Bayesian optimization to estimate hyperfine couplings from 19F ENDOR spectra

Host-guest geometry in paramagnetic cavitands elucidated by 19F electron-nuclear double resonance

Elucidating structural information of supramolecular host-guest systems is pivotal for understanding molecular recognition and designing functional materials. This study explores the binding modes of fluorinated benzylamine guests in cyclodextrin-based paramagnetic cavitands, employing Gd(III)-capped cyclodextrins (Gd-α-CD and Gd-β-CD, comprising six and seven glucopyranoside units, respectively) and high-field 19F electron-nuclear double resonance (ENDOR). The 19F ENDOR spectra revealed distinct behaviors based on the fluorine position and cyclodextrin cavity size. For para-fluorinated benzylamine guests, Gd-β-CD displayed a bimodal distribution of Gd-F distances, corresponding to two distinct binding modes, whereas Gd-α-CD exhibited a single binding mode. In contrast, meta-fluorinated benzylamines demonstrated a single binding mode for both Gd-α-CD and Gd-β-CD, underscoring the influence of cavity size and fluorine substitution in the guest on binding specificity. ENDOR measurements performed at the EPR central transition of Gd(III) are generally expected to yield Gd-F distances without orientation-specific details. Surprisingly, in Gd-CDs systems, an unexpected orientation selectivity was observed, enabling the extraction of both Gd-F distances and orientation of the guest molecule relative to the cavitand's Gd(III) zero-field splitting (ZFS) tensor. This two-faceted capability of 19F-ENDOR allows for determining host-guest complexation geometry and provides insights into ZFS orientation within the cavitand structure.

Frequency and time domain 19F ENDOR spectroscopy: role of nuclear dipolar couplings to determine distance distributions

19F electron-nuclear double resonance (ENDOR) spectroscopy is emerging as a method of choice to determine molecular distances in biomolecules in the angstrom to nanometer range. However, line broadening mechanisms in 19F ENDOR spectra can obscure the detected spin-dipolar coupling that encodes the distance information, thus limiting the resolution and accessible distance range. So far, the origin of these mechanisms has not been understood. Here, we employ a combined approach of rational molecular design, frequency and time domain ENDOR methods as well as quantum mechanical spin dynamics simulations to analyze these mechanisms. We present the first application of Fourier transform ENDOR to remove power broadening and measure T2n of the 19F nucleus. We identify nuclear dipolar couplings between the fluorine and protons up to 14 kHz as a major source of spectral broadening. When removing these interactions by H/D exchange, an unprecedented spectral width of 9 kHz was observed suggesting that, generally, the accessible distance range can be extended. In a spin labeled RNA duplex we were able to predict the spectral ENDOR line width, which in turn enabled us to extract a distance distribution. This study represents a first step towards a quantitative determination of distance distributions in biomolecules from 19F ENDOR.

Pulsed EPR Methods in the Angstrom to Nanometre Scale Shed Light on the Conformational Flexibility of a Fluoride Riboswitch

Riboswitches control gene regulation upon external stimuli such as environmental factors or ligand binding. The fluoride sensing riboswitch from Thermotoga petrophila is a complex regulatory RNA proposed to be involved in resistance to F- cytotoxicity. The details of structure and dynamics underpinning the regulatory mechanism are currently debated. Here we demonstrate that a combination of pulsed electron paramagnetic resonance (ESR/EPR) spectroscopies, detecting distances in the angstrom to nanometre range, can probe distinct regions of conformational flexibility in this riboswitch. PELDOR (pulsed electron-electron double resonance) revealed a similar preorganisation of the sensing domain in three forms, i.e. the free aptamer, the Mg2+-bound apo, and the F--bound holo form. 19F ENDOR (electron-nuclear double resonance) was used to investigate the active site structure of the F--bound holo form. Distance distributions without a priori structural information were compared with in silico modelling of spin label conformations based on the crystal structure. While PELDOR, probing the periphery of the RNA fold, revealed conformational flexibility of the RNA backbone, ENDOR indicated low structural heterogeneity at the ligand binding site. Overall, the combination of PELDOR and ENDOR with sub-angstrom precision gave insight into structural organisation and flexibility of a riboswitch, not easily attainable by other biophysical techniques.

Spin labels for 19F ENDOR distance determination: resolution, sensitivity and distance predictability

19F electron-nuclear double resonance (ENDOR) has emerged as an attractive method for determining distance distributions in biomolecules in the range of 0.7-2 nm, which is not easily accessible by pulsed electron dipolar spectroscopy. The 19F ENDOR approach relies on spin labeling, and in this work, we compare various labels' performance. Four protein variants of GB1 and ubiquitin bearing fluorinated residues were labeled at the same site with nitroxide and trityl radicals and a Gd(III) chelate. Additionally, a double-histidine variant of GB1 was labeled with a Cu(II) nitrilotriacetic acid chelate. ENDOR measurements were carried out at W-band (95 GHz) where 19F signals are well separated from 1H signals. Differences in sensitivity were observed, with Gd(III) chelates providing the highest signal-to-noise ratio. The new trityl label, OXMA, devoid of methyl groups, exhibited a sufficiently long phase memory time to provide an acceptable sensitivity. However, the longer tether of this label effectively reduces the maximum accessible distance between the 19F and the Cα of the spin-labeling site. The nitroxide and Cu(II) labels provide valuable additional geometric insights via orientation selection. Prediction of electron-nuclear distances based on the known structures of the proteins were the closest to the experimental values for Gd(III) labels, and distances obtained for Cu(II) labeled GB1 are in good agreement with previously published NMR results. Overall, our results offer valuable guidance for selecting optimal spin labels for 19F ENDOR distance measurement in proteins.

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

Fluorine electron-nuclear double resonance (19F 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 19F ENDOR almost 2-fold. We first demonstrate this on a model fluorine-containing Gd(III) complex with a well-resolved 19F 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 19F and Gd(III), in which the Gd-F distance is too long to produce a well-resolved 19F 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 19F ENDOR approach may be applicable to Gd-F distances as large as 20 Å, widening the current ENDOR distance window.

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

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 explored the capability of Mims 19F ENDOR experiments on reporting intermolecular distances in trityl- and 19F-labeled DNA duplexes at three electron paramagnetic resonance (EPR) frequencies (34, 94, and 263 GHz). For spin labeling, we used the hydrophobic Finland trityl radical and hydrophilic OX063 trityl radical. Fluorine labels were introduced into two positions of a DNA oligonucleotide. The results indicated that hyperfine splittings visible in the ENDOR spectra are consistent with the most populated interspin distances between 19F and the trityl radical predicted from molecular dynamic (MD) simulations. Moreover, for some cases, ENDOR spectral simulations based on MD results were able to reproduce the conformational distribution reflected in the experimental ENDOR line broadening. Additionally, MD simulations provided more detailed information about the melting of terminal base pairs of the oligonucleotides and about the configuration of the trityls relative to a DNA end.