Stability of the nitroxide biradical AMUPol in intact and lysed mammalian cells

Spatially resolved DNP-assisted NMR illuminates the conformational ensemble of α-synuclein in intact viable cells

The protein α-syn adopts a wide variety of conformations including an intrinsically disordered monomeric form and an α-helical-rich membrane-associated form that is thought to play an important role in cellular membrane processes. However, despite the high affinity of α-syn for membranes, evidence that the α-helical form is adopted inside cells has been indirect. DNP-assisted solid-state NMR on frozen cellular samples can report directly on the entire conformational ensemble. By controlling the distribution of the DNP agent throughout the cellular biomass, such experiments can provide quantitative information upon the entire structural ensemble or provide information about spatially resolved subpopulations. When the polarization agent is dispersed homogeneously throughout the cell, a minority of the α-syn inside HEK293 cells adopts a highly α-helical-rich conformation. When the polarization agent is peripherally localized, the α-helical-rich conformation predominates, indicating that it is preferentially adopted near the cellular periphery. This demonstrates how selectively altering the spatial distribution of the DNP agent can be a powerful tool to observe spatially distinct structural ensembles. This approach paves the way for more nuanced investigations into the conformations that proteins adopt in different areas of the cell.

Stability of the polarization agent AsymPolPOK in intact and lysed mammalian cells

Dynamic nuclear polarization (DNP) solid-state NMR enables detection of proteins inside cells through sensitivity enhancement from nitroxide biradical polarization agents. AsymPolPOK, a novel water-soluble asymmetric nitroxide biradical, offers superior sensitivity and faster build-up times compared to existing agents like AMUPol. Here, we characterize AsymPolPOK's behavior in mammalian HEK293 cells, examining its cellular distribution, reduction kinetics, and DNP performance. We demonstrate that electroporation achieves uniform cellular delivery of AsymPolPOK, including nuclear permeation, with no cytotoxicity at millimolar concentrations. However, the cellular environment rapidly reduces AsymPolPOK to its monoradical form, with one nitroxide center showing greater reduction resistance than the other. While AsymPolPOK maintains high DNP enhancements and short build-up times in lysates, its performance in intact cells depends critically on delivery method and exposure time to cellular constituents. Electroporation yields higher, more uniform enhancements compared to incubation, but prolonged exposure to the cellular environment diminishes DNP performance in both cases. These findings establish AsymPolPOK's potential for in-cell DNP NMR while highlighting the need for developing more bio-resistant polarization agents to further advance cellular structural biology studies.

Spatially resolved DNP-assisted NMR illuminates the conformational ensemble of α-synuclein in intact viable cells

The protein α-syn adopts a wide variety of conformations including an intrinsically disordered monomeric form and an α-helical rich membrane-associated form that is thought to play an important role in cellular membrane processes. However, despite the high affinity of α-syn for membranes, evidence that the α-helical form is adopted inside cells has been indirect. DNP-assisted solid state NMR on frozen cellular samples can report on protein conformations inside cells. Moreover, by controlling the distribution of the DNP polarization agent throughout the cellular biomass, such experiments can provide quantitative information upon the entire structural ensemble or provide information about spatially resolved sub-populations. Using DNP-assisted magic angle spinning (MAS) NMR we establish that purified α-syn in the membrane-associated and intrinsically disordered forms have distinguishable spectra. We then introduced isotopically labeled monomeric α-syn into cells. When the DNP polarization agent is dispersed homogenously throughout the cell, we found that a minority of the α-syn inside cells adopted a highly α-helical rich conformation. When the DNP polarization agent is peripherally localized, we found that the α-helical rich conformation predominates. Thus, we provide direct evidence that α-helix rich conformations of α-syn are adopted near the cellular periphery inside cells under physiological conditions. Moreover, we demonstrate how selectively altering the spatial distribution of the DNP polarization agent can be a powerful tool to observe spatially distinct structural ensembles. This approach paves the way for more nuanced investigations into the conformations that proteins adopt in different areas of the cell.

An Efficient and Stable Polarizing Agent for In-Cell Magic-Angle Spinning Dynamic Nuclear Polarization NMR Spectroscopy

Nuclear Magnetic Resonance (NMR) spectroscopy would be a method of choice to follow biochemical events in cells because it can analyze molecules in complex environments. However, the intrinsically low sensitivity of NMR makes in-cell measurements challenging. Dynamic Nuclear Polarization (DNP) has emerged as a method to circumvent this limitation, but most polarizing agents developed for DNP are unstable in reducing cellular environments. Here, we introduce the use of Gd(III)-based DNP polarizing agents for in-cell NMR spectroscopy. Specifically, we show their persistent stability in cellular formulations, and we investigate the DNP performance of the Gd(III)-based complex [Gd(tpatcn)] in human embryonic kidney cell lysates and intact cells. For cell lysates, DNP enhancements up to -27 are obtained on the cellular signals, reproducible even after storage at room temperature for days. Mixing the [Gd(tpatcn)] solution with intact cells enables the observation of cellular signals with DNP, and DNP enhancement factors of about -40 are achieved.

Stability of the polarization agent AsymPolPOK in intact and lysed mammalian cells

Dynamic nuclear polarization (DNP) solid-state NMR enables detection of proteins at endogenous concentrations in cells through sensitivity enhancement from nitroxide biradical polarization agents. AsymPolPOK, a novel water-soluble asymmetric nitroxide biradical, offers superior sensitivity and faster build-up times compared to existing agents like AMUPol. Here, we characterize AsymPolPOK in mammalian HEK293 cells, examining its cellular distribution, reduction kinetics, and DNP performance. We demonstrate that electroporation achieves uniform cellular delivery of AsymPolPOK, including nuclear permeation, with no cytotoxicity at millimolar concentrations. However, the cellular environment rapidly reduces AsymPolPOK to its monoradical form, with one nitroxide center showing greater reduction resistance than the other. While AsymPolPOK maintains high DNP enhancements and short build-up times in lysates, its performance in intact cells depends critically on delivery method and exposure time to cellular constituents. Electroporation yields higher, more uniform enhancements compared to incubation, but prolonged exposure to the cellular environment diminishes DNP performance in both cases. These findings establish the potential of AsymPolPOK as a polarization agent for in-cell DNP NMR while highlighting the need for developing more bio-resistant polarization agents to further advance cellular structural biology studies.

Expanding the tool box for native structural biology: 19F dynamic nuclear polarization with fast magic angle spinning

Obtaining atomic-level information on components in the cell is a major focus in structural biology. Elucidating specific structural and dynamic features of proteins and their interactions in the cellular context is crucial for understanding cellular processes. We introduce 19F dynamic nuclear polarization (DNP) combined with fast magic-angle-spinning (MAS) nuclear magnetic resonance (NMR) spectroscopy as a powerful technique to study proteins in mammalian cells. We demonstrate our approach on the severe acute respiratory syndrome coronavirus 2 5F-Trp-NNTD protein, electroporated into human cells. DNP signal enhancements of 30- to 40-fold were observed, translating into over 1000-fold experimental time savings. High signal-to-noise ratio spectra were acquired on nanomole quantities of a protein in cells in minutes. 2D 19F-19F dipolar correlation spectra with remarkable sensitivity and resolution were obtained, exhibiting 19F-19F cross peaks associated with fluorine atoms as far as ~10 angstroms apart. This work paves the way for 19F DNP-enhanced MAS NMR applications in cells for probing protein structure, dynamics, and ligand interactions.

In cell NMR reveals cells selectively amplify and structurally remodel amyloid fibrils

Amyloid forms of α-synuclein adopt different conformations depending on environmental conditions. Advances in structural biology have accelerated fibril characterization. However, it remains unclear which conformations predominate in biological settings because current methods typically not only require isolating fibrils from their native environments, but they also do not provide insight about flexible regions. To address this, we characterized α-syn amyloid seeds and used sensitivity enhanced nuclear magnetic resonance to investigate the amyloid fibrils resulting from seeded amyloid propagation in different settings. We found that the amyloid fold and conformational preferences of flexible regions are faithfully propagated in vitro and in cellular lysates. However, seeded propagation of amyloids inside cells led to the minority conformation in the seeding population becoming predominant and more ordered, and altered the conformational preferences of flexible regions. The examination of the entire ensemble of protein conformations in biological settings that is made possible with this approach may advance our understanding of protein misfolding disorders and facilitate structure-based drug design efforts.

Stabilizing Nitroxide Spin Labels for Structural and Conformational Studies of Biomolecules by Maleimide Treatment

Nitroxide (NO) spin radicals are effective in characterizing structures, interactions and dynamics of biomolecules. The EPR applications in cell lysates or intracellular milieu require stable spin labels, but NO radicals are unstable in such conditions. We showed that the destabilization of NO radicals in cell lysates or even in cells is caused by NADPH/NADH related enzymes, but not by the commonly believed reducing reagents such as GSH. Maleimide stabilizes the NO radicals in the cell lysates by consumption of the NADPH/NADH that are essential for the enzymes involved in destabilizing NO radicals, instead of serving as the solo thiol scavenger. The maleimide treatment retains the crowding properties of the intracellular components and allows to perform long-time EPR measurements of NO labeled biomolecules close to the intracellular conditions. The strategy of maleimide treatment on cell lysates for the EPR applications has been demonstrated on double electron-electron resonance (DEER) measurements on a number of NO labeled protein samples. The method opens a broad application range for the NO labeled biomolecules by EPR in conditions that resemble the intracellular milieu.

An EPR Study on Highly Stable Nitroxyl-Nitroxyl Biradicals for Dynamic Nuclear Polarization Applications at High Magnetic Fields

Nitroxide biradicals are efficient polarizing agents in dynamic nuclear polarization (DNP) solid-state nuclear magnetic resonance. Many recently reported radicals possess substantial DNP efficiency in organic solvents but have poor solubility in water media which is unfavorable for biological applications. In this paper, we report DNP efficiency at a high magnetic field for two water-soluble biradicals resistant to reducing media. Water solubility was achieved by obtaining the radicals in the form of quaternary ammonium salts. Parameters of hyperfine interaction and exchange interaction were quantified by EPR spectroscopy, and their influence on the DNP effect was determined. The resistance of the biradicals to strongly reducing media was characterized. High stability was achieved using tetraethyl substituents and pyrrolidine moieties.

A Comparative Study of Nitroxide-Based Biradicals for Dynamic Nuclear Polarization in Cellular Environments

Dynamic nuclear polarization (DNP) is a powerful tool to enhance the NMR signals of molecules by transferring polarization from unpaired electron spins to nuclei through microwave irradiation. The resulting signal enhancements can enable the analysis of samples that have previously been intractable by NMR spectroscopy, including proteins, nucleic acids, and metabolites in cells. To carry out DNP, the sample is doped with a polarization agent, a biradical containing two nitroxide moieties. DNP applications in cells, however, present significant challenges as nitroxides are often susceptible to the reducing cellular environment. Here, we introduce a novel polarization agent, POPAPOL, that exhibits increased lifetimes under reducing conditions. We also compare its bioresistance and DNP performance with three popular, commercially available polarization agents. Our work indicates that pyrrolidine-based nitroxides can outperform piperidine-based nitroxides in cellular environments, and that future polarization agent designs must carefully balance DNP performance and stability for cellular applications.

Highly bioresistant, hydrophilic and rigidly linked trityl-nitroxide biradicals for cellular high-field dynamic nuclear polarization

Cellular dynamic nuclear polarization (DNP) has been an effective means of overcoming the intrinsic sensitivity limitations of solid-state nuclear magnetic resonance (ssNMR) spectroscopy, thus enabling atomic-level biomolecular characterization in native environments. Achieving DNP signal enhancement relies on doping biological preparations with biradical polarizing agents (PAs). Unfortunately, PA performance within cells is often limited by their sensitivity to the reductive nature of the cellular lumen. Herein, we report the synthesis and characterization of a highly bioresistant and hydrophilic PA (StaPol-1) comprising the trityl radical OX063 ligated to a gem-diethyl pyrroline nitroxide via a rigid piperazine linker. EPR experiments in the presence of reducing agents such as ascorbate and in HeLa cell lysates demonstrate the reduction resistance of StaPol-1. High DNP enhancements seen in small molecules, proteins and cell lysates at 18.8 T confirm that StaPol-1 is an excellent PA for DNP ssNMR investigations of biomolecular systems at high magnetic fields in reductive environments.