Heavy metal-free 19F NMR probes for quantitative measurements of glutathione reductase activity using silica nanoparticles as a signal quencher

For the quantitative assessment of the glutathione reductase (GR) activity with a (19)F NMR spectroscopy, we developed the heavy metal-free probes based on silica nanoparticles modified with water-soluble perfluorinated dendrimers via the disulfide linkers. Before enzymatic reaction, the molecular rotation of the perfluorinated dendrimers is highly restricted, and the magnitude of (19)F NMR signals from the perfluorinated dendrimers can be suppressed. By the reductive cleavage of the disulfide linkers with the reduced glutathione-mediated enzymatic reaction of GR, perfluorinated dendrimers can be released from the surfaces of the nanoparticles. Consequently, the (19)F NMR signals of perfluorinated dendrimers were recovered. The enzymatic activity of GR was determined from the increase of the magnitude of (19)F NMR signals. Finally, to demonstrate the feasibility of the probe in the presence of miscellaneous molecules under bio-mimetic conditions, the comparison study was executed with the cancer cell lysate. The value determined from our method showed a good agreement with that from the conventional method.     

19F NMR study of protein-induced rhombic perturbations on the electronic structure of the active site of myoglobin

 A novel C ₂-symmetric ring-fluorinated hemin, 13,17-bis(2-carboxyethyl)-2,8,12,18-tetramethyl-3,7-difluoroporphyrinatoiron(III), has been synthesized and was incorporated into sperm whale apomyoglobin to investigate protein-induced rhombic perturbations on the electronic structure of the active site of myoglobin (Mb) using ¹⁹F NMR spectroscopy. NMR signals for ¹⁹F atoms introduced as substituents on the present heme in ferrous low-spin and high-spin and ferric low-spin complexes have been observed and their shifts sharply reflect not only the electronic nature of the heme iron, but also in-plane asymmetry of the heme electronic structure. The two-fold symmetric electronic structure of the ring-fluorinated hemin is clearly manifested in the ¹⁹F and ¹H NMR spectra of its dicyano complex. The chemical equivalence of the two fluorine atoms of the heme is removed in the active site of myoglobin and the splitting of the two ¹⁹F NMR signals provides a quantitative probe for characterizing the rhombic perturbation of the heme electronic structure induced by the heme-protein interaction. The in-plane asymmetry of heme electronic structures in carbonmonoxy and deoxy Mbs have been analyzed for the first time on the basis of the shift difference between the two ¹⁹F NMR signals of the heme and is interpreted in terms of iron-ligand binding and/or the orbital ground state of the heme. A potential utility of ¹⁹F NMR, combined with the use of a symmetric fluorinated hemin, in characterizing the heme electronic structure of myoglobin in a variety of iron oxidation, spin, and ligation states, is presented. Received: 23 December 1999 / Accepted: 3 April 2000     

Structural Studies of Bcl-xL/ligand Complexes using 19F NMR

Fluorine atoms are often incorporated into drug molecules as part of the lead optimization process in order to improve affinity or modify undesirable metabolic and pharmacokinetic profiles. From an NMR perspective, the abundance of fluorinated drug leads provides an exploitable niche for structural studies using ¹⁹F NMR in the drug discovery process. As ¹⁹F has no interfering background signal from biological sources, ¹⁹F NMR studies of fluorinated drugs bound to their protein receptors can yield easily interpretable and unambiguous structural constraints. ¹⁹F can also be selectively incorporated into proteins to obtain additional constraints for structural studies. Despite these advantages, ¹⁹F NMR has rarely been exploited for structural studies due to its broad lines in macromolecules and their ligand complexes, leading to weak signals in ¹H/¹⁹F heteronuclear NOE experiments. Here we demonstrate several different experimental strategies that use ¹⁹F NMR to obtain ligand–protein structural constraints for ligands bound to the anti-apoptotic protein Bcl-xL, a drug target for anti-cancer therapy. These examples indicate the applicability of these methods to typical structural problems encountered in the drug development process.     

An NMR method for characterizing conformation changes in proteins

An NMR method for detecting and estimating the magnitude of conformation changes in proteins is described. By measuring both ¹⁹F and ¹H chemical shifts in a -CH₂F probe ring current shifts can be determined separately from shifts due to van der Waals interactions and electric fields. The method has been applied to lysozyme and a conformation change in a complex of the enzyme with β-methyl monofluoro-N-acetylglucosamine has been detected. The effect is due to the ionization of Asp 52, one of the catalytic groups, and the magnitude of the change is estimated to be about 1 Å. A mechanism for this conformation change is proposed.     

Bimodal quantitative monitoring for enzymatic activity with simultaneous signal increases in 19F NMR and fluorescence using silica nanoparticle-based molecular probes

We describe the bimodal quantitative assay for enzymatic activity in (19)F NMR spectroscopy and fluorescence spectroscopy using a nanoparticle-based molecular probe. Perfluorinated dendrimers were tethered on silica nanoparticles with a phosphate-caged fluorescein as a linker. Before enzymatic reaction, the molecular rotation of the perfluorinated dendrimers should be highly restricted, and the (19)F NMR signals from the perfluorinated dendrimers were too broad to be detected relative to the noise level. Fluorescence signals of fluorescein were suppressed by the presence of the diphosphate groups. Following the enzymatic reaction with an alkaline phosphatase, perfluorinated dendrimers and fluorescein were released, and the NMR signals of perfluorinated dendrimers and strong fluorescence from fluorescein were correspondingly observed. The enzymatic activity and reaction rates of the hydrolysis of alkaline phosphatase were detected from the increases of fluorescence and (19)F NMR signals. Finally, the feasibility of the probe in the presence of miscellaneous molecules under biomimetic conditions was demonstrated by determining of the enzymatic activity in cell lysate. Quantitative analysis using both (19)F NMR spectroscopy and fluorescence spectroscopy can be accomplished.     

19F Nuclear Magnetic Resonance as a Tool To Investigate Microbial Degradation of Fluorophenols to Fluorocatechols and Fluoromuconates

A method was developed to study the biodegradation and oxidative biodehalogenation of fluorinated phenols by ¹⁹F nuclear magnetic resonance (NMR). Characterization of the ¹⁹F NMR spectra of metabolite profiles of a series of fluorophenols, converted by purified phenol hydroxylase, catechol 1,2-dioxygenase, and/or by the yeast-like fungus Exophiala jeanselmei, provided possibilities for identification of the ¹⁹F NMR chemical shift values of fluorinated catechol and muconate metabolites. As an example, the ¹⁹F NMR method thus defined was used to characterize the time-dependent metabolite profiles of various halophenols in either cell extracts or in incubations with whole cells of E. jeanselmei. The results obtained for these two systems are similar, except for the level of muconates observed. Altogether, the results of the present study describe a ¹⁹F NMR method which provides an efficient tool for elucidating the metabolic pathways for conversion of fluorine-containing phenols by microorganisms, with special emphasis on possibilities for biodehalogenation and detection of the type of fluorocatechols and fluoromuconates involved. In addition, the method provides possibilities for studying metabolic pathways in vivo in whole cells.     

In vivo 19F NMR chemical-shift imaging of Ancistrocladus species

Summary ¹⁹F nuclear magnetic resonance (NMR) imaging and¹⁹F NMR chemical-shift imaging (¹⁹F CSI) have been used to localize fluorinated compounds administered to stems ofAncistrocladus heyneanus andA. abbreviatus for the elucidation of biosynthetic pathways in living plants. This first application of¹⁹F CSI on plants proved CSI to be a valuable technique for mapping fluorinated molecules in plants. Exemplarily using trifluoroacetate as a model compound allowed to select appropriate feeding methods and to optimize both concentration and duration of the application to the plant. The time course of the uptake and distribution of trifluoroacetate was monitored by both¹⁹F imaging and¹⁹F CSI. Fluorinated metabolites formed by uptake of 3-fluoro-3-deoxy-D-glucose were detected with¹⁹F CSI.Abbreviations 3-FDG 3-fluoro-3-deoxy-D-glucose - CSI chemicalshift imaging - NMR nuclear magnetic resonance - SNR signal-to-noise ratio - TFA trifluoroacetate Dedicated to Professor Manfred Christi on the occasion of his 60th birthday     

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.     

Approaches for the measurement of solvent exposure in proteins by <Superscript>19</Superscript>F NMR

Fluorine NMR is a useful tool to probe protein folding, conformation and local topology owing to the sensitivity of the chemical shift to the local electrostatic environment. As an example we make use of ¹⁹F NMR and 3-fluorotyrosine to evaluate the conformation and topology of the tyrosine residues (Tyr-99 and Tyr-138) within the EF-hand motif of the C-terminal domain of calmodulin (CaM) in both the calcium-loaded and calcium-free states. We critically compare approaches to assess topology and solvent exposure via solvent isotope shifts, ¹⁹F spin–lattice relaxation rates, ¹H–¹⁹F nuclear Overhauser effects, and paramagnetic shifts and relaxation rates from dissolved oxygen. Both the solvent isotope shifts and paramagnetic shifts from dissolved oxygen sensitively reflect solvent exposed surface areas.     

Development of a Maleimide Amino Acid for Use as a Tool for Peptide Conjugation and Modification

An amino acid possessing a maleimide side chain was developed and synthesized in good yield. With a propensity to undergo the Michael addition reaction, the creation of a maleimide amino acid derivative was targeted for use as a highly functional tool for enabling peptide conjugation and structural modifications. After addressing the inherent potential side reactions of maleimides during solid phase peptide synthesis, the ability to incorporate the maleimide amino acid in an RGDS peptide sequence was demonstrated. ¹H NMR and mass spectroscopic techniques enabled thorough characterization of the peptide sequence, confirming the presence of the maleimide functionality. Once characterized, the ability to use the maleimide moiety as a peptide modification tool was investigated. Specifically, it was shown that the maleimide functional group could be exploited, given the proper reaction conditions, to anchor a peptide to a surface and create a cyclic conformation from a linear sequence. Furthermore, bioactivity of the peptide containing maleimide amino acid was evaluated by studying cellular interactions with surfaces functionalized with an integrin binding sequence.     

Signal turn-on probe for nucleic acid detection based on (19)F nuclear magnetic resonance

To image gene expression in vivo, we designed and synthesized a novel signal turn-on probe for ¹⁹F nuclear magnetic resonance (MR) imaging based on paramagnetic relaxation enhancement. The stem-loop structured oligodeoxyribonucleotide (ODN) having a molecular beacon sequence for point mutated K-ras mRNA was doubly labeled with bis(trifluoromethyl)benzene moiety and Gd-1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid chelate moiety at the each termini of the ODN probe, respectively. We found that the ¹⁹F MR signal of the bis(trifluoromethyl)benzene moiety tethered at the 5′ termini of the probe turned on by the addition of complementary ODN. The probe has the potential to image gene expressions in vivo.     

<Superscript>19</Superscript>F labelled glycosaminoglycan probes for solution NMR and non-linear (CARS) microscopy

Studying polysaccharide-protein interactions under physiological conditions by conventional techniques is challenging. Ideally, macromolecules could be followed by both in vitro spectroscopy experiments as well as in tissues using microscopy, to enable a proper comparison of results over these different scales but, often, this is not feasible. The cell surface and extracellular matrix polysaccharides, glycosaminoglycans (GAGs) lack groups that can be detected selectively in the biological milieu. The introduction of ¹⁹F labels into GAG polysaccharides is explored and the interaction of a labelled GAG with the heparin-binding protein, antithrombin, employing ¹⁹F NMR spectroscopy is followed. Furthermore, the ability of ¹⁹F labelled GAGs to be imaged using CARS microscopy is demonstrated. ¹⁹F labelled GAGs enable both ¹⁹F NMR protein-GAG binding studies in solution at the molecular level and non-linear microscopy at a microscopic scale to be conducted on the same material, essentially free of background signals.     

Perfluoro‐tert‐butyl‐homoserine as a sensitive 19F NMR reporter for peptide–membrane interactions in solution

Fluorine (¹⁹F) NMR is a valuable tool for studying dynamic biological processes. However, increasing the sensitivity of fluorinated reporter molecules is a key to reducing acquisition times and accessing transient biological interactions. Here, we evaluate the utility a novel amino acid, l ‐O‐(perfluoro‐t‐butyl)‐homoserine (pFtBSer), that can easily be synthesized and incorporated into peptides and provides greatly enhanced sensitivity over currently used ¹⁹F biomolecular NMR probes. Incorporation of pFtBSer into the potent antimicrobial peptide MSI‐78 results in a sharp ¹⁹F NMR singlet that can be readily detected at concentrations of 5 µm and lower. We demonstrate that pFtBSer incorporation into MSI‐78 provides a sensitive tool to study binding through ¹⁹F NMR chemical shift and nuclear relaxation changes. These results establish future potential for pFtBSer to be incorporated into various proteins where NMR signal sensitivity is paramount, such as in‐cell investigations. Copyright © 2013 European Peptide Society and John Wiley & Sons, Ltd.     

19F NMR metabolomics for the elucidation of microbial degradation pathways of fluorophenols

Of all NMR-observable isotopes ¹⁹F is the one most convenient for studies on the biodegradation of environmental pollutants and especially for fast initial metabolic screening of newly isolated organisms. In the past decade we have identified the ¹⁹F NMR characteristics of many fluorinated intermediates in the microbial degradation of fluoroaromatics including especially fluorophenols. In the present paper we give an overview of results obtained for the initial steps in the aerobic microbial degradation of fluorophenols, i.e. the aromatic hydroxylation to di-, tri- or even tetrahydroxybenzenes ultimately suitable as substrates for the second step, ring cleavage by dioxygenases. In addition we present new results from studies on the identification of metabolites resulting from reaction steps following aromatic ring cleavage, i.e. resulting from the conversion of fluoromuconates by chloromuconate cycloisomerase. Together the presented data illustrate the potential of the ¹⁹F NMR technique for (1) fast initial screening of biodegradative pathways, i.e. for studies on metabolomics in newly isolated microorganisms, and (2) identification of relatively unstable pathway intermediates like fluoromuconolactones and fluoromaleylacetates. Journal of Industrial Microbiology & Biotechnology (2001) 26, 22–34. Received 20 April 2000/ Accepted in revised form 22 May 2000     

The use of p-fluorobenzenesulfonyl chloride as a reagent for studies of proteins by fluorine nuclear magnetic resonance

The reagent p-fluorobenzenesulfonyl chloride modifies the protein side chains of tyrosine, lysine, and histidine and the alpha-NH2 group. The p-fluorobenzenesulfonyl (Fbs-) group, identified by the 19F nuclear magnetic resonance signal, exhibits a different 19F chemical shift for each functional group modified. The Fourier-transformed spectra of the Fbs- group displayed the expected nine-line multiplet in Fbs- amino acids and simple Fbs- peptides but not in the Fbs- proteins, where the resolution was less. Lysozyme, RNase, DNase, and chymotrypsin react with this reagent and each Fbs- protein exhibits a distinctive pattern of 19F NMR signals due to the label, suggesting that the reaction of the reagent varies with the reactivity of the side chains in a protein. The three major 19F signals of the unfolded Fbs-RNase in 8 M urea are due to the Fbs- label on the imidazolium, alpha-NH2, and epsilon-NH2 groups. Based upon results from amino acid and 19F NMR analyses of the tryptic-chymotryptic peptides of Fbs-RNase, portions of the imidazolium and epsilon-NH2 resonances were assigned to the Fbs- label on His-105 and Lys-41, respectively, while the alpha-NH2 resonance was entirely due to the Fbs- label on the alpha-NH2 of Lys-1. Because Fbs-RNase has an unchanged, near-ultraviolet circular dichroism spectrum and because it retains approximately 80% of the RNase activity, the conformation of Fbs-RNase is probably not altered from the folded conformation of the native enzyme. Upon unfolding in 8 M urea or heating at 70 degrees C, Fbs-RNase gave a 19F NMR spectrum differing from that of the folded Fbs-RNase. In the presence of uridylic acid, Lys-41 was the only residue protected from modification by the reagent with a concomitant reduction of the epsilon-NH2 resonance, and the RNase thus modified was fully active. Hence, 19F NMR analysis of protein, via the reaction with p-fluorobenzenesulfonyl chloride, provided not only information about the protein conformation but also direct measurements of the modification status.     

Synthesis,molecular docking,and antioxidant activity of new fluorescent tetrafluoroterphenyl analogues

Nucleophilic aromatic substitution (S_NAr) chemistry has been applied to develop many functionalized pentafluorobenzene derivatives. Those compounds are highly specific at the para position of the fluorinated ring. Therefore, they are typical adducts for the preparation of antioxidant molecular systems. In this context, we report the use of S_NAr chemistry as a suitable and simple approach for the synthesis of fluorescent antioxidant perfluorinated materials bearing ether bonds in various para-substituted alkoxy chains and with high purity and excellent yields. The fluoroterphenyl core was prepared via alkylation, Cu(I)-assisted decarboxylation, and cross-coupling using the potassium salt of fluorobenzoate, followed by the reaction with different alcohols. The structures of the synthesized fluoroterphenyl adducts were investigated using FT-IR, ¹H NMR, ¹³C NMR, and ¹⁹F NMR spectroscopy. The emission spectra and absorption spectra showed solvatochromism. The newly prepared tetrafluoroterphenyl analogues were investigated by antioxidant examination using the 2,2-diphenyl-1-picrylhydrazyl assay. Results were compared with ascorbic acid and butylated hydroxytoluene as references, and revealed that the tetrafluoroterphenyl analogues containing a decyl chain had the highest activity, with an IC₅₀ value of 22.36 ± 0.19 g/ml. The produced tetrafluoroterphenyl analogues were used in molecular docking strategies with a Protein Data Bank protein ID 5IKQ. The antioxidant investigations and docking results were convergent.     

Novel fluorinated lipopeptides from Bacillus sp. CS93 via precursor-directed biosynthesis

While attempting to improve production of fluoro-iturin A in Bacillus sp. CS93 new mono- and di-fluorinated fengycins were detected in culture supernatants by ¹⁹F NMR and tandem mass spectrometry, after incubation of the bacterium with 3-fluoro-l-tyrosine. The fluorinated amino acid was presumably incorporated in place of one or both of the tyrosyl residues in fengycin. Investigations to generate additional new fluorinated derivatives were undertaken using commercially available fluorinated phenylalanines and 2-fluoro- and 2,3-difluoro-tyrosine that were synthesised by Negishi cross-coupling of iodoalanine and fluorinated bromo-phenols. The anti-fungal activity of the fluorinated lipopeptides was assayed against Trichophyton rubrum and found to be similar to that of the non-fluorinated metabolites.     

5-Fluorotryptophan as dual probe for ground-state heterogeneity and excited-state dynamics in apoflavodoxin

The apoflavodoxin protein from Azotobacter vinelandii harboring three tryptophan (Trp) residues, was biosynthetically labeled with 5-fluorotryptophan (5-FTrp). 5-FTrp has the advantage that chemical differences in its microenvironment can be sensitively visualized via ¹⁹F NMR. Moreover, it shows simpler fluorescence decay kinetics. The occurrence of FRET was earlier observed via the fluorescence anisotropy decay of WT apoflavodoxin and the anisotropy decay parameters are in excellent agreement with distances between and relative orientations of all Trp residues. The anisotropy decay in 5-FTrp apoflavodoxin demonstrates that the distances and orientations are identical for this protein. This work demonstrates the added value of replacing Trp by 5-FTrp to study structural features of proteins via ¹⁹F NMR and fluorescence spectroscopy.     

Biodegradation of polyfluorinated biphenyl in bacteria

Fluorinated aromatic compounds are significant environmental pollutants, and microorganisms play important roles in their biodegradation. The effect of fluorine substitution on the transformation of fluorobiphenyl in two bacteria was investigated. Pseudomonas pseudoalcaligenes KF707 and Burkholderia xenovorans LB400 used 2,3,4,5,6-pentafluorobiphenyl and 4,4??-difluorobiphenyl as sole sources of carbon and energy. The catabolism of the fluorinated compounds was examined by gas chromatography?Cmass spectrometry and fluorine-19 nuclear magnetic resonance spectroscopy (¹⁹F NMR), and revealed that the bacteria employed the upper pathway of biphenyl catabolism to degrade these xenobiotics. The novel fluorometabolites 3-pentafluorophenyl-cyclohexa-3,5-diene-1,2-diol and 3-pentafluorophenyl-benzene-1,2-diol were detected in the supernatants of biphenyl-grown resting cells incubated with 2,3,4,5,6-pentafluorobiphenyl, most likely as a consequence of the actions of BphA and BphB. 4-Fluorobenzoate was detected in cultures incubated with 4,4??-difluorobiphenyl and ¹⁹F NMR analysis of the supernatant from P. pseudoalcaligenes KF707 revealed the presence of additional water-soluble fluorometabolites.     

NMR measurements of Ca2+ and H+ transport mediated by A23187 and reconstituted plasma membrane Ca2+-ATPase

NMR-based assays for measuring the fluxes of Ca²⁺, H⁺, and ATP in liposomal systems are presented. The ¹⁹F NMR Ca²⁺-chelating molecule 5,5-difluoro-1,2-bis(o-amino-phenoxy)ethane-N,N,N′,N′-tetraacetic acid (5FBAPTA) was trapped inside large unilamellar vesicles and used to monitor passive and A23187-mediated Ca²⁺ transport into them. The data were analyzed using progress curves of the transport reaction. They demonstrated the general applicability of 5FBAPTA as a ¹⁹F NMR probe of active Ca²⁺ transport. ³¹P NMR time-courses were used to monitor simultaneously the ATP hydrolysing activity of the reconstituted human erythrocyte Ca²⁺-ATPase and the concomitant acidification of the reaction medium in a suspension of small unilamellar vesicles. Using an estimate of the extraliposomal buffering capacity, the H⁺/ATP coupling stoichiometry, in the presence of A23187, was estimated from the NMR-derived data at steady state; it amounted to 1.4±0.3. This result is discussed with respect to the issue of molecular `slip' in the context of a non-equilibrium thermodynamics model of the pump (accompanying paper in this issue). Importantly, NMR, in contrast to optical detection methods, can potentially register all fluxes and (electro)chemical gradients involved in the Ca²⁺-ATPase-mediated H⁺/Ca²⁺counterport, in a single experiment. Received: 19 June 1997 / Accepted: 3 December 1997