work that, using the W-band (95GHz) ELDOR- (electron-electron double resonance) detected NMR (EDNMR) method, different principal nitrogen hyperfine, Azz, and quadrupole, Pzz, tensor values of a nitroxide radical in glassy 2-propanol matrix can be measured with high accuracy. They belong to nitroxides with different hydrogen-bond situations. The satisfactory resolution and superior sensitivity of EDNMR as compared to the standard ENDOR (electron-nuclear double resonance) method are demonstrated.

Extracellular loop 4 of the proline transporter PutP controls the periplasmic entrance to ligand binding sites

The Na(+)/proline symporter (PutP), like several other Na(+)-coupled symporters, belongs to the so-called LeuT-fold structural family, which features ten core transmembrane domains (cTMs) connected by extra- and intracellular loops. The role of these loops has been discussed in context with the gating function in the alternating access model of secondary active transport processes. Here we report the complete spin-labeling site scan of extracellular loop 4 (eL4) in PutP that reveals the presence of two α-helical segments, eL4a and eL4b. Among the eL4 residues that are directly implicated in the functional dynamics of the transporter, Phe314 in eL4b anchors the loop by means of hydrophobic contacts to cTM1 close to the ligand binding sites. We propose that ligand-induced conformational changes at the binding sites are transmitted via the anchoring residue to eL4 and through eL4 further to adjacent cTMs, leading to closure of the extracellular gate.

Hydrogen bonding of nitroxide spin labels in membrane proteins

On the basis of experiments at 275 GHz, we reconsider the dependence of the continuous-wave EPR spectra of nitroxide spin-labeled protein sites in sensory- and bacteriorhodopsin on the micro-environment.

Structural and dynamical characteristics of trehalose and sucrose matrices at different hydration levels as probed by FTIR and high-field EPR

Some organisms can survive complete dehydration and high temperatures by adopting an anhydrobiotic state in which the intracellular medium contains large amounts of disaccharides, particularly trehalose and sucrose. Trehalose is most effective also in protecting isolated in vitro biostructures. In an attempt to clarify the molecular mechanisms of disaccharide bioprotection, we compared the structure and dynamics of sucrose and trehalose matrices at different hydration levels by means of high-field W-band EPR and FTIR spectroscopy. The hydration state of the samples was characterized by FTIR spectroscopy and the structural organization was probed by EPR using a nitroxide radical dissolved in the respective matrices. Analysis of the EPR spectra showed that the structure and dynamics of the dehydrated matrices as well as their evolution upon re-hydration differ substantially between trehalose and sucrose. The dehydrated trehalose matrix is homogeneous in terms of distribution of the residual water and spin-probe molecules. In contrast, dehydrated sucrose forms a heterogeneous matrix. It is comprised of sucrose polycrystalline clusters and several bulk water domains. The amorphous form was found only in 30% (volume) of the sucrose matrix. Re-hydration leads to a structural homogenization of the sucrose matrix, whilst in the trehalose matrix several domains develop differing in the local water/radical content and radical mobility. The molecular model of the matrices provides an explanation for the different protein-matrix dynamical coupling observed in dried ternary sucrose and trehalose matrices, and accounts for the superior efficacy of trehalose as a bioprotectant. Furthermore, for bacterial photosynthetic reaction centers it is shown that at low water content the protein-matrix coupling is modulated by the sugar/protein molar ratio in sucrose matrices only. This effect is suggested to be related to the preference for sucrose, rather than trehalose, as a bioprotective disaccharide in some anhydrobiotic organisms.

High-field EPR on membrane proteins - crossing the gap to NMR

In this review on advanced EPR spectroscopy, which addresses both the EPR and NMR communities, considerable emphasis is put on delineating the complementarity of NMR and EPR concerning the measurement of molecular interactions in large biomolecules. From these interactions, detailed information can be revealed on structure and dynamics of macromolecules embedded in solution- or solid-state environments. New developments in pulsed microwave and sweepable cryomagnet technology as well as ultrafast electronics for signal data handling and processing have pushed to new horizons the limits of EPR spectroscopy and its multifrequency extensions concerning the sensitivity of detection, the selectivity with respect to interactions, and the resolution in frequency and time domains. One of the most important advances has been the extension of EPR to high magnetic fields and microwave frequencies, very much in analogy to what happens in NMR. This is exemplified by referring to ongoing efforts for signal enhancement in both NMR and EPR double-resonance techniques by exploiting dynamic nuclear or electron spin polarization via unpaired electron spins and their electron-nuclear or electron-electron interactions. Signal and resolution enhancements are particularly spectacular for double-resonance techniques such as ENDOR and PELDOR at high magnetic fields. They provide greatly improved orientational selection for disordered samples that approaches single-crystal resolution at canonical g-tensor orientations - even for molecules with small g-anisotropies. Exchange of experience between the EPR and NMR communities allows for handling polarization and resolution improvement strategies in an optimal manner. Consequently, a dramatic improvement of EPR detection sensitivity could be achieved, even for short-lived paramagnetic reaction intermediates. Unique structural and dynamic information is thus revealed that can hardly be obtained by any other analytical techniques. Micromolar quantities of sample molecules have become sufficient to characterize stable and transient reaction intermediates of complex molecular systems - offering highly interesting applications for chemists, biochemists and molecular biologists. In three case studies, representative examples of advanced EPR spectroscopy are reviewed: (I) High-field PELDOR and ENDOR structure determination of cation-anion radical pairs in reaction centers from photosynthetic purple bacteria and cyanobacteria (Photosystem I); (II) High-field ENDOR and ELDOR-detected NMR spectroscopy on the oxygen-evolving complex of Photosystem II; and (III) High-field electron dipolar spectroscopy on nitroxide spin-labelled bacteriorhodopsin for structure-function studies. An extended conclusion with an outlook to further developments and applications is also presented.

Site-directed spin labeling EPR spectroscopy in protein research

Site-directed spin labeling (SDSL) in combination with electron paramagnetic resonance (EPR) spectroscopy has emerged as an efficient tool to elucidate the structure and the conformational dynamics of proteins under conditions close to the native state. This review article summarizes the basics as well as the recent progress in SDSL and EPR methods, especially for investigations on protein structure, protein function, and interaction of proteins with other proteins or nucleic acids. Labeling techniques as well as EPR methods are introduced and exemplified with applications to systems that have been studied in the author’s laboratory in the past 15 years, headmost the sensory rhodopsin-transducer complex mediating the photophobic response of the halophilic archaeum Natronomonas pharaonis. Further examples underline the application of SDSL EPR spectroscopy to answer specific questions about the system under investigation, such as the nature and influence of interactions of proteins with other proteins or nucleic acids. Finally, it is discussed how SDSL EPR can be combined with other biophysical techniques to combine the strengths of the different methodologies.

Structural insight into proteorhodopsin oligomers

Oligomerization has important functional implications for many membrane proteins. However, obtaining structural insight into oligomeric assemblies is challenging, as they are large and resist crystallization. We focus on proteorhodopsin (PR), a protein with seven transmembrane α-helices that was found to assemble to hexamers in densely packed lipid membrane, or detergent-solubilized environments. Yet, the structural organization and the subunit interface of these PR oligomers were unknown. We used site-directed spin-labeling together with electron spin-resonance lineshape and Overhauser dynamic nuclear polarization analysis to construct a model for the specific orientation of PR subunits within the hexameric complex. We found intersubunit distances to average 16 Å between neighboring 55 residues and that residues 177 are >20 Å apart from each other. These distance constraints show that PR has a defined and radial orientation within a hexamer, with the 55-site of the A-B loop facing the hexamer core and the 177-site of the E-F loop facing the hexamer exterior. Dynamic nuclear polarization measurements of the local solvent dynamics complement the electron spin-resonance-based distance analysis, by resolving whether protein surfaces at positions 55, 58, and 177 are exposed to solvent, or covered by protein-protein or protein-detergent contacts.

Enzymatic single-molecule kinetic isotope effects

Ensemble-based measurements of kinetic isotope effects (KIEs) have advanced physical understanding of enzyme-catalyzed reactions, but controversies remain. KIEs are used as reporters of rate-limiting H-transfer steps, quantum mechanical tunnelling, dynamics and multiple reactive states. Single molecule (SM) enzymatic KIEs could provide new information on the physical basis of enzyme catalysis. Here, single pair fluorescence energy transfer (spFRET) was used to measure SM enzymatic KIEs on the H-transfer catalyzed by the enzyme pentaerythritol tetranitrate reductase. We evaluated a range of methods for extracting the SM KIE from single molecule spFRET time traces. The SM KIE enabled separation of contributions from nonenzymatic protein and fluorophore processes and H-transfer reactions. Our work demonstrates SM KIE analysis as a new method for deconvolving reaction chemistry from intrinsic dynamics.

EPR techniques to probe insertion and conformation of spin-labeled proteins in lipid bilayers

Electron paramagnetic resonance (EPR) spectroscopy of spin-labeled membrane proteins is a valuable biophysical technique to study structural details and conformational transitions of proteins close to their physiological environment, e.g., in liposomes, membrane bilayers, and nanodiscs. Unlike in nuclear magnetic resonance spectroscopy, having only one or few specific side chains labeled at a time with paramagnetic probes makes the size of the object under investigation irrelevant in terms of technique sensitivity. As a drawback, extensive site-directed mutagenesis is required in order to analyze the properties of the protein under investigation. EPR can provide detailed information on side chain dynamics of large membrane proteins or protein complexes embedded in membranes with an exquisite sensitivity for flexible regions and on water accessibility profiles across the membrane bilayer. Moreover, distances between the two spin-labeled side chains in membrane proteins can be detected with high precision in the 1.5-6 nm range at cryogenic temperatures. The application of EPR to membrane proteins still presents some challenges in terms of sample preparation, sensitivity, and data interpretation; thus no ready-to-go methodological recipes can be given. However this chapter describes the state of the art in the application of nitroxide-based site-directed spin labeling EPR to membrane proteins, with specific focus on the different types of information which can be obtained with continuous wave and pulsed techniques and on the challenges in sample preparation and data analysis for functional and structural membrane protein studies.

Dynamical Line-Shifts in High-Field Electron Spin Resonance: Applications to Polymer Physics

High-field high-frequency Electron Paramagnetic Resonance spectroscopy (HF 2 -EPR) is a powerful tool to investigate, with ultra-high angular resolution, the rotational dynamics of complex systems like polymers, viscous fluids and glasses. Usually, information is drawn by detailed numerical analysis of the overall lineshape. Here, we present a simplified analytical model of the line shifts due to the rotational dynamics of the paramagnetic centre. The model captures the basic features of the reorientation process (time scale and size of the angular jump). It is compared with experimental results concerning the reorientation of a paramagnetic guest molecule dissolved in polystyrene. We find that, if the rotational model to describe the reorientation of the radical is consistent, the best-fit parameters yield equally acceptable best-fits of the overall spectrum by numerical simulations and dynamical line shifts by independent analytic expressions.

High-Field EPR Spectroscopic Characterization of Spin Probes in Aqueous Ionic Liquid Mixtures

Binary mixtures of the hydrophilic room temperature ionic liquid 1-butyl-3-methylimidazolium tetrafluoroborate ([bmim+][BF4 -]) and water have been probed using high-field/high-frequency electron paramagnetic resonance (EPR) spectroscopy. By adding nitroxide radicals as paramagnetic tracers, the solution structure could be assessed from typical solutes' points of view. Three probe molecules, differing in charge and hydrogen bonding affinity, have been employed: the dianionic Fremy's salt, amphiphilic TEMPO, and hydrophilic TEMPOL. High-field pulse EPR spectroscopy has been used to determine hyperfine interaction tensors and g-matrices under cryogenic conditions. Polarity-proticity plots reveal the interaction of the nitroxide moiety with apolar (TEMPO) and ionic (FS) nano-domains, depending on the probe structure. Only small variations are observed on changing the water content suggesting that the probes are well shielded from aqueous subdomains. The results indicate that addition of water in fact stabilizes IL-rich mesostructures by embedding them in pools of water.

Transmembrane signal transduction in archaeal phototaxis: the sensory rhodopsin II-transducer complex studied by electron paramagnetic resonance spectroscopy

Archaeal photoreceptors, together with their cognate transducer proteins, mediate phototaxis by regulating cell motility through two-component signal transduction pathways. This sensory pathway is closely related to the bacterial chemotactic system, which has been studied in detail during the past 40 years. Structural and functional studies applying site-directed spin labelling and electron paramagnetic resonance spectroscopy on the sensory rhodopsin II/transducer (NpSRII/NpHtrII) complex of Natronomonas pharaonis have yielded insights into the structure, the mechanisms of signal perception, the signal transduction across the membrane and provided information about the subsequent information transfer within the transducer protein towards the components of the intracellular signalling pathway. Here, we provide an overview about the findings of the last decade, which, combined with the wealth of data from research on the Escherichia coli chemotaxis system, served to understand the basic principles microorganisms use to adapt to their environment. We document the time course of a signal being perceived at the membrane, transferred across the membrane and, for the first time, how this signal modulates the dynamic properties of a HAMP domain, a ubiquitous signal transduction module found in various protein classes.

Ultrasensitive measurements of microbial rhodopsin photocycles using photochromic FRET

Microbial rhodopsins are an important class of light-activated transmembrane proteins whose function is typically studied on bulk samples. Herein, we apply photochromic fluorescence resonance energy transfer to investigate the dynamics of these proteins with sensitivity approaching the single-molecule limit. The brightness of a covalently linked organic fluorophore is modulated by changes in the absorption spectrum of the endogenous retinal chromophore that occur as the molecule undergoes a light-activated photocycle. We studied the photocycles of blue-absorbing proteorhodopsin and sensory rhodopsin II (SRII). Clusters of 2-3 molecules of SRII clearly showed a light-induced photocycle. Single molecules of SRII showed a photocycle upon signal averaging over several illumination cycles.

Determination of the 14N quadrupole coupling constant of nitroxide spin probes by W-band ELDOR-detected NMR

Nitroxide spin probe electron paramagnetic resonance (EPR) has proven to be a very successful method to probe local polarity and solvent hydrogen bonding properties at the molecular level. The g(xx) and the (14)N hyperfine A(zz) principal values are the EPR parameters of the nitroxide spin probe that are sensitive to these properties and are therefore monitored experimentally. Recently, the (14)N quadrupole interaction of nitroxides has been shown to be also highly sensitive to polarity and H-bonding (A. Savitsky et al., J. Phys. Chem. B 112 (2008) 9079). High-field electron spin echo envelope modulation (ESEEM) was used successfully to determine the P(xx) and P(yy) principal components of the (14)N quadrupole tensor. The P(zz) value was calculated from the traceless character of the quadrupole tensor. We introduce here high-field (W-band, 95 GHz, 3.5 T) electron-electron double resonance (ELDOR)-detected NMR as a method to obtain the (14)N P(zz) value directly, together with A(zz). This is complemented by W-band hyperfine sublevel correlation (HYSCORE) measurements carried out along the g(xx) direction to determine the principal P(xx) and P(yy) components. Through measurements of TEMPOL dissolved in solvents of different polarities, we show that A(zz) increases, while |P(zz)| decreases with polarity, as predicted by Savitsky et al.

Site-directed spin-labeling of DNA by the azide-alkyne 'click' reaction: nanometer distance measurements on 7-deaza-2'-deoxyadenosine and 2'-deoxyuridine nitroxide conjugates spatially separated or linked to a 'dA-dT' base pair

Nucleobase-directed spin-labeling by the azide-alkyne 'click' (CuAAC) reaction has been performed for the first time with oligonucleotides. 7-Deaza-7-ethynyl-2'-deoxyadenosine (1) and 5-ethynyl-2'-deoxyuridine (2) were chosen to incorporate terminal triple bonds into DNA. Oligonucleotides containing 1 or 2 were synthesized on a solid phase and spin labeling with 4-azido-2,2,6,6-tetramethylpiperidine 1-oxyl (4-azido-TEMPO, 3) was performed by post-modification in solution. Two spin labels (3) were incorporated with high efficiency into the DNA duplex at spatially separated positions or into a 'dA-dT' base pair. Modification at the 5-position of the pyrimidine base or at the 7-position of the 7-deazapurine residue gave steric freedom to the spin label in the major groove of duplex DNA. By applying cw and pulse EPR spectroscopy, very accurate distances between spin labels, within the range of 1-2 nm, were measured. The spin-spin distance was 1.8±0.2 nm for DNA duplex 17(dA*(7,10))⋅11 containing two spin labels that are separated by two nucleotides within one individual strand. A distance of 1.4±0.2 nm was found for the spin-labeled 'dA-dT' base pair 15(dA*(7))⋅16(dT*(6)). The 'click' approach has the potential to be applied to all four constituents of DNA, which indicates the universal applicability of the method. New insights into the structural changes of canonical or modified DNA are expected to provide additional information on novel DNA structures, protein interaction, DNA architecture, and synthetic biology.

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.

Protein-protein interaction changes in an archaeal light-signal transduction

Negative phototaxis in Natronomonas pharaonis is initiated by transient interaction changes between photoreceptor and transducer. pharaonis phoborhodopsin (ppR; also called pharaonis sensory rhodopsin II, psR-II) and the cognate transducer protein, pHtrII, form a tight 2 : 2 complex in the unphotolyzed state, and the interaction is somehow altered during the photocycle of ppR. We have studied the signal transduction mechanism in the ppR/pHtrII system by means of low-temperature Fourier-transform infrared (FTIR) spectroscopy. In the paper, spectral comparison in the absence and presence of pHtrII provided fruitful information in atomic details, where vibrational bands were identified by the use of isotope-labeling and site-directed mutagenesis. From these studies, we established the two pathways of light-signal conversion from the receptor to the transducer; (i) from Lys205 (retinal) of ppR to Asn74 of pHtrII through Thr204 and Tyr199, and (ii) from Lys205 of ppR to the cytoplasmic loop region of pHtrII that links Gly83.

DFT study of nitroxide radicals: explicit modeling of solvent effects on the structural and electronic characteristics of 4-amino-2,2,6,6-tetramethyl-piperidine-N-oxyl

An explicit DFT modeling of water surroundings on the electron paramagnetic resonance properties of 4-amino-2,2,6,6-tetramethyl-piperidine-N-oxyl (TA) has been performed. A stepwise hydration of TA is accompanied with certain changes in geometrical parameters (bond lengths and angles) and redistribution of partial electric charges in TA. An aqueous cluster of 45 water molecules can be considered as an appropriate model for a complete aqueous shell around TA, although most of the structural and electronic characteristics of TA already converge at about 10 water molecules. Water surroundings induce an increase in electron spin density on the nitrogen atom of the nitroxide fragment due to stabilization of the polar resonance structure > N(+*)-O(-) at the expense of less polar structure > N-O*. The water-induced rise of the isotropic splitting constant a(iso), calculated from the contact term of the hyperfine interaction, comprises Deltaa(iso)(rho(N2)) = 2.2-2.5 G, which is typical of experimental value for TA. There are two contributions to the solvent effect on the a(iso)(rho(N2)) value: the redistribution of spin density in the nitroxide fragment (polarity effect) and water-induced distortions of TA geometry. Microscopic variations in a hydrogen-bonded water network cause noticeable fluctuations of the splitting constant a(iso)(rho(N2)). Calculations of the atomic spin density (sigma(N2)) allowed us to compute the splitting constant from the relationship a(iso)(sigma(N2)) = Qsigma(N2), where Q = 36.2 G. A practical advantage of using this relationship is that it gives 'smoothed' values of the splitting constant, which are sensitive to the environment polarity but remain tolerant to microscopic fluctuations of the hydrogen-bonded water network around a spin-label molecule.

Spin-Label EPR for Determining Polarity and Proticity in Biomolecular Assemblies: Transmembrane Profiles

Hyperfine couplings and g-values of nitroxyl spin labels are sensitive to polarity and hydrogen bonding in the environment probed. The dependences of these electronic paramagnetic resonance (EPR) properties on environmental dielectric permittivity and proticity are reviewed. Calibrations are given, in terms of the Block-Walker reaction field and local proton donor concentration, for the nitroxides that are commonly used in spin labeling of lipids and proteins. Applications to studies of the transverse polarity profiles in lipid bilayers, which constitute the permeability barrier of biological membranes, are reviewed. Emphasis is given to parallels with the permeation profiles of oxygen and nitric oxide that are determined from spin-label relaxation enhancements by using nonlinear continuous-wave EPR and saturation recovery EPR, and with permeation profiles of D(2)O that are determined by using (2)H electron spin echo envelope modulation spectroscopy.

Spin labeling EPR

Site-directed spin labeling in combination with electron paramagnetic resonance spectroscopy has emerged as an efficient tool to elucidate the structure and conformational dynamics of biomolecules under native-like conditions. This article summarizes the basics as well as recent progress of site-directed spin labeling. Continuous wave EPR spectra analyses and pulse EPR techniques are reviewed with special emphasis on applications to the sensory rhodopsin-transducer complex mediating the photophobic response of the halophilic archaeum Natronomonas pharaonis and the photosynthetic reaction center from Rhodobacter sphaeroides R26.

Site-directed spin-labeling study of the light-harvesting complex CP29

The topology of the long N-terminal domain (approximately 100 amino-acid residues) of the photosynthetic Lhc CP29 was studied using electron spin resonance. Wild-type protein containing a single cysteine at position 108 and nine single-cysteine mutants were produced, allowing to label different parts of the domain with a nitroxide spin label. In all cases, the apoproteins were either solubilized in detergent or they were reconstituted with their native pigments (holoproteins) in vitro. The spin-label electron spin resonance spectra were analyzed in terms of a multicomponent spectral simulation approach, based on hybrid evolutionary optimization and solution condensation. These results permit to trace the structural organization of the long N-terminal domain of CP29. Amino-acid residues 97 and 108 are located in the transmembrane pigment-containing protein body of the protein. Positions 65, 81, and 90 are located in a flexible loop that is proposed to extend out of the protein from the stromal surface. This loop also contains a phosphorylation site at Thr81, suggesting that the flexibility of this loop might play a role in the regulatory mechanisms of the light-harvesting process. Positions 4, 33, 40, and 56 are found to be located in a relatively rigid environment, close to the transmembrane protein body. On the other hand, position 15 is located in a flexible region, relatively far away from the transmembrane domain.

Pulsed EPR determination of water accessibility to spin-labeled amino acid residues in LHCIIb

Membrane proteins reside in a structured environment in which some of their residues are accessible to water, some are in contact with alkyl chains of lipid molecules, and some are buried in the protein. Water accessibility of residues may change during folding or function-related structural dynamics. Several techniques based on the combination of pulsed electron paramagnetic resonance (EPR) with site-directed spin labeling can be used to quantify such water accessibility. Accessibility parameters for different residues in major plant light-harvesting complex IIb are determined by electron spin echo envelope modulation spectroscopy in the presence of deuterated water, deuterium contrast in transversal relaxation rates, analysis of longitudinal relaxation rates, and line shape analysis of electron-spin-echo-detected EPR spectra as well as by the conventional techniques of measuring the maximum hyperfine splitting and progressive saturation in continuous-wave EPR. Systematic comparison of these parameters allows for a more detailed characterization of the environment of the spin-labeled residues. These techniques are applicable independently of protein size and require approximately 10-20 nmol of singly spin-labeled protein per sample. For a residue close to the N-terminus, in a domain unresolved in the existing x-ray structures of light-harvesting complex IIb, all methods indicate high water accessibility.

Dynamic nuclear polarization enhanced nuclear magnetic resonance and electron spin resonance studies of hydration and local water dynamics in micelle and vesicle assemblies

We present a unique analysis tool for the selective detection of local water inside soft molecular assemblies (hydrophobic cores, vesicular bilayers, and micellar structures) suspended in bulk water. Through the use of dynamic nuclear polarization (DNP), the (1)H NMR signal of water is amplified, as it interacts with stable radicals that possess approximately 658 times higher spin polarization. We utilized stable nitroxide radicals covalently attached along the hydrophobic tail of stearic acid molecules that incorporate themselves into surfactant-based micelle or vesicle structures. Here, we present a study of local water content and fluid viscosity inside oleate micelles and vesicles and Triton X-100 micelles to serve as model systems for soft molecular assemblies. This approach is unique because the amplification of the NMR signal is performed in bulk solution and under ambient conditions with site-specific spin labels that only detect the water that is directly interacting with the localized spin labels. Continuous wave (cw) electron spin resonance (ESR) analysis provides rotational dynamics of the spin-labeled molecular chain segments and local polarity parameters that can be related to hydration properties, whereas we show that DNP-enhanced (1)H NMR analysis of fluid samples directly provides translational water dynamics and permeability of the local environment probed by the spin label. Our technique therefore has the potential to become a powerful analysis tool, complementary to cw ESR, to study hydration characteristics of surfactant assemblies, lipid bilayers, or protein aggregates, where water dynamics is a key parameter of their structure and function. In this study, we find that there is significant penetration of water inside the oleate micelles with a higher average local water viscosity (approximately 1.8 cP) than in bulk water, and Triton X-100 micelles and oleate vesicle bilayers mostly exclude water while allowing for considerable surfactant chain motion and measurable water permeation through the soft structure.