2-Fluorotyrosine is a valuable but understudied amino acid for protein-observed 19F NMR

Insights into the Structure and Dynamics of Proteins from 19F Solution NMR Spectroscopy

19F NMR spectroscopy has recently witnessed a resurgence as an attractive analytical tool for the study of the structure and dynamics of biomolecules in vitro and in cells, despite reports of its applications in biomolecular NMR since the 1970s. The high gyromagnetic ratio, large chemical shift dispersion, and complete absence of the spin 1/2 19F nucleus from biomolecules results in background-free, high-resolution 19F NMR spectra. The introduction of 19F probes in a few selected locations in biomolecules reduces spectral crowding despite its increased line width in comparison to typical 1H NMR line widths and allows rapid site-specific measurements from simple 1D spectra alone. The design and synthesis of novel 19F probes with reduced line widths and increased chemical shift sensitivity to the surrounding environment, together with advances in labeling techniques, NMR methodology, and hardware, have overcome several drawbacks of 19F NMR spectroscopy. The increased interest and widespread use of 19F NMR spectroscopy of biomolecules is gradually establishing it as a sensitive and high-resolution probe of biomolecular structure and dynamics, supplementing traditional 13C/15N-based methods. This Review focuses on the advances in 19F solution NMR spectroscopy of proteins in the past 5 years, with an emphasis on novel 19F tags and labeling techniques, NMR experiments to probe protein structure and conformational dynamics in vitro, and in-cell NMR applications.

Environmentally Ultrasensitive Fluorine Probe to Resolve Protein Conformational Ensembles by 19F NMR and Cryo-EM

Limited chemical shift dispersion represents a significant barrier to studying multistate equilibria of large membrane proteins by 19F NMR. We describe a novel monofluoroethyl 19F probe that dramatically increases the chemical shift dispersion. The improved conformational sensitivity and line shape enable the detection of previously unresolved states in one-dimensional (1D) 19F NMR spectra of a 134 kDa membrane transporter. Changes in the populations of these states in response to ligand binding, mutations, and temperature correlate with population changes of distinct conformations in structural ensembles determined by single-particle cryo-electron microscopy (cryo-EM). Thus, 19F NMR can guide sample preparation to discover and visualize novel conformational states and facilitate image analysis and three-dimensional (3D) classification.

Assessing the applicability of 19F labeled tryptophan residues to quantify protein dynamics

Nuclear magnetic resonance (NMR) spectroscopy is uniquely suited to study the dynamics of biomolecules in solution. Most NMR studies exploit the spins of proton, carbon and nitrogen isotopes, as these atoms are highly abundant in proteins and nucleic acids. As an alternative and complementary approach, fluorine atoms can be introduced into biomolecules at specific sites of interest. These labels can then be used as sensitive probes for biomolecular structure, dynamics or interactions. Here, we address if the replacement of tryptophan with 5-fluorotryptophan residues has an effect on the overall dynamics of proteins and if the introduced fluorine probe is able to accurately report on global exchange processes. For the four different model proteins (KIX, Dcp1, Dcp2 and DcpS) that we examined, we established that ¹⁵N CPMG relaxation dispersion or EXSY profiles are not affected by the 5-fluorotryptophan, indicating that this replacement of a proton with a fluorine has no effect on the protein motions. However, we found that the motions that the 5-fluorotryptophan reports on can be significantly faster than the backbone motions. This implies that care needs to be taken when interpreting fluorine relaxation data in terms of global protein motions. In summary, our results underscore the great potential of fluorine NMR methods, but also highlight potential pitfalls that need to be considered.

Tracking Fluorine during Aqueous Photolysis and Advanced UV Treatment of Fluorinated Phenols and Pharmaceuticals Using a Combined 19F-NMR, Chromatography, and Mass Spectrometry Approach

Fluorine incorporation into organic molecules has increased due to desirable changes in the molecular physiochemical properties. Common fluorine motifs include: aliphatic fluorines and -CF₃, or -F containing groups bonded directly onto an aromatic (Ar-CF₃ and Ar-F) or heteroaromatic ring. Photolysis of these compounds, either in natural or engineered systems, is a potential source of new fluorinated byproducts. Given the potential persistence and toxicity of fluorinated byproducts, monitoring of product formation during photolysis of various fluorinated motifs is needed. ¹⁹F-NMR is a means to detect and quantify these species. Ar-CF₃ and Ar-F model compounds (2-, 3-, and 4-(trifluoromethyl)phenol, 2-, 3-, 4-fluorophenol, and 2,6-, 3,5-difluorophenol) were photolyzed under a variety of aqueous conditions: pH 5, pH 7, pH 10, 1 mM H₂O₂ at pH 7 to form •OH, and 0.5 mM SO₃ ^2- at pH 10 to form e_aq ^-. Pharmaceuticals with the Ar-CF₃ (fluoxetine) and Ar-F plus pyrazole-CF₃ (sitagliptin) motifs were treated similarly. Parent molecule concentrations were monitored with high pressure liquid chromatography with a UV detector. Fluorine in the parent and product molecules was quantified with ¹⁹F-NMR and complete fluorine mass balances were obtained. High resolution mass spectrometry was used to further explore product identities. The major product for Ar-F compounds was fluoride. The Ar-CF₃ model compounds led to fluoride and organofluorine products dependent on motif placement and reaction conditions. Trifluoroacetic acid was a product of 4-(trifluoromethyl)phenol and fluoxetine. Additional detected fluoxetine products identified using mass spectrometry resulted from addition of -OH to the aromatic ring, but a dealkylation product could not be distinguished from fluoxetine by ¹⁹F-NMR. Sitagliptin formed multiple products that all retained the pyrazole-CF₃ motif while the Ar-F motif produced fluoride. ¹⁹F-NMR, mass spectrometry, and chromatography methods provide complementary information on the formation of fluorinated molecules by modification or fragmentation of the parent structure during photolysis, allowing screening for fluorinated photoproducts and development of fluorine mass balances.

Site-Specific Incorporation of 7-Fluoro-L-tryptophan into Proteins by Genetic Encoding to Monitor Ligand Binding by 19F NMR Spectroscopy

A mutant aminoacyl-tRNA synthetase identified by a library selection system affords site-specific incorporation of 7-fluoro-L-tryptophan in response to an amber stop codon. The enzyme allows the production of proteins with a single hydrogen atom replaced by a fluorine atom as a sensitive nuclear magnetic resonance (NMR) probe. The substitution of a single hydrogen atom by another element that is as closely similar in size and hydrophobicity as possible minimizes possible perturbations in the structure, stability, and solubility of the protein. The fluorine atom enables site-selective monitoring of the protein response to ligand binding by ¹⁹F NMR spectroscopy, as demonstrated with the Zika virus NS2B-NS3 protease.

Lanmodulin Remains Unfold and Fails to Interact with Lanthanide Ions in Escherichia coli Cells

We report the conformation of a newly discovered specific lanthanide ions (Ln3+) binding protein, Lanmodulin (LanM), and its inteaction with Ln3+ in Escherichia coli cells using In-cell NMR. We found...

Resolution of chemical shift anisotropy in 19F ENDOR spectroscopy at 263 GHz/9.4 T

Pulsed ¹⁹F ENDOR spectroscopy provides a selective method for measuring angstrom to nanometer distances in structural biology. Here, the performance of ¹⁹F ENDOR at fields of 3.4 T and 9.4 T is compared using model compounds containing one to three ¹⁹F atoms. CF₃ groups are included in two compounds, for which the possible occurrence of uniaxial rotation might affect the distance distribution. At 9.4 T, pronounced asymmetric features are observed in many of the presented ¹⁹F ENDOR spectra. Data analysis by spectral simulations shows that these features arise from the chemical shift anisotropy (CSA) of the ¹⁹F nuclei. This asymmetry is also observed at 3.4 T, albeit to a much smaller extent, confirming the physical origin of the effect. The CSA parameters are well consistent with DFT predicted values and can be extracted from simulation of the experimental data in favourable cases, thereby providing additional information about the geometrical and electronic structure of the spin system. The feasibility of resolving the CSA at 9.4 T provides important information for the interpretation of line broadening in ENDOR spectra also at lower fields, which is relevant for developing methods to extract distance distributions from ¹⁹F ENDOR spectra.

Soluble Methane Monooxygenase Component Interactions Monitored by 19F NMR

Soluble methane monooxygenase (sMMO) is a multicomponent metalloenzyme capable of catalyzing the fissure of the C-H bond of methane and the insertion of one atom of oxygen from O2 to yield methanol. Efficient multiple-turnover catalysis occurs only in the presence of all three sMMO protein components: hydroxylase (MMOH), reductase (MMOR), and regulatory protein (MMOB). The complex series of sMMO protein component interactions that regulate the formation and decay of sMMO reaction cycle intermediates is not fully understood. Here, the two tryptophan residues in MMOB and the single tryptophan residue in MMOR are converted to 5-fluorotryptophan (5FW) by expression in defined media containing 5-fluoroindole. In addition, the mechanistically significant N-terminal region of MMOB is 19F-labeled by reaction of the K15C variant with 3-bromo-1,1,1-trifluoroacetone (BTFA). The 5FW and BTFA modifications cause minimal structural perturbation, allowing detailed studies of the interactions with sMMOH using 19F NMR. Resonances from the 275 kDa complexes of sMMOH with 5FW-MMOB and BTFA-K15C-5FW-MMOB are readily detected at 5 μM labeled protein concentration. This approach shows directly that MMOR and MMOB competitively bind to sMMOH with similar KD values, independent of the oxidation state of the sMMOH diiron cluster. These findings suggest a new model for regulation in which the dynamic equilibration of MMOR and MMOB with sMMOH allows a transient formation of key reactive complexes that irreversibly pull the reaction cycle forward. The slow kinetics of exchange of the sMMOH:MMOB complex is proposed to prevent MMOR-mediated reductive quenching of the high-valent reaction cycle intermediate Q before it can react with methane.

Advances in the study of GPCRs by 19F NMR

Crystallography and cryo-electron microscopy have advanced atomic resolution perspectives of inactive and active states of G protein-coupled receptors (GPCRs), alone and in complex with G proteins or arrestin. ¹⁹F NMR can play a role in ascertaining activation mechanisms and understanding the complete energy landscape associated with signal transduction. Fluorinated reporters are introduced biosynthetically via fluorinated amino acid analogs or chemically, via thiol-specific fluorinated reporters. The chemical shift sensitivity of these reporters makes it possible to discern details of conformational ensembles. In addition to spectroscopic details, paramagnetic species can be incorporated through orthogonal techniques to obtain distance information on fluorinated reporters, while T₂-and T₁-based relaxation experiments provide details on exchange kinetics in addition to fluctuations within a given state.

Methodological advancements for characterising protein side chains by NMR spectroscopy

The surface of proteins is covered by side chains of polar amino acids that are imperative for modulating protein functionality through the formation of noncovalent intermolecular interactions. However, despite their tremendous importance, the unique structures of protein side chains require tailored approaches for investigation by nuclear magnetic resonance spectroscopy and so have traditionally been understudied compared with the protein backbone. Here, we review substantial recent methodological advancements within nuclear magnetic resonance spectroscopy to address this issue. Specifically, we consider advancements that provide new insight into methyl-bearing side chains, show the potential of using non-natural amino acids and reveal the actions of charged side chains. Combined, the new methods promise unprecedented characterisations of side chains that will further elucidate protein function.

The precious fluorine on the ring: fluorine NMR for biological systems

The fluorine-19 nucleus was recognized early to harbor exceptional properties for NMR spectroscopy. With 100% natural abundance, a high gyromagnetic ratio (83% sensitivity compared to 1H), a chemical shift that is extremely sensitive to its surroundings and near total absence in biological systems, it was destined to become a favored NMR probe, decorating small and large molecules. However, after early excitement, where uptake of fluorinated aromatic amino acids was explored in a series of animal studies, 19F-NMR lost popularity, especially in large molecular weight systems, due to chemical shift anisotropy (CSA) induced line broadening at high magnetic fields. Recently, two orthogonal approaches, (i) CF3 labeling and (ii) aromatic 19F-13C labeling leveraging the TROSY (Transverse Relaxation Optimized Spectroscopy) effect have been successfully applied to study large biomolecular systems. In this perspective, we will discuss the fascinating early work with fluorinated aromatic amino acids, which reveals the enormous potential of these non-natural amino acids in biological NMR and the potential of 19F-NMR to characterize protein and nucleic acid structure, function and dynamics in the light of recent developments. Finally, we explore how fluorine NMR might be exploited to implement small molecule or fragment screens that resemble physiological conditions and discuss the opportunity to follow the fate of small molecules in living cells.

What does fluorine do to a protein? Thermodynamic, and highly-resolved structural insights into fluorine-labelled variants of the cold shock protein

Fluorine labelling represents one promising approach to study proteins in their native environment due to efficient suppressing of background signals. Here, we systematically probe inherent thermodynamic and structural characteristics of the Cold shock protein B from Bacillus subtilis (BsCspB) upon fluorine labelling. A sophisticated combination of fluorescence and NMR experiments has been applied to elucidate potential perturbations due to insertion of fluorine into the protein. We show that single fluorine labelling of phenylalanine or tryptophan residues has neither significant impact on thermodynamic stability nor on folding kinetics compared to wild type BsCspB. Structure determination of fluorinated phenylalanine and tryptophan labelled BsCspB using X-ray crystallography reveals no displacements even for the orientation of fluorinated aromatic side chains in comparison to wild type BsCspB. Hence we propose that single fluorinated phenylalanine and tryptophan residues used for protein labelling may serve as ideal probes to reliably characterize inherent features of proteins that are present in a highly biological context like the cell.