Distance determination in human ubiquitin by pulsed double electron-electron resonance and double quantum coherence ESR methods

Recently, distance measurements by pulsed ESR (electron spin resonance) have been obtained using pulsed DEER (double electron-electron resonance) and DQC (double quantum coherence) in SDSL (site directed spin labeling) proteins. These methods can observe long range dipole interactions (15-80A). We applied these methods to human ubiquitin proteins. The distance between the 20th and the 35th cysteine was estimated in doubly spin labeled human ubiquitin. Pulsed DEER requires two microwave sources. However, a phase cycle is not usually required in this method. On the other hand, DQC-ESR at X-band ( approximately 9GHz) can acquire a large echo signal by using pulses of short duration and high power, but this method has an ESEEM (electron spin echo envelope modulation) problem. We used a commercial pulsed ESR spectrometer and compared these two methods.     

Maltose Binding Protein Is Partially Structured in Its Molten Globule State

Seven double cysteine mutants of maltose binding protein (MBP) were generated with one each in the active cleft at position 298 and the second cysteine distributed over both domains of the protein. These cysteines were spin labeled and distances between the labels in biradical pairs determined by pulsed double electron–electron resonance (DEER) measurements. The values were compared with theoretical predictions of distances between the labels in biradicals constructed by molecular modeling from the crystal structure of MBP without maltose and were found to be in excellent agreement. MBP is in a molten globule state at pH 3.3 and is known to still bind its substrate maltose. The nitroxide spin label was sufficiently stable under these conditions. In preliminary experiments, DEER measurements were carried out with one of the mutants yielding a broad distance distribution as was to be expected if there is no explicit tertiary structure and the individual helices pointing into all possible directions.     

Dead-time free measurement of dipole-dipole interactions between electron spins. 2000

A four-pulse version of the pulse double electron–electron resonance (DEER) experiment is presented, which is designed for the determination of interradical distances on a nanoscopic lengthscale. With the new pulse sequence electron–electron couplings can be studied without dead-time artifacts, so that even broad distributions of electron–electron distances can be characterized. A version of the experiment that uses a pulse train in the detection period exhibits improved signal-to-noise ratio. Tests on two nitroxide biradicals with known length indicate that the accessible range of distances extends from about 1.5 to 8 nm. The four-pulse DEER spectra of an ionic spin probe in an ionomer exhibit features due to probe molecules situated both on the same and on different ion clusters. The former feature provides information on the cluster size and is inaccessible with previous methods.     

Observer-selective double electron-electron-spin resonance, a pulse sequence to improve orientation selection

By pulsed double electron-electron resonance (DEER), distances between spin labels in disordered systems up to 8 nm can be measured. In addition, the relative orientation of the interacting radicals can be determined, provided that the bandwidth of the pulses is sufficiently small. On the other hand, the bandwidth has to exceed the dipolar interaction considerably, because otherwise the DEER modulations become distorted and the modulation depth decreases, making distance determination impossible. Therefore, small bandwidths, i.e. long pulses, place a lower limit on the distance that can be determined. Two new pulse sequences, observer-selective DEER (os-DEER) and dead-time free os-DEER, are introduced that make it possible to use long observer pulses with bandwidths that are smaller than the dipolar interaction. The new pulse sequences do not suffer from the distortions caused by the limited bandwidth of the observer pulses, as demonstrated by measurements on a nitroxide biradical. With observer pulses of 140 ns, i.e., significantly longer than the 32 ns used in the conventional DEER sequence, a dipolar interaction of 7.8 MHz has been measured.     

An NMR Investigation of the Conformational Effect of Nitroxide Spin Labels on Ala-Rich Helical Peptides

Nitroxide spin labels, in conjunction with electron spin resonance (ESR) experiments, are extensively employed to probe the structure and dynamics of biomolecules. One of the most ubiquitous spin labeling reagents is the methanethiosulfonate spin label which attaches a spin label selectively to Cys residues via a disulfide bond (Cys-SL). However, the actual effect of the nitroxide spin label upon the conformation of the peptide or protein cannot be unambiguously determined by ESR. In this study, a series of 16-residue Ala-rich helical peptides was characterized by nuclear magnetic resonance techniques. The C_αH chemical shift analysis, NOEs, and³J_NHαcoupling constants for peptides with no Cys, free Cys, and Cys-SL (with the N–O group reduced) were compared. These results indicate that while replacement of an Ala with a Cys residue causes a loss of overall helical structure, the Cys-SL residue is helix supporting, as would be expected for a non-β-branched aliphatic amino acid. Thus, the Cys-SL residue does not perturb helical structure and, instead, exhibits helix-stabilizing characteristics similar to that found for Ala, Met, and Leu.     

The determination of pair distance distributions by pulsed ESR using Tikhonov regularization

Pulsed ESR techniques with the aid of site-directed spin labeling have proven useful in providing unique structural information about proteins. The determination of distance distributions in electron spin pairs directly from the dipolar time evolution of the pulsed ESR signals by means of the Tikhonov regularization method is reported. The difficulties connected with numerically inverting this ill-posed mathematical problem are clearly illustrated. The Tikhonov regularization with the regularization parameter determined by the L-curve criterion is then described and tested to confirm its accuracy and reliability. The method is applied to recent experimental results on doubly labeled proteins that have been studied using two pulsed ESR techniques, double quantum coherence (DQC) ESR and double electron-electron resonance (DEER). The extracted distance distributions are able to provide valuable information about the conformational constraints in various partially folded states of proteins. This study supplies a mathematically reliable method for extracting pair distributions from pulsed ESR experimental data and has extended the use of pulsed ESR to provide results of greater value for structural biology.     

Isotope selection in distance measurements between nitroxides

Self-assembly of spin-labeled synthetic macromolecules or biomacromolecules can lead to structures that contain more than two nitroxide radicals. Label-to-label distance distributions are then poorly resolved since established electron paramagnetic resonance techniques for distance measurements cannot select between the different pairs of nitroxides. A separation into different contributions can be achieved by partially labeling the nitroxide radicals by (15)N or by deuterium and applying pulse electron electron double resonance techniques. With (15)N labeling, strong suppression of either the (14)N or the (15)N contribution can be achieved by suitable choices of the excitation bandwidths and frequencies of the observer subsequence and pump pulse and linear combination of data sets. With deuterium labeling, interactions between only the isotope-labeled nitroxides can be selected by a two-dimensional version of the four-pulse double electron electron resonance experiment. This selection is based on the deep electron spin echo envelope modulation of deuterated nitroxides.     

Dead-time free measurement of dipole-dipole interactions between electron spins

A four-pulse version of the pulse double electron-electron resonance (DEER) experiment is presented, which is designed for the determination of interradical distances on a nanoscopic length-scale. With the new pulse sequence electron-electron couplings can be studied without dead-time artifacts, so that even broad distributions of electron-electron distances can be characterized. A version of the experiment that uses a pulse train in the detection period exhibits improved signal-to-noise ratio. Tests on two nitroxide biradicals with known length indicate that the accessible range of distances extends from about 1.5 to 8 nm. The four-pulse DEER spectra of an ionic spin probe in an ionomer exhibit features due to probe molecules situated both on the same and on different ion clusters. The former feature provides information on the cluster size and is inaccessible with previous methods.     

Self-Aggregation and Orientation of the Ion Channel-Forming Zervamicin IIA in the Membranes of ePC Vesicles Studied by cw EPR and ESEEM Spectroscopy

The ion channel-forming peptide antibiotic zervamicin A was studied in egg phosphocholin lipid membranes of large multilamellar vesicles (LMV) at 77 K. Continuous wave electron paramagnetic resonance (EPR) and electron spin echo envelope modulation (ESEEM) methods combined with site-specific electron spin labeling were used to study the aggregation and immersion depth of two analog molecules, i.e., each monolabeled either at the N- or C-terminal end of the helical molecule. Analysis of the shape of the EPR spectra indicates that zervamicin molecules form aggregates in which the dipolar interaction between the spin labels at the N-terminus is substantially larger than that between the labels at the C-terminus. The ESEEM method was used to study the interaction between the nitroxide radical spin labels of the zervamicin molecules and deuterium nuclei in LMV, which were prepared using a D₂O buffer. It is established that the largest amplitude of deuterium modulation of the unpaired electron is observed for zervamicin molecules labeled at the N-terminus. Based on the analysis of the Fourier parameters of the deuterium modulated spectrum, a model of the immersion depth of the terminal ends of the zervamicin molecule in a lipid bilayer is formulated. All of the spin labels at the N-terminus are grouped at the lipid–water interface, whereas 60% of labels at the C-terminus are located at the lipid–water interface and 40% are more deeply inserted into the lipid bilayer.     

Resolving Conformational and Rotameric Exchange in Spin-Labeled Proteins Using Saturation Recovery EPR

The function of many proteins involves equilibria between conformational substates, and to elucidate mechanisms of function it is essential to have experimental tools to detect the presence of conformational substates and to determine the time scale of exchange between them. Site-directed spin labeling (SDSL) has the potential to serve this purpose. In proteins containing a nitroxide side chain (R1), multicomponent electron paramagnetic resonance (EPR) spectra can arise either from equilibria involving different conformational substates or rotamers of R1. To employ SDSL to uniquely identify conformational equilibria, it is thus essential to distinguish between these origins of multicomponent spectra. Here we show that this is possible based on the time scale for exchange of the nitroxide between distinct environments that give rise to multicomponent EPR spectra; rotamer exchange for R1 lies in the ≈0.1–1 μs range, while conformational exchange is at least an order of magnitude slower. The time scales of exchange events are determined by saturation recovery EPR, and in favorable cases, the exchange rate constants between substates with lifetimes of approximately 1–70 μs can be estimated by the approach.     

Distance between a native cofactor and a spin label in the reaction centre of Rhodobacter sphaeroides by a two-frequency pulsed electron paramagnetic resonance method and molecular dynamics simulations

The distance between the paramagnetic state of a native cofactor and a spin label is measured in the photosynthetic reaction centre from the bacterium Rhodobacter sphaeroides R26. A two-frequency pulsed electron paramagnetic resonance method [double-electron-electron spin resonance (DEER)] is used. A distance of 3.05 nm between the semiquinone anion state of the primary acceptor (Q(A)) and the spin label at the native cysteine at position 156 in the H-subunit is found. Molecular-dynamics (MD) simulations are performed to interpret the distance. A 6 ns run comprising the entire RC protein yields a distance distribution that is close to the experimental one. The average distance found by the MD simulation is smaller than the distance obtained by DEER by at least 0.2 nm. To better represent the experiments performed at low temperature (60K), a MD method to mimic the freezing-in of the room-temperature conformations is introduced. Both MD methods yield similar distances, but the second method has a trend towards a wider distance distribution.     

An electron microscopic study of the archaeal feast/famine regulatory protein: 3. Labeling of the N-terminus using nickel

Histidine residues added to the N-terminus of a polypeptide (i.e. a His-tag) was used, for the first time to our knowledge, for electron labeling of the protein upon its electron spectroscopic imaging. Originally such a His-tag was developed by another group to purify modified proteins by taking advantage of their affinity to nickel. The feast/famine regulatory protein pot0434017 (FL11) was modified by adding six His residues to its N-terminus, so that each His pair would chelate a nickel ion. An electron microscope was operated at 200 KeV, and the electrons that lost the energy by ~875 eV upon interaction with the metal were selectively focused. The majority, 60–70%, of the spots detected in the electron micrographs were paired by distances shorter than 80 Å, and over 70% of them were paired by distances shorter than 40 Å. It is concluded that the protein molecules formed dimers, and the termini of most of the protein molecules were labeled with nickel by this method.     

TR-EPR of single and double spin-labeled C60 derivatives in frozen matrices

Time-resolved electron paramagnetic resonance spectra of two single spin-labeled and two double spin-labeled C₆₀ derivatives in frozen solution are recorded with pulsed laser excitation and 100 ns time resolution. Quartet and quintet excited species are detected which arise from the electron spin coupling of the triplet excited fullerene moiety with the unpaired spin(s) of the nitroxide label(s). Despite the similar molecular structure, in both series of single and double labeled derivatives a different behavior was found, which is due to substantial difference of the energy of exchange coupling.     

Measuring Cu2+-Nitroxide Distances Using Double Electron–Electron Resonance and Saturation Recovery

Distance measurements were obtained between a bound Cu²⁺ and a spin label on two polypeptides of differing length using the double electron–electron resonance (DEER) and saturation recovery experiments. Distance distributions obtained from the DEER results resolved differences between the average distance and distribution of distances for each peptide. An average distance was also obtained for each peptide using the relaxation-based saturation recovery experiment. Predicted average distances for the relaxation-based method, <r_ESR>, were calculated using the distance distributions from the DEER experiment. The predicted <r_ESR> values were similar to those measured by saturation recovery; both were biased to shorter values compared with the DEER results. The breadth of the distance distributions had a significant effect on the average distance measured by saturation recovery. This work highlights the advantage of using DEER to measure metal-nitroxide distances in that the average distances measured are less biased than in relaxation-based techniques.     

Double Electron–Electron Resonance Between Trapped Electron and Hole in a Semiconductor

We demonstrate the spin interactions between dispersedly trapped electrons and holes in a semiconductor using the double electron–electron resonance (DEER) method of the pulsed electron paramagnetic resonance (EPR) techniques. An aluminum-doped titanium dioxide crystal is adopted as a spin system, in which optically generated electrons and holes are trapped, to reveal EPR signals that appear close to each other at a selected crystal orientation under an external magnetic field. We used the four-pulse DEER method by applying two microwave frequencies to a microwave cavity for pumping electrons and probing holes at the optimum temperature of 32 K. The dipolar modulation in the probed signal by pumping interacting spins was successfully detected. The observed non-oscillating decay shape indicates that the detected interaction is caused by widely distributed trapped electron and hole spins over long distances. We were able to extract a spin-pair distribution function by the first derivative of a background-corrected curve, referring to a previously reported method.     

Pulsed dipolar spectroscopy distance measurements in biomacromolecules labeled with Gd(III) markers

This work demonstrates the feasibility of using Gd(III) tags for long-range Double Electron Electron Resonance (DEER) distance measurements in biomacromolecules. Double-stranded 14- base pair Gd(III)-DNA conjugates were synthesized and investigated at K(a) band. For the longest Gd(III) tag the average distance and average deviation between Gd(III) ions determined from the DEER time domains was about 59±12?. This result demonstrates that DEER measurements with Gd(III) tags can be routinely carried out for distances of at least 60?, and analysis indicates that distance measurements up to 100? are possible. Compared with commonly used nitroxide labels, Gd(III)-based labels will be most beneficial for the detection of distance variations in large biomacromolecules, with an emphasis on large scale changes in shape or distance. Tracking the folding/unfolding and domain interactions of proteins and the conformational changes in DNA are examples of such applications.     

Analysis of nitroxide spin label motion in a protein-protein complex using multiple frequency EPR spectroscopy

X- and W-band EPR spectra, at room and low temperatures, are reported for nitroxide spin labels attached to cysteine residues selectively introduced into two proteins, the DNase domain of colicin-E9 and its immunity protein, Im9. The dynamics of each site of attachment on the individual proteins and in the tight DNase-Im9 complex have been analysed by computer simulations of the spectra using a model of Brownian dynamics trajectories for the spin label and protein. Ordering potentials have been introduced to describe mobility of labels restricted by the protein domain. Label mobility varies with position from completely immobilised, to motionally restricted and to freely rotating. Bi-modal dynamics of the spin label have been observed for several sites. We show that W-band spectra are particularly useful for detection of anisotropy of spin label motion. On complex formation significant changes are observed in the dynamics of labels at the binding interface region. This work reveals multi-frequency EPR as a sensitive and valuable tool for detecting conformational changes in protein structure and dynamics especially in protein-protein complexes.     

Structure and dynamics of annexin 12 bound to a planar lipid bilayer

Site directed spin labeling is used to investigate the protein annexin 12 absorbed on a single planar phospholipid bilayer of approximately 2-3 cm(2). Electron paramagnetic resonance spectra of nitroxide side chain at several topological sites reveal a conserved tertiary fold of the protein in the absorbed state, in agreement with earlier diffraction results. The angular dependent spectra of the two-dimensional microcrystals are shown to provide information on the degree of ordering of spin labels in a alpha-helix and in turn on the orientation of the alpha-helix with respect to the surface.     

The Temperature Dependence of Nitroxide Spin–Label Interaction Parameters: a High-Field EPR Study of Intramolecular Motional Contributions

High-field W-band electron paramagnetic resonance (EPR) spectroscopy was utilized to study the temperature dependence of the magnetic interaction parameters (g-, hyperfine-, quadrupole tensors) of two types of doublet-state nitroxide spin probes in glass-forming ortho-terphenyl solution: a five-membered ring system of pyrroline type (model for the commonly used methane thiosulfonate spin label) and a six-membered ring system of piperidine type (model for the commonly used TOAC spin label). The analysis of the g- and hyperfine tensors in terms of their isotropic and anisotropic parts reveals at least two mechanisms of motion that are responsible for the temperature dependence of the interaction parameters. The first mechanism is attributed to the overall small-angle motion of the nitroxide molecule in the glassy matrix; it leads to an averaging of the anisotropies of the EPR parameters. The second mechanism originates in an intramolecular out-of-plane motion of oxygen in the nitroxide group. This type of motion is evidenced by comparing the experimental findings for the spin-interaction parameters with the results of density functional theory calculations. The harmonic oxygen out-of-plane vibrations result in a variation of both the isotropic and anisotropic parts of the g- and hyperfine tensors. In contrast, the quadrupole tensor is not influenced by this vibration mechanism in the temperature range under study (90–240 K). Consequences of the applicability of such typical nitroxide radicals for probing details of their protein environment and for studying librational dynamics in frozen solutions are discussed.     

Two-Dimensional Distance Correlation Maps from Pulsed Triple Electron Resonance (TRIER) on Proteins with Three Paramagnetic Centers

Recently, we introduced the pulsed triple electron resonance (TRIER) experiment, which correlates dipolar frequencies of molecules with three electron spins. These correlation patterns contain valuable information: in combination with double electron–electron resonance (DEER) they allow to interpret distance distributions of biological systems that exist in more than one conformation. Together with an improved sequence and new data processing, we were now for the first time able to obtain two-dimensional distance correlation maps of the previously investigated model compounds as well as of spin-labeled proteins. For this we applied two-dimensional approximate Pake transformation to TRIER data. This enabled us to get distance correlation plots from two triple-labeled protein samples that were in good agreement with DEER data and simulations. With such information it should then be possible to assign peaks in DEER distance distributions for macromolecules that can exist in more than one conformation.