Models for slow anisotropic rotational diffusion in saturation transfer electron paramagnetic resonance at 9 and 35 GHz

A Highly Ordered Nitroxide Side Chain for Distance Mapping and Monitoring Slow Structural Fluctuations in Proteins

Site-directed spin labeling electron paramagnetic resonance (SDSL-EPR) is an established tool for exploring protein structure and dynamics. Although nitroxide side chains attached to a single cysteine via a disulfide linkage are commonly employed in SDSL-EPR, their internal flexibility complicates applications to monitor slow internal motions in proteins and to structure determination by distance mapping. Moreover, the labile disulfide linkage prohibits the use of reducing agents often needed for protein stability. To enable the application of SDSL-EPR to the measurement of slow internal dynamics, new spin labels with hindered internal motion are desired. Here, we introduce a highly ordered nitroxide side chain, designated R9, attached at a single cysteine residue via a non-reducible thioether linkage. The reaction to introduce R9 is highly selective for solvent-exposed cysteine residues. Structures of R9 at two helical sites in T4 Lysozyme were determined by X-ray crystallography and the mobility in helical sequences was characterized by EPR spectral lineshape analysis, Saturation Transfer EPR, and Saturation Recovery EPR. In addition, interspin distance measurements between pairs of R9 residues are reported. Collectively, all data indicate that R9 will be useful for monitoring slow internal structural fluctuations, and applications to distance mapping via dipolar spectroscopy and relaxation enhancement methods are anticipated.

Supplementary Information

The online version contains supplementary material available at 10.1007/s00723-023-01618-8.

High field/high frequency saturation transfer electron paramagnetic resonance spectroscopy: increased sensitivity to very slow rotational motions

Saturation transfer electron paramagnetic resonance (ST-EPR) spectroscopy has been employed to characterize the very slow microsecond to millisecond rotational dynamics of a wide range of nitroxide spin-labeled proteins and other macromolecules in the past three decades. The vast majority of this previous work has been carried out on spectrometers that operate at X-band ( approximately 9 GHz) microwave frequency with a few investigations reported at Q-band ( approximately 34 GHz). EPR spectrometers that operate in the 94-250-GHz range and that are capable of making conventional linear EPR measurements on small aqueous samples have now been developed. This work addresses potential advantages of utilizing these same high frequencies for ST-EPR studies that seek to quantitatively analyze the very slow rotational dynamics of spin-labeled macromolecules. For example, the uniaxial rotational diffusion (URD) model has been shown to be particularly applicable to the study of the rotational dynamics of integral membrane proteins. Computational algorithms have been employed to define the sensitivity of ST-EPR signals at 94, 140, and 250 GHz to the correlation time for URD, to the amplitude of constrained URD, and to the orientation of the spin label relative to the URD axis. The calculations presented in this work demonstrate that these higher microwave frequencies provide substantial increases in sensitivity to the correlation time for URD, to small constraints in URD, and to the geometry of the spin label relative to the URD axis as compared with measurements made at X-band. Moreover, the calculations at these higher frequencies indicate sensitivity to rotational motions in the 1-100-ms time window, particularly at 250 GHz, thereby extending the slow motion limit for ST-EPR by two orders of magnitude relative to X- and Q-bands.

The sensitivity of saturation transfer electron paramagnetic resonance spectra to restricted amplitude uniaxial rotational diffusion

Computational methods have been developed to model the effects of constrained or restricted amplitude uniaxial rotational diffusion (URD) on saturation transfer electron paramagnetic resonance (ST-EPR) signals observed from nitroxide spin labels. These methods, which have been developed to model the global rotational motion of intrinsic membrane proteins that can interact with the cytoskeleton or other peripheral proteins, are an extension of previous work that described computationally efficient algorithms for calculating ST-EPR spectra for unconstrained URD (Hustedt and Beth, 1995, Biophys. J. 69:1409-1423). Calculations are presented that demonstrate the dependence of the ST-EPR signal (V'(2)) on the width (Delta) of a square-well potential as a function of the microwave frequency, the correlation time for URD, and the orientation of the spin-label with respect to the URD axis. At a correlation time of 10 micros, the V'(2) signal is very sensitive to Delta in the range from 0 to 60 degrees, marginally sensitive from 60 degrees to 90 degrees, and insensitive beyond 90 degrees. Sensitivity to Delta depends on the correlation time for URD with higher sensitivity to large values of Delta at the shorter correlation times, on the microwave frequency, and on the orientation of the spin-label relative to the URD axis. The computational algorithm has been incorporated into a global nonlinear least-squares analysis approach, based upon the Marquardt-Levenberg method (Blackman et al., 2001, Biophys. J. 81:3363-3376). This has permitted determination of the correlation time for URD and the width of the square-well potential by automated fitting of experimental ST-EPR data sets obtained from a spin-labeled membrane protein and provided a new automated method for analysis of data obtained from any system that exhibits restricted amplitude URD.

Simulation of saturation transfer electron paramagnetic resonance spectra for rotational motion with restricted angular amplitude

We have simulated both conventional (V1) and saturation transfer (V'2) electron paramagnetic resonance spectra for the case of Brownian rotational diffusion restricted in angular amplitude. Numerical solutions of the diffusion-coupled Bloch equations were obtained for an axially symmetric 14N nitroxide spin label with its principal axis rotating within a Gaussian angular distribution of full width delta theta at half maximum. Spectra were first calculated for a macroscopically oriented system with cylindrical symmetry (e.g., a bundle of muscle fibers or a stack of membrane bilayers), with the Gaussian angular distribution centered at theta 0 with respect to the magnetic field. These spectra were then summed over theta 0 to obtain the spectrum of a randomly oriented sample (e.g., a dispersion of myofibrils or membrane vesicles). The angular amplitude delta theta was varied from 0 degrees, corresponding to isotropic motion (order parameter = 0). For each value of delta theta, the rotational correlation time, tau r, was varied from 10(-7) to 10(-2) s, spanning the range from maximal to minimal saturation transfer. We provide plots that illustrate the dependence of spectral parameters on delta theta and tau r. For an oriented system, the effects of changing delta theta and tau r are easily distinguishable, and both parameters can be determined unambiguously by comparing simulated and experimental spectra. For a macroscopically disordered system, the simulated spectra are still quite sensitive to delta theta, but a decrease in tau r produces changes similar to those from an increase in delta theta. If delta theta can be determined independently, then the results of the present study can be used to determine tau r from experimental spectra. Similarly, if tau r is known, then delta theta can be determined.

Investigation of biological systems by high resolution 2-mm wave band ESR

The application of high resolution ESR to the investigation of various biological systems is discussed. The advantages of the technique in the study of structural, conformational and dynamic characteristics have been exemplified by spin-labeled human serum albumin, egg lysozyme, liposome membranes, inverted micelles, alpha-chymotrypsin, cotton fiber and cellulose. The polarity of the microenvironment and the mechanism of molecular mobility of the objects under study have been determined. The combination of high resolution and saturation transfer techniques has been shown to give a detailed analysis of very slow molecular motions in biological objects. Peroxide radicals in biosystems have been identified from their ESR spectra at the 2-mm wave band.

A spin label ESR and saturation transfer ESR study of alpha-tocopherol containing model membranes

An investigation into the effect of alpha-tocopherol on phospholipid model membranes has been carried out by electron spin resonance (ESR) and saturation transfer ESR. The use of stearic acid and of perdeutero -di-t-butyl nitroxide spin probes has allowed us to monitor, in particular, the effect of alpha-tocopherol on both the phospholipid chain order and the phospholipid chain mobility. The results obtained are mainly consistent with a differing action of alpha-tocopherol in the gel and in the liquid crystalline phases: in the former it induces a decrease of order and an increase in fluidity; while in the latter phase an indication of a slight increase in ordering and a clear decrease in fluidity are registered.

Selective detection of the rotational dynamics of the protein-associated lipid hydrocarbon chains in sarcoplasmic reticulum membranes

We have developed a saturation transfer EPR (ST-EPR) method to measure selectively the rotational dynamics of those lipids that are motionally restricted by integral membrane proteins and have applied this methodology to measure lipid-protein interactions in native sarcoplasmic reticulum (SR) membranes. This analysis involves the measurement of spectral saturation using a series of six stearic acid spin labels that are labeled with a nitroxide at different carbon atom positions. A large amount of spectral saturation is observed for spin labels in native SR membranes, but not for spin labels in dispersions of extracted SR lipids, implying that the motional properties of those lipids interacting with the Ca-ATPase, i.e., the boundary or annular lipid, can be directly measured without the need for spectral subtraction procedures. A comparison of the motional properties of the restricted lipid, measured by ST-EPR, with those measured by digital subtraction of conventional EPR spectra qualitatively agree, for in both cases the Ca-ATPase restricts the rotational mobility of a population of lipids, whose rotational mobility increases as the nitroxide is positioned toward the center of the bilayer. However, the ability of ST-EPR to directly measure the motionally restricted lipid in a model-independent means provides the greater precision necessary to measure small changes in the rotational dynamics of the lipid at the protein-lipid interface, providing a valuable tool in clarifying the relationship between the physical nature of the protein-lipid interface and membrane function.

Methodology for increased precision in saturation transfer electron paramagnetic resonance studies of rotational dynamics

Microsecond rotational motions of nitroxide spin labels are measured primarily with saturation transfer electron paramagnetic resonance (ST-EPR). In the present study we have used model system experiments to quantitatively evaluate different ST-EPR spectral parameters, both in-phase and out-of-phase, with an emphasis on techniques for suppressing the interference from weakly immobilized probes. Analyses of both systematic and random errors show that maximum sensitivity to small changes in correlation time and minimum ambiguity of interpretation are best achieved by combining measurements of both spectral line-shape, i.e., the ratio of line-heights, and spectral intensity, i.e., the absolute amplitude of either a position within a spectrum or a spectral integral. Errors in the measurement of correlation times for the two types of parameters tend to be complementary. Integrated intensity parameters are particularly useful in measuring microsecond probe motions in the presence of weakly immobilized components. We confirm that integrated intensity parameters are sometimes effective in rejecting signals from weakly immobilized probes, but the effectiveness of this rejection is more limited than previously supposed and depends on the type of parameter being measured. We describe procedures for evaluating and minimizing errors due to weakly immobilized probes, emphasizing the advantages of a new kind of intensity parameter obtained from integrated in-phase spectra. We provide detailed descriptions of experimental procedures, along with calibration plots of the most useful spectral parameters vs. rotational correlation time, which should make it possible for workers in other laboratories, using different instruments and sample geometries, to reproduce spectra quantitatively and to make accurate correlation time measurements.

Applications of new saturation transfer electron paramagnetic resonance methodology to the rotational dynamics of the Ca-ATPase in sarcoplasmic reticulum membranes

The presence of small amounts of weakly immobilized probes can result in large systematic errors in the measurement of correlation times (tau r) from saturation transfer EPR spectra. However, we have recently developed experimental methodology to minimize these errors (Squier and Thomas, Biophys. J., 49:921-935). In the present study we have applied this methodology to the measurement of the rotational motion of the Ca-ATPase in sarcoplasmic reticulum. This analysis involves the estimate of tau r from line-shape parameters (spectral line-height ratios) and intensity parameters (spectral integral), coupled with digital subtractions to remove spectral components corresponding to weakly immobilized probes. We have analyzed the ST-EPR spectra of the Ca-ATPase over a range of temperatures and find that, unlike line-shape parameters, intensity parameters are little affected by the subtraction of the weakly immobilized spectral component (W). Thus, tau r values from intensity parameters are a more reliable measurement of rotational motion. As reported previously, an analysis with line-shape parameters yields a nonlinear Arrhenius plot of protein mobility. However, the plot is linear when intensity parameters or corrected spectra are used, consistent with the theory for the hydrodynamic properties of a membrane protein of unchanging size and shape in a fluid bilayer. An analysis with line-shape parameters yields different effective tau r values in different spectral regions, and these tau r values are temperature-dependent. However, correction of spectra for W yields temperature-independent tau r ratios, indicating that the motional anisotropy is temperature-independent. Obtaining a good match for the weakly immobilized spectral component remains a major difficulty in the quantitative analysis of ST-EPR spectra using line-shape parameters. This study shows that intensity parameters can be used to avoid this problem, making the ST-EPR technique applicable in cases that were previously resistant to analysis.

New biophysical techniques and their application to the study of membranes

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