Rational design of dinitroxide biradicals for efficient cross-effect dynamic nuclear polarization

A series of 37 dinitroxide biradicals have been prepared and their performance studied as polarizing agents in cross-effect DNP NMR experiments at 9.4 T and 100 K in 1,1,2,2-tetrachloroethane (TCE). We observe that in this regime the DNP performance is strongly correlated with the substituents on the polarizing agents, and electron and nuclear spin relaxation times, with longer relaxation times leading to better enhancements. We also observe that deuteration of the radicals generally leads to better DNP enhancement but with longer build-up time. One of the new radicals introduced here provides the best performance obtained so far under these conditions.

Gd(III) complexes for electron-electron dipolar spectroscopy: Effects of deuteration, pH and zero field splitting

Spectral parameters of Gd(III) complexes are intimately linked to the performance of the Gd(III)-nitroxide or Gd(III)-Gd(III) double electron-electron resonance (DEER or PELDOR) techniques, as well as to that of relaxation induced dipolar modulation enhancement (RIDME) spectroscopy with Gd(III) ions. These techniques are of interest for applications in structural biology, since they can selectively detect site-to-site distances in biomolecules or biomolecular complexes in the nanometer range. Here we report relaxation properties, echo detected EPR spectra, as well as the magnitude of the echo reduction effect in Gd(III)-nitroxide DEER for a series of Gadolinium(III) complexes with chelating agents derived from tetraazacyclododecane. We observed that solvent deuteration does not only lengthen the relaxation times of Gd(III) centers but also weakens the DEER echo reduction effect. Both of these phenomena lead to an improved signal-to-noise ratios or, alternatively, longer accessible distance range in pulse EPR measurements. The presented data enrich the knowledge on paramagnetic Gd(III) chelate complexes in frozen solutions, and can help optimize the experimental conditions for most types of the pulse measurements of the electron-electron dipolar interactions.

Shape Persistence of Polyproline II Helical Oligoprolines

Oligoprolines are commonly used as molecular scaffolds. Past studies on the persistence length of their secondary structure, the polyproline II (PPII) helix, and on the fraction of backbone cis amide bonds have provided conflicting results. We resolved this debate by studying a series of spin-labeled proline octadecamers with EPR spectroscopy. Distance distributions between an N-terminal Gd(III) -DOTA (DOTA=1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid) label and a nitroxide label at one of five evenly spaced backbone sites allowed us to discriminate between the flexibility of the PPII helix and the cis amide contributions. An upper limit of 2 % cis amide bonds per residue was found in a 7:3 (v/v) water/glycerol mixture, whereas cis amides were not observed in trifluoroethanol. Extrapolation of Monte Carlo models from the glass transition to ambient temperature predicts a persistence length of ≈3-3.5 nm in both solvents. The method is generally applicable to any type of oligomer for which the persistence length is of interest.

Sensitivity enhancement by population transfer in Gd(iii) spin labels

Frequency-swept chirp pulses with bandwidths > 1 GHz rearrange electron spin populations in the S = 7/2 spin of Gd(iii) ions for better sensitivity, as demonstrated with distance measurements between Gd(iii) ions.

RIDME Spectroscopy with Gd(III) Centers

The relaxation induced dipolar modulation enhancement (RIDME) technique is applied at W-band microwave frequencies around 94 GHz to a pair of Gd(III) complexes that are connected by a rodlike spacer, and the extraction of the interspin distance distribution is discussed. A dipolar pattern derived from RIDME experimental data is a superposition of Pake-like dipolar patterns corresponding to the fundamental dipolar interaction and higher harmonics thereof. Intriguingly, the relative weights of the stretched patterns do not depend significantly on mixing time. As much larger modulation depths can be achieved than in double electron-electron resonance distance measurements at the same frequency, Gd(III)-Gd(III) RIDME may become attractive for structural characterization of biomacromolecules and biomolecular complexes.

EPR-aided approach for solution structure determination of large RNAs or protein-RNA complexes

High-resolution structural information on RNA and its functionally important complexes with proteins is dramatically underrepresented compared with proteins but is urgently needed for understanding cellular processes at the molecular and atomic level. Here we present an EPR-based protocol to help solving large RNA and protein-RNA complex structures in solution by providing long-range distance constraints between rigid fragments. Using enzymatic ligation of smaller RNA fragments, large doubly spin-labelled RNAs can be obtained permitting the acquisition of long distance distributions (>80 Å) within a large protein-RNA complex. Using a simple and fast calculation in torsion angle space of the spin-label distributions with the program CYANA, we can derive simple distance constraints between the spin labels and use them together with short-range distance restraints derived from NMR to determine the structure of a 70 kDa protein-RNA complex composed of three subcomplexes.

Conformational cycle of the vitamin B12 ABC importer in liposomes detected by double electron-electron resonance (DEER)

Double electron-electron resonance is used here to investigate intermediates of the transport cycle of the Escherichia coli vitamin B12 ATP-binding cassette importer BtuCD-F. Previously, we showed the ATP-induced opening of the cytoplasmic gate I in TM5 helices, later confirmed by the AMP-PNP-bound BtuCD-F crystal structure. Here, other key residues are analyzed in TM10 helices (positions 307 and 322) and in the cytoplasmic gate II, i.e. the loop between TM2 and TM3 (positions 82 and 85). Without BtuF, binding of ATP induces detectable changes at positions 307 and 85 in BtuCD in liposomes. Together with BtuF, ATP triggers the closure of the cytoplasmic gate II in liposomes (reported by both positions 82 and 85). This forms a sealed cavity in the translocation channel in agreement with the AMP-PNP·BtuCD-F x-ray structure. When vitamin B12 and AMP-PNP are simultaneously present, the extent of complex formation is reduced, but the short 82-82 interspin distance detected indicates that the substrate does not affect the closed conformation of this gate. The existence of the BtuCD-F complex under these conditions is verified with spectroscopically orthogonal nitroxide and Gd(III)-based labels. The cytoplasmic gate II remains closed also in the vanadate-trapped state, but it reopens in the ADP-bound state of the complex. Therefore, we suggest that the substrate likely trapped in ATP·BtuCD-F can be released after ATP hydrolysis but before the occluded ADP-bound conformation is reached.

Solid-phase polarization matrixes for dynamic nuclear polarization from homogeneously distributed radicals in mesostructured hybrid silica materials

Mesoporous hybrid silica-organic materials containing homogeneously distributed stable mono- or dinitroxide radicals covalently bound to the silica surface were developed as polarization matrixes for solid-state dynamic nuclear polarization (DNP) NMR experiments. For TEMPO-containing materials impregnated with water or 1,1,2,2-tetrachloroethane, enhancement factors of up to 36 were obtained at ∼100 K and 9.4 T without the need for a glass-forming additive. We show that the homogeneous radical distribution and the subtle balance between the concentration of radical in the material and the fraction of radicals at a sufficient inter-radical distance to promote the cross-effect are the main determinants for the DNP enhancements we obtain. The material, as well as an analogue containing the poorly soluble biradical bTUrea, is used as a polarizing matrix for DNP NMR experiments of solutions containing alanine and pyruvic acid. The analyte is separated from the polarization matrix by simple filtration.

EPR relaxation-enhancement-based distance measurements on orthogonally spin-labeled T4-lysozyme

Lanthanide-induced enhancement of the longitudinal relaxation of nitroxide radicals in combination with orthogonal site-directed spin labeling is presented as a systematic distance measurement method intended for studies of bio-macromolecules and bio-macromolecular complexes. The approach is tested on a water-soluble protein (T4-lysozyme) for two different commercially available lanthanide labels, and complemented by previously reported data on a membrane-inserted polypeptide. Single temperature measurements are shown to be sufficient for reliable distance determination, with an upper measurable distance limit of about 5-6 nm. The extracted averaged distances represent the closest approach in Ln(III) -nitroxide distance distributions. Studies of conformational changes and of bio-macromolecule association-dissociation are proposed as possible application area of the relaxation-enhancement-based distance measurements.

Large molecular weight nitroxide biradicals providing efficient dynamic nuclear polarization at temperatures up to 200 K

A series of seven functionalized nitroxide biradicals (the bTbK biradical and six derivatives) are investigated as exogenous polarization sources for dynamic nuclear polarization (DNP) solid-state NMR at 9.4 T and with ca. 100 K sample temperatures. The impact of electron relaxation times on the DNP enhancement (ε) is examined, and we observe that longer inversion recovery and phase memory relaxation times provide larger ε. All radicals are tested in both bulk 1,1,2,2-tetrachloroethane solutions and in mesoporous materials, and the difference in ε between the two cases is discussed. The impact of the sample temperature and magic angle spinning frequency on ε is investigated for several radicals each characterized by a range of electron relaxation times. In particular, TEKPol, a bulky derivative of bTbK with a molecular weight of 905 g·mol(-1), is presented. Its high-saturation factor makes it a very efficient polarizing agent for DNP, yielding unprecedented proton enhancements of over 200 in both bulk and materials samples at 9.4 T and 100 K. TEKPol also yields encouraging enhancements of 33 at 180 K and 12 at 200 K, suggesting that with the continued improvement of radicals large ε may be obtained at higher temperatures.

Orthogonal spin labeling and Gd(III)-nitroxide distance measurements on bacteriophage T4-lysozyme

We present the first example of chemoselective site-specific spin labeling of a monomeric protein with two spectroscopically orthogonal spin labels: a gadolinium(III) chelate complex and a nitroxide radical. A detailed analysis of the performance of two commercially available Gd(III) ligands in the Gd(III)-nitroxide pulse double electron-electron resonance (DEER or PELDOR) experiment is reported. A modification of the flip angle of the pump pulse in the Gd(III)-nitroxide DEER experiment is proposed to optimize sensitivity.

Multiple Pathway Relaxation Enhancement in the System Composed of Three Paramagnetic Species: Nitroxide Radical-Ln(3+)-O2

Longitudinal relaxation of nitroxide spin-labels has been measured for a membrane-incorporated α-helical polypeptide in the presence and absence of residual amounts of membrane-dissolved O2 and paramagnetic Dy(3+) ions. Such a model system, containing three different types of paramagnetic species, provides an important example of nonadditivity of two different relaxation channels for the nitroxide spins.

Enzymatic synthesis of multi spin-labeled DNA

Electron paramagnetic resonance (EPR) spectroscopy was applied extensively in studies of nucleic acid structures and dynamics. Two modified 2'-deoxyuridine triphosphates were synthesized bearing a spin label linked to the base by a rigid linker to ensure a tight coupling of spin label dynamics. The incorporation of both spin-labeled nucleotides could be shown in primer extension reactions in presence of DNA polymerases from eukaryotic, prokaryotic, and archaic origin. In further experiments we were able to introduce multiple spin labels during primer extension reactions.

Binding of single gold atoms on thin MgO(001) films

In the present Letter the first electron paramagnetic resonance spectra of single metal atoms on a single crystalline oxide surface are presented. For Au atoms on a MgO(001) film investigated here an analysis of the angular dependent resonance positions and the hyperfine coupling to (17)O shows that the atoms are bound on top of oxygen ions on the terrace of the film. This result is in perfect agreement with scanning tunneling microscopy measurements at 5 K presented here. The measured hyperfine matrix components allow an experimental verification of the theoretically proposed binding mechanism of Au atoms on MgO. In particular, the large reduction of the isotropic hyperfine coupling constant of supported Au as compared to free atoms is not due to a charge transfer at the interface but a hybridization of orbitals and a resulting polarization of the unpaired electron.