Probing the micelle-bound aggregation-prone state of α-synuclein with (19)F NMR spectroscopy

Fluorinated Tags to Study Protein Conformation and Interactions Using 19F NMR

The incorporation of fluorine atoms into a biomacromolecule provides a background-free and environmentally sensitive reporter of structure, conformation and interactions using 19F NMR. There are several methods to introduce the 19F reporter - either by synthetic incorporation via solid phase peptide synthesis; by suppressing the incorporation or biosynthesis of a natural amino acid and supplementing the growth media with a fluorinated counterpart during protein expression; and by genetic code expansion to add new amino acids to the amino acid alphabet. This review aims to discuss progress in the field of introducing fluorinated handles into biomolecules for NMR studies by post-translational bioconjugation or 'fluorine-tagging'. We will discuss the range of chemical tagging 'warheads' that have been used, explore the applications of fluorine tags, discuss ways to enhance reporter sensitivity and how the signal to noise ratios can be boosted. Finally, we consider some key challenges of the field and offer some ideas for future directions.

19F NMR as a tool in chemical biology

We previously reviewed the use of 19F NMR in the broad field of chemical biology [Cobb, S. L.; Murphy, C. D. J. Fluorine Chem. 2009, 130, 132-140] and present here a summary of the literature from the last decade that has the technique as the central method of analysis. The topics covered include the synthesis of new fluorinated probes and their incorporation into macromolecules, the application of 19F NMR to monitor protein-protein interactions, protein-ligand interactions, physiologically relevant ions and in the structural analysis of proteins and nucleic acids. The continued relevance of the technique to investigate biosynthesis and biodegradation of fluorinated organic compounds is also described.

Use of 19 F Differential Labelling for the Simultaneous Detection and Monitoring of Three Individual Proteins in a Serum Environment

Protein behavior in complex mixtures, such as biological fluids, is often modeled by simplified buffer systems in solution. Here we have used the recently described differential ¹⁹ F labelling approach (with NMR detection) to monitor and compare the solution behaviour of three proteins at once: human serum albumin (HSA), transferrin (TrF), and immunoglobulin G (IgG), both in serum and in buffer. We demonstrate that monitoring three proteins simultaneously and independently in biological fluid is possible, and that the presence of other endogenous components greatly changes the association characteristics of these proteins. For example, in the simplified model buffer system, all three proteins diffuse at a similar rate, while in serum HSA diffuses around three times faster than TrF, and four times faster than IgG. This ¹⁹ F NMR approach allows characterization of the behaviour of complex multiprotein systems in their native environment, e. g., in biological fluids.

19F NMR as a Tool for Monitoring Individual Differentially Labeled Proteins in Complex Mixtures

The ability to monitor the behavior of individual proteins in complex mixtures has many potential uses, ranging from analysis of protein interactions in highly concentrated solutions, modeling biological fluids or the intracellular environment, to optimizing biopharmaceutical co-formulations. Differential labeling NMR approaches, which traditionally use ¹⁵N or ¹³C isotope incorporation during recombinant expression, are not always practical in cases when endogenous proteins are obtained from an organism, or where the expression system does not allow for efficient labeling, especially for larger proteins. This study proposes differential labeling of proteins by covalent attachment of ¹⁹F groups with distinct chemical shifts, giving each protein a unique spectral signature which can be monitored by ¹⁹F NMR without signal overlap, even in complex mixtures, and without any interfering signals from the buffer or other unlabeled components. Parameters, such as signal intensities, translational diffusion coefficients, and transverse relaxation rates, which report on the behavior of individual proteins in the mixture, can be recorded even for proteins as large as antibodies at a wide range of concentrations.

Protein 19F-labeling using transglutaminase for the NMR study of intermolecular interactions

The preparation of stable isotope-labeled proteins is important for NMR studies, however, it is often hampered in the case of eukaryotic proteins which are not readily expressed in Escherichia coli. Such proteins are often conveniently investigated following post-expression chemical isotope tagging. Enzymatic ¹⁵N-labeling of glutamine side chains using transglutaminase (TGase) has been applied to several proteins for NMR studies. ¹⁹F-labeling is useful for interaction studies due to its high NMR sensitivity and susceptibility. Here, ¹⁹F-labeling of glutamine side chains using TGase and 2,2,2-trifluoroethylamine hydrochloride was established for use in an NMR study. This enzymatic ¹⁹F-labeling readily provided NMR detection of protein-drug and protein-protein interactions with complexes of about 100 kDa since the surface residues provided a good substrate for TGase. The ¹⁹F-labeling method was 3.5-fold more sensitive than ¹⁵N-labeling, and could be combined with other chemical modification techniques such as lysine ¹³C-methylation. ¹³C-dimethylated-¹⁹F-labeled FKBP12 provided more accurate information concerning the FK506 binding site.

Alpha-Synuclein Disease Mutations Are Structurally Defective and Locally Affect Membrane Binding

The intrinsically disordered human protein alpha-Synuclein (αS) has a prominent role in Parkinson's disease (PD) pathology. Several familial variants of αS are correlated with inherited PD. Disease mutations have been shown to have an impact on lipid membrane binding. Here, using electron paramagnetic resonance spectroscopy in combination with site-directed spin labeling, we show that familial PD-associated variants are structurally defective in membrane binding and alter the local binding properties of the protein.

Simultaneous detection of distinct ubiquitin chain topologies by 19F NMR

The dynamic interplay between ubiquitin (Ub) chain construction and destruction is critical for the regulation of many cellular pathways. To understand these processes, it would be ideal to simultaneously detect different Ub chains as they are created and destroyed in the cell. This objective cannot be achieved with existing detection strategies. Here, we report on the use of ¹⁹F Nuclear Magnetic Resonance (NMR) spectroscopy to detect and characterize conformationally distinct Ub oligomers. By exploiting the environmental sensitivity of the ¹⁹F nucleus and the conformational diversity found among Ub chains of different linkage types, we can simultaneously resolve the ¹⁹F NMR signals for mono-Ub and three distinct di-Ub oligomers (K6, K48, and K63) in heterogeneous mixtures. The utility of this approach is demonstrated by the ability to interrogate the selectivity of deubiquitinases with multiple Ub substrates in real time. We also demonstrate that ¹⁹F NMR can be used to discern Ub linkages that are formed by select E3 ligases found in pathogenic bacteria. Collectively, our results assert the potential of ¹⁹F NMR for monitoring Ub signaling in cells to reveal fundamental insights about the associated cellular pathways.

Using (19)F NMR to probe biological interactions of proteins and peptides

Fluorine is a valuable probe for investigating the interactions of biological molecules because of its favorable NMR characteristics, its small size, and its near total absence from biology. Advances in biosynthetic methods allow fluorine to be introduced into peptides and proteins with high precision, and the increasing sensitivity of NMR spectrometers has facilitated the use of (19)F NMR to obtain molecular-level insights into a wide range of often-complex biological interactions. Here, we summarize the advantages of solution-state (19)F NMR for studying the interactions of peptides and proteins with other biological molecules, review methods for the production of fluorine-labeled materials, and describe some representative recent examples in which (19)F NMR has been used to study conformational changes in peptides and proteins and their interactions with other biological molecules.

Resolution of oligomeric species during the aggregation of Aβ1-40 using (19)F NMR

In the commonly used nucleation-dependent model of protein aggregation, aggregation proceeds only after a lag phase in which the concentration of energetically unfavorable nuclei reaches a critical value. The formation of oligomeric species prior to aggregation can be difficult to detect by current spectroscopic techniques. By using real-time (19)F NMR along with other techniques, we are able to show that multiple oligomeric species can be detected during the lag phase of Aβ1-40 fiber formation, consistent with a complex mechanism of aggregation. At least six types of oligomers can be detected by (19)F NMR. These include the reversible formation of large β-sheet oligomer immediately after solubilization at high peptide concentration, a small oligomer that forms transiently during the early stages of the lag phase, and four spectroscopically distinct forms of oligomers with molecular weights between ∼30 and 100 kDa that appear during the later stages of aggregation. The ability to resolve individual oligomers and track their formation in real-time should prove fruitful in understanding the aggregation of amyloidogenic proteins and in isolating potentially toxic nonamyloid oligomers.

5-fluoro-D,L-tryptophan as a dual NMR and fluorescent probe of α-synuclein

Analysis of conventional proton nuclear magnetic resonance (NMR) experiments on intrinsically disordered proteins (IDPs) is challenging because of the highly flexible and multiple rapidly exchanging conformations typifying this class of proteins. One method to circumvent some of these difficulties is to incorporate nonnative fluorine ((19)F) nuclei at specific sites within the polypeptide. (19)F NMR is particularly suitable for characterization of unfolded structures because (19)F chemical shifts are highly sensitive to local environments and conformations. Furthermore, the incorporation of fluorine analogs of fluorescent amino acids such as 5-fluoro-D: ,L: -tryptophan (5FW) allows for complementary studies of protein microenvironment via fluorescence spectroscopy. Herein, we describe methods to produce, purify, characterize, and perform steady-state fluorescence and 1D NMR experiments on 5FW analogs of the IDP α-synuclein.

A rationally designed six-residue swap generates comparability in the aggregation behavior of α-synuclein and β-synuclein

The aggregation process of α-synuclein, a protein closely associated with Parkinson's disease, is highly sensitive to sequence variations. It is therefore of great importance to understand the factors that define the aggregation propensity of specific mutational variants as well as their toxic behavior in the cellular environment. In this context, we investigated the extent to which the aggregation behavior of α-synuclein can be altered to resemble that of β-synuclein, an aggregation-resistant homologue of α-synuclein not associated with disease, by swapping residues between the two proteins. Because of the vast number of possible swaps, we have applied a rational design procedure to single out a mutational variant, called α2β, in which two short stretches of the sequence in the NAC region have been replaced in α-synuclein from β-synuclein. We find not only that the aggregation rate of α2β is close to that of β-synuclein, being much lower than that of α-synuclein, but also that α2β effectively changes the cellular toxicity of α-synuclein to a value similar to that of β-synuclein upon exposure of SH-SY5Y cells to preformed oligomers. Remarkably, control experiments on the corresponding mutational variant of β-synuclein, called β2α, confirmed that the mutations that we have identified also shift the aggregation behavior of this protein toward that of α-synuclein. These results demonstrate that it is becoming possible to control in quantitative detail the sequence code that defines the aggregation behavior and toxicity of α-synuclein.

Interaction of α-synuclein and a cell penetrating fusion peptide with higher eukaryotic cell membranes assessed by ¹⁹F NMR

We show that fluorine NMR can be used to monitor the insertion and change in conformation of a ¹⁹F-labeled cell-penetrating peptide upon interacting with the cellular plasma membrane. α-Synuclein and a construct comprising a cell-penetrating peptide covalently attached to its N-terminus were studied. Important information about the interaction of the proteins with CHO-K1 cells was obtained by monitoring the diminution of ¹⁹F resonances of 3-fluoro-l-tyrosine labeled proteins. For α-synuclein, a decrease in the resonance from position 39 was observed indicating that only the N-terminal third region of the protein interacts with plasma membrane. However, when the fusion construct was incubated with the cells, a decrease in the resonance from the fusion peptide region was noted with no change in the resonances from α-synuclein region. Longer incubation, studied by using confocal fluorescence microscopy, revealed that the fusion construct translocates into the cells, but α-synuclein alone did not cross the membrane in significant amounts.

Using fluorine nuclear magnetic resonance to probe changes in the structure and dynamics of membrane-active peptides interacting with lipid bilayers

The antimicrobial peptide MSI-78 serves as a model system for studying interactions of bioactive peptides with membranes. Using a series of MSI-78 peptides that incorporate l-4,4,4-trifluoroethylglycine, a small and sensitive (19)F nuclear magnetic resonance probe, we investigated how the local structure and dynamics of the peptide change when it binds to the lipid bilayer. The fluorinated MSI-78 analogues exhibited position-specific changes in (19)F chemical shift ranging from 1.28 to -1.35 ppm upon binding to lipid bicelles. The largest upfield shifts are associated with the most hydrophobic positions in the peptide. Changes in solvent isotope effects (H(2)O/D(2)O) on (19)F chemical shifts were observed for the peptides that are consistent with the MSI-78 solvent-inaccessible hydrophobic core upon binding bicelles. Transverse relaxation measurements of the (19)F nucleus, using the Carr-Purcell-Meiboom-Gill pulse sequence, were used to examine changes in the local mobility of MSI-78 that occur upon binding to the lipid bilayer. Positions in the hydrophobic core of peptide-membrane complex show the greatest decrease in mobility upon binding of the lipid bilayer, whereas residues that interact with lipid headgroups are more mobile. The most mobile positions are at the N- and C-termini of the peptide. These results provide support for the proposed mechanism of membrane disruption by MSI-78 and reveal new details about the dynamic changes that accompany membrane binding.