<sup>19</sup>F electron nuclear double resonance (ENDOR) spectroscopy for distance measurements using trityl spin labels in DNA duplexes

Asanbaeva, Nargiz B.; Новопашина, Д. С.; Rogozhnikova, Olga Yu.; Tormyshev, Victor M.; Kehl, A.; Суханов, А. А.; Shernyukov, Аndrey V.; Genaev, A. M.; Lomzov, Alexander A.; Bennati, Marina; Meyer, Andreas; Bagryanskaya, Elena G.

doi:10.1039/d3cp02969g

Cited by 6 publications

(4 citation statements)

References 49 publications

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“…21 In the case of rigid spin labels, additional structural information can be obtained by determining the orientation of the spin label in the structure of the biomolecule. Trityl 22,25 and Gd(III) 23,27 labels have been also used for distance determination by 19 F ENDOR, with the advantage of not requiring a set of orientation selection measurements owing to the isotropic nature of their EPR spectrum. Recently, phenoxyl 24 and Cu(II) 26 have also been used for distance measurements.…”

Section: ■ Introductionmentioning

confidence: 99%

“…In ENDOR, hyperfine interactions between the electron spin in a paramagnetic center and the surrounding nuclei are measured. Traditionally, it has been applied to extract the local spatial and electronic structure of intrinsic paramagnetic metal ions or metal clusters in proteins, − while, at present, ENDOR experiments for distance determination on spin-labeled biomolecules are being developed. − For measuring weak hyperfine interactions, which are dipolar in nature, Mims ENDOR is the technique of choice, as demonstrated for a nitroxide label situated 1 nm away from a 31 P nucleus in a membrane bilayer …”

Section: Introductionmentioning

confidence: 99%

“…Finally, performing these measurements at the Q-band, taking advantage of currently easily accessible pulsed EPR spectrometers, is possible, and 19 F ENDOR distance measurements at the Q-band have already been reported for trityl-and Cu(II)-labeled biomolecules. 25,26 However, at lower frequencies, interference between 19 F and 1 H ENDOR lines may occur, especially for high-spin electron transitions, since the corresponding 1 H ENDOR lines can extend far out from the Larmor frequency according to eq 1. If this is the case, subtraction of spectra obtained in the absence of 19 F is necessary, as recently shown for Cu(II)− 19 F ENDOR.…”

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Extending the Range of Distances Accessible by ¹⁹F Electron–Nuclear Double Resonance in Proteins Using High-Spin Gd(III) Labels

Bogdanov,

Frydman,

Seal

et al. 2024

J. Am. Chem. Soc.

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Fluorine electron-nuclear double resonance ( 19 F ENDOR) has recently emerged as a valuable tool in structural biology for distance determination between F atoms and a paramagnetic center, either intrinsic or conjugated to a biomolecule via spin labeling. Such measurements allow access to distances too short to be measured by double electron−electron resonance (DEER). To further extend the accessible distance range, we exploit the high-spin properties of Gd(III) and focus on transitions other than the central transition (|−1/2⟩ ↔ |+1/2⟩), that become more populated at high magnetic fields and low temperatures. This increases the spectral resolution up to ca. 7 times, thus raising the long-distance limit of 19 F ENDOR almost 2fold. We first demonstrate this on a model fluorine-containing Gd(III) complex with a well-resolved 19 F spectrum in conventional central transition measurements and show quantitative agreement between the experimental spectra and theoretical predictions. We then validate our approach on two proteins labeled with 19 F and Gd(III), in which the Gd−F distance is too long to produce a well-resolved 19 F ENDOR doublet when measured at the central transition. By focusing on the |−5/2⟩ ↔ |−3/2⟩ and |−7/2⟩ ↔ |−5/2⟩ EPR transitions, a resolution enhancement of 4.5-and 7-fold was obtained, respectively. We also present data analysis strategies to handle contributions of different electron spin manifolds to the ENDOR spectrum. Our new extended 19 F ENDOR approach may be applicable to Gd−F distances as large as 20 Å, widening the current ENDOR distance window.

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Section: ■ Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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confidence: 99%

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Extending the Range of Distances Accessible by ¹⁹F Electron–Nuclear Double Resonance in Proteins Using High-Spin Gd(III) Labels

Bogdanov,

Frydman,

Seal

et al. 2024

J. Am. Chem. Soc.

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“…■ EXPERIMENTAL AND COMPUTATIONAL METHODS Molecular dynamics simulations were performed via the Amber20 36 software package using GAFF force field (Version 1.81). For trityl moieties, force field parameters obtained previously 37 were used. Charge derivation was made by AM1-BCC method with sqm and Antechamber utilities included in the package AmberTools21.…”

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confidence: 99%

Dynamic Nuclear Polarization Using Electron Spin Cluster

Chaklashiya,

Equbal,

Shernyukov

et al. 2024

J. Phys. Chem. Lett.

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Dynamic nuclear polarization (DNP) utilizing narrow-line electron spin clusters (ESCs) to achieve nuclear spin resonance matching (ESC-DNP) by microwave irradiation is a promising way to achieve NMR signal enhancements with a wide design scope requiring low microwave power at high magnetic field. Here we present the design for a trityl-based tetra-radical (TetraTrityl) to achieve DNP for 1H NMR at 7 T, supported by experimental data and quantum mechanical simulations. A slow-relaxing (T 1e ≈ 1 ms) 4-ESC is found to require at least two electron spin pairs at <8 Å e–e spin distance to yield 1H ESC-DNP enhancement, while squeezing the rest of the e–e spin distances to <12 Å results in optimal 1H ESC-DNP enhancements. Fast-relaxing ESCs (T 1e ≈ 10 μs) are found to require a weakly coupled narrow-line radical (sensitizer) to extract polarization from the ESC. These results provide design principles for achieving a power-efficient DNP at high field via ESC-DNP.

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Puls EPR Methoden im Angstöm‐ bis Nanometerbereich geben Aufschluss über die konformationelle Flexibilität eines Fluorid‐Riboschalters

Remmel,

Meyer,

Ackermann

et al. 2024

Angewandte Chemie

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Riboschalter steuern die Genregulation in Reaktion auf externe Reize wie Umweltfaktoren oder Ligandenbindung. Der fluoriderkennende Riboschalter aus Thermotoga petrophila ist eine komplexe regulatorische RNA, von der angenommen wird, an der Resistenz gegen die zytotoxische Wirkung von Fluorid beteiligt zu sein. Details der Struktur und Dynamik, die dem regulatorischen Mechanismus zugrunde liegen, werden derzeit diskutiert. Hier zeigen wir, dass mit einer Kombination aus Puls Elektronen‐Paramagnetischer‐Resonanz (ESR/EPR) Spektroskopien, die Abstände im Angström‐ bis Nanometerbereich detektiert, spezifische Bereiche konformationeller Flexibilität in diesem Riboschalter untersucht werden können. PELDOR (pulsed electron‐electron double resonance) zeigte eine ähnliche Präorganisation der Sensordomäne in drei Formen: der freien Aptamerform, der Mg2+‐gebundenen apo‐Form und der F−‐gebundenen holo‐Form. 19F ENDOR (electron‐nuclear double resonance) wurde verwendet, um die Struktur des aktiven Zentrums der F−‐gebundenen holo‐Form zu untersuchen. Abstandsverteilungen ohne vorherige strukturelle Informationen wurden mit auf der Kristallstruktur basierenden in silico Modellierungen der Spinmarkerkonformationen verglichen. Während PELDOR, welches die Peripherie der RNA Faltung untersucht, die konformationelle Flexibilität des RNA Rückgrats aufdeckte, zeigte ENDOR eine geringe strukturelle Heterogenität der Ligandenbindungstasche. Die Kombination aus PELDOR und ENDOR lieferte sub‐Angström‐präzise Einblicke in die strukturelle Organisation und Flexibilität eines Riboschalters, die mit anderen biophysikalischen Techniken nur schwer zu erreichen sind.

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¹⁹F electron nuclear double resonance (ENDOR) spectroscopy for distance measurements using trityl spin labels in DNA duplexes

Abstract: The combination of fluorine labeling and pulsed electron-nuclear double resonance (ENDOR) is emerging as a powerful technique for obtaining structural information about proteins and nucleic acids. In this work, we...

Cited by 6 publications

References 49 publications

Extending the Range of Distances Accessible by ¹⁹F Electron–Nuclear Double Resonance in Proteins Using High-Spin Gd(III) Labels

Extending the Range of Distances Accessible by ¹⁹F Electron–Nuclear Double Resonance in Proteins Using High-Spin Gd(III) Labels

Dynamic Nuclear Polarization Using Electron Spin Cluster

Puls EPR Methoden im Angstöm‐ bis Nanometerbereich geben Aufschluss über die konformationelle Flexibilität eines Fluorid‐Riboschalters

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19F electron nuclear double resonance (ENDOR) spectroscopy for distance measurements using trityl spin labels in DNA duplexes

Abstract: The combination of fluorine labeling and pulsed electron-nuclear double resonance (ENDOR) is emerging as a powerful technique for obtaining structural information about proteins and nucleic acids. In this work, we...

Cited by 6 publications

References 49 publications

Extending the Range of Distances Accessible by 19F Electron–Nuclear Double Resonance in Proteins Using High-Spin Gd(III) Labels

Extending the Range of Distances Accessible by 19F Electron–Nuclear Double Resonance in Proteins Using High-Spin Gd(III) Labels

Dynamic Nuclear Polarization Using Electron Spin Cluster

Puls EPR Methoden im Angstöm‐ bis Nanometerbereich geben Aufschluss über die konformationelle Flexibilität eines Fluorid‐Riboschalters

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¹⁹F electron nuclear double resonance (ENDOR) spectroscopy for distance measurements using trityl spin labels in DNA duplexes

Extending the Range of Distances Accessible by ¹⁹F Electron–Nuclear Double Resonance in Proteins Using High-Spin Gd(III) Labels

Extending the Range of Distances Accessible by ¹⁹F Electron–Nuclear Double Resonance in Proteins Using High-Spin Gd(III) Labels