Computational approaches to investigate fluoride binding, selectivity and transport across the membrane.

The use of molecular dynamics (MD) simulations to study biomolecular systems has proven reliable in elucidating atomic-level details of structure and function. In this chapter, MD simulations were used to uncover new insights into two phylogenetically unrelated bacterial fluoride (F-) exporters: the CLCF F-/H+ antiporter and the Fluc F- channel. The CLCF antiporter, a member of the broader CLC family, has previously revealed unique stoichiometry, anion-coordinating residues, and the absence of an internal glutamate crucial for proton import in the CLCs. Through MD simulations enhanced with umbrella sampling, we provide insights into the energetics and mechanism of the CLCF transport process, including its selectivity for F- over HF. In contrast, the Fluc F- channel presents a novel architecture as a dual topology dimer, featuring two pores for F- export and a central non-transported sodium ion. Using computational electrophysiology, we simulate the electrochemical gradient necessary for F- export in Fluc and reveal details about the coordination and hydration of both F- and the central sodium ion. The procedures described here delineate the specifics of these advanced techniques and can also be adapted to investigate other membrane protein systems.

NMR methods to detect fluoride binding and transport by membrane proteins.

Solid-state nuclear magnetic resonance (NMR) methods can probe the motions of membrane proteins in liposomes at the atomic level, and propel the understanding of biomolecular processes for which static structures cannot provide a satisfactory description. High-resolution crystallography snapshots have provided a structural basis for fluoride channels. NMR is a powerful tool to build upon these snapshots and depict a dynamic picture of fluoride channels in native-like lipid bilayers. In this contribution, we discuss solid-state and solution NMR experiments to detect fluoride binding and transport by fluoride channels. Ongoing developments in membrane protein sample preparation and ssNMR methodology, particularly in using 1H, 19F and 13C-detection schemes, offer additional opportunities to study structure and functional aspects of fluoride channels.

Electrophysiology of fluoride channels in the yeasts Saccharomyces cerevisiae and Candida albicans.

Tight regulation of molecules moving through the cell membrane is particularly important for free-living microorganisms because of their small cell volumes and frequent changes in the chemical composition of the extracellular environment. This is true for nutrients, but even more so for toxic molecules. Traditionally, the transport of these diverse molecules in microorganisms has been studied on cell populations rather than on single cells, mainly because of technical difficulties. The goal of this chapter is to make available a detailed method to prepare yeast spheroplasts to study the movement of fluoride ions across the plasma membrane of single cells by the patch-clamp technique. In this procedure, three steps are critical to achieve high resistance (GΩ) seals between the membrane and the glass electrode: (1) appropriate removal of the cell wall by enzymatic treatment; (2) balance between the osmotic strength of sealing solutions and cell membrane turgor; and (3) meticulous morphological inspection of spheroplasts suitable for gigaseal formation. We show now that this method, originally developed for Saccharomyces cerevisiae, can also be applied to Candida albicans, an opportunistic human pathogen.

Lanthanum-fluoride electrode-based methods to monitor fluoride transport in cells and reconstituted lipid vesicles.

Fluoride (F-) export proteins, including F- channels and F- transporters, are widespread in biology. They contribute to cellular resistance against fluoride ion, which has relevance as an ancient xenobiotic, and in more modern contexts like organofluorine biosynthesis and degradation or dental medicine. This chapter summarizes quantitative methods to measure fluoride transport across membranes using fluoride-specific lanthanum-fluoride electrodes. Electrode-based measurements can be used to measure unitary fluoride transport rates by membrane proteins that have been purified and reconstituted into lipid vesicles, or to monitor fluoride efflux into living microbial cells. Thus, fluoride electrode-based measurements yield quantitative mechanistic insight into one of the major determinants of fluoride resistance in microorganisms, fungi, yeasts, and plants.

Direct fluoride monitoring using a fluorogenic RNA-based biosensor.

Fluorinated compounds, whether naturally occurring or from anthropogenic origin, have been extensively exploited in the last century. Degradation of these compounds by physical or biochemical processes is expected to result in the release of fluoride. Several fluoride detection mechanisms have been previously described. However, most of these methods are not compatible with high- and ultrahigh-throughput screening technologies, lack the ability to real-time monitor the increase of fluoride concentration in solution, or rely on costly reagents (such as cell-free expression systems). Our group recently developed "FluorMango" as the first completely RNA-based and direct fluoride-specific fluorogenic biosensor. To do so, we merged and engineered the Mango-III light-up RNA aptamer and the fluoride-specific aptamer derived from a riboswitch, crcB. In this chapter, we explain how this RNA-based biosensor can be produced in large scale before providing examples of how it can be used to quantitatively detect (end-point measurement) or monitor in real-time fluoride release in complex biological systems by translating it into measurable fluorescent signal.

Characterisation of experimental flowable composites containing fluoride-doped calcium phosphates as promising remineralising materials.

OBJECTIVE: Remineralising composites with antibacterial properties may seal the cavity and prevent secondary caries. This study aimed at developing experimental flowable composites containing different concentrations of fluoride-doped calcium phosphate fillers and evaluating their remineralising and antibacterial properties. METHODS: Experimental resin-based composites containing different concentrations (0-20 %) of fluoride-doped calcium phosphate fillers (VS10/VS20) were formulated. The release of calcium (Ca), phosphate (PO) and fluoride (F) ions was assessed for 30 days. Remineralisation properties were evaluated through ATR-FTIR and SEM/EDX after storage in simulated body fluid (SBF). The metabolic activity and viability of Streptococcus gordonii was also evaluated through ATP, CFU and live/dead confocal microscopy. The evaluation of specific monomer elution from the experimental composites was conducted using high-performance liquid chromatography (HPLC). RESULTS: The composites containing VS10 showed the highest release of Ca, those containing VS20 released more F over time (p < 0.05), while there was no significant difference in terms of PO ions release between the groups (p > 0.05). A quick 7-day mineral precipitation was observed in the tested composites containing VS10 or VS20 at 10 %; these materials also showed the greatest antibacterial activity (p < 0.05). Moreover, the tested composites containing VS10 presented the lowest elution of monomers (p < 0.05). CONCLUSIONS: Innovative composites were developed with low monomers elution, evident antibacterial activity against S. gordonii and important remineralisation properties due to specific ions release. CLINICAL SIGNIFICANCE: Novel composites containing fluoride-doped calcium phosphates may be promising to modulate bacteria growth, promote remineralisation and reduce the risk of cytotoxicity related to monomers' elution.

Fluoride Ion Binding and Translocation in the CLCF Fluoride/Proton Antiporter: Molecular Insights from Combined Quantum-Mechanical/Molecular-Mechanical Modeling.

CLCF fluoride/proton antiporters move fluoride ions out of bacterial cells, leading to fluoride resistance in these bacteria. However, many details about their operating mechanisms remain unclear. Here, we report a combined quantum-mechanical/molecular-mechanical (QM/MM) study of a CLCF homologue from Enterococci casseliflavus (Eca), in accord with the previously proposed windmill mechanism. Our multiscale modeling sheds light on two critical steps in the transport cycle: (i) the external gating residue E118 pushing a fluoride in the external binding site into the extracellular vestibule and (ii) an incoming fluoride reconquering the external binding site by forcing out E118. Both steps feature competitions for the external binding site between the negatively charged carboxylate of E118 and the fluoride. Remarkably, the displaced E118 by fluoride accepts a proton from the nearby R117, initiating the next transport cycle. We also demonstrate the importance of accurate quantum descriptions of fluoride solvation. Our results provide clues to the mysterious E318 residue near the central binding site, suggesting that the transport activities are unlikely to be disrupted by the glutamate interacting with a well-solvated fluoride at the central binding site. This differs significantly from the structurally similar CLC chloride/proton antiporters, where a fluoride trapped deep in the hydrophobic pore causes the transporter to be locked down. A free-energy barrier of 10-15 kcal/mol was estimated via umbrella sampling for a fluoride ion traveling through the pore to repopulate the external binding site.

Enhanced remineralisation ability and antibacterial properties of sol-gel glass ionomer cement modified by fluoride containing strontium-based bioactive glass or strontium-containing fluorapatite.

OBJECTIVES: This study aimed to compare two types of bioactive additives which were strontium-containing fluorinated bioactive glass (SrBGF) or strontium-containing fluorapatite (SrFA) added to sol-gel derived glass ionomer cement (SGIC). The objective was to develop antibacterial and mineralisation properties, using bioactive additives, to minimize the occurrence of caries lesions in caries disease. METHODS: Synthesized SrBGF and SrFA nanoparticles were added to SGIC at 1 wt% concentration to improve antibacterial properties against S. mutans, promote remineralisation, and hASCs and hDPSCs viability. Surface roughness and ion-releasing behavior were also evaluated to clarify the effect on the materials. Antibacterial activity was measured via agar disc diffusion and bacterial adhesion. Remineralisation ability was assessed by applying the material to demineralised teeth and subjecting them to a 14-day pH cycle, followed by microCT and SEM-EDS analysis. RESULTS: The addition of SrFA into SGIC significantly improved its antibacterial property. SGIC modified with either SrBGF or SrFA additives could similarly induce apatite crystal precipitation onto demineralised dentin and increase dentin density, indicating its ability to remineralise dentin. Moreover, this study also showed that SGIC modified with SrBGF or SrFA additives had promising results on the in vitro cytotoxicity of hASC and hDPSC. SIGNIFICANT: SrFA has superior antibacterial property as compared to SrBGF while demonstrating equal remineralisation ability. Furthermore, the modified SGIC showed promising results in reducing the cytotoxicity of hASCs and hDPSCs, indicating its potential for managing caries.

α-Silylated Diazoalkynes: New Tools for Bioconjugation of Proteins.

α-Silylated diazoalkynes are stabilized diazo compounds that can selectively react with carboxylic residues in buffered aqueous media. In-situ fluoride induced desilylation increases this reactivity, leading to a very fast reaction. Application to the selective functionalization of RNase A, followed by post-functionalization using click chemistry, is described. These new reagents expand the toolbox for native protein modification at carboxylic residues.

Sulfate Doping Promotes Agglomeration of Calcium Fluoride Crystals.

Calcium salt precipitation is an effective solution to wastewater fluoride pollution. The purity and precipitation efficiency of calcium fluoride is critical for its removal and recovery. This study aimed to reveal the role of coexisting sulfates in the precipitation of calcium fluoride. A low sulfate concentration promoted calcium fluoride precipitation. The size of calcium fluoride-aggregated particle clusters increased from 750 to 2000 nm when the molar ratio of sulfate to fluoride was increased from 0 to 3:100. Sulfate doped in the calcium fluoride crystals neutralized the positive charge of the calcium fluoride. Online atomic force microscopy measurements showed that sulfate reduced the repulsive force between calcium fluoride crystals and increased the adhesion force from 1.62 to 2.46 nN, promoting the agglomeration of calcium fluoride crystals. Sulfate improved the precipitation efficiency of calcium fluoride by promoting agglomeration; however, the purity of calcium fluoride was reduced by doping. Sulfate reduced the induction time of calcium fluoride crystallization and improved the nucleation rate of calcium fluoride. Sulfate should be retained to improve the precipitation of calcium fluoride and to avoid its loss from the effluents. However, it is necessary to separate sulfate from fluoride to obtain high-purity calcium fluoride. Therefore, sulfate concentration regulation in high-fluoride wastewater is key to achieving the efficient removal and recovery of fluoride ions.

Enzyme Engineering Renders Chlorinase the Activity of Fluorinase.

Organofluorine compounds have attracted substantial attention owing to their wide application in agrochemistry. Fluorinase (FlA) is a unique enzyme in nature that can incorporate fluorine into an organic molecule. Chlorinase (SalL) has a similar mechanism as fluorinase and can use chloride but not fluoride as a substrate to generate 5'-chloro-deoxyadenosine (5'-ClDA) from S-adenosyl-l-methionine (SAM). Therefore, identifying the features that lead to this selectivity for halide ions is highly important. Here, we engineered SalL to gain the function of FlA. We found that residue Tyr70 plays a key role in this conversion through alanine scanning. Site-saturation mutagenesis experiments demonstrated that Y70A/C/S/T/G all exhibited obvious fluorinase activity. The G131S mutant of SalL, in which the previously thought crucial residue Ser158 for fluoride binding in FlA was introduced, did not exhibit fluorination activity. Compared with the Y70T single mutant, the double mutant Y70T/W129F increased 5'-fluoro-5-deoxyadenosine (5'-FDA) production by 76%. The quantum mechanics (QM)/molecular mechanics (MM) calculations suggested that the lower energy barriers and shorter nucleophilic distance from F- to SAM in the mutants than in the SalL wild-type may contribute to the activity. Therefore, our study not only renders SalL the activity of FlA but also sheds light on the enzyme selectivity between fluoride versus chloride.

Ratiometric fluorescence-based and chromogenic sensors for the detection of fluoride ions and their application in real samples.

This review focuses on the results of synthetic ratiometric fluorescent and colorimetric probes, which have been applied to qualitatively and quantitatively detect fluoride anions in cells, living organisms, and real samples. Primary attention is given to progress made in the working mechanism and applications of these probes to detect fluoride ions in living systems. In addition, design strategies and detection limit for these probes are discussed. This review aims to deliver a comprehensive compilation of the examples reported from 2005 to 2021 on the developments of ratiometric chromogenic and fluorogenic chemosensors for fluoride anions. A total of 20 different ratiometric/colorimetric sensors have been selected for the novelty in their design, sensitivity, detection limit, dynamic range, and speed of detection based on the three fundamental principles of F- ion detection, namely Si-O bond cleavage; excimer emission; and intramolecular charge transfer emission through the B-F monomer, B-F-B bridged dimers, and deprotonation of the amide N-H. Special emphasis has been given to categorize the fluorophores that work in aqueous media, and possible strategies that might be adopted to design green sensors are discussed. Finally, a tabular summary of the comparative studies of all the sensors based on their sensitivity, detection limit, working solvent, and applications is provided. This extensive review may expedite improvements in the development of advanced fluorescent probes for vast and stimulating applications in the future.

Synthesis and Evaluation of Glycosyl Luciferins.

Measuring glycosidase activity is important to monitor any aberrations in carbohydrate hydrolase activity, but also for the screening of potential glycosidase inhibitors. To this end, synthetic substrates are needed which provide an enzyme-dependent read-out upon hydrolysis by the glycosidase. Herein, we present two new routes for the synthesis of caged luminescent carbohydrates, which can be used for determining glycosidase activity with a luminescent reporter molecule. The substrates were validated with glycosidase and revealed a clear linear range and enzyme-dependent signal upon the in situ generation of the luciferin moiety from the corresponding nitrile precursors. Besides, we showed that these compounds could directly be synthesized from unprotected glycosyl-α-fluorides in a two-step procedure with yields up to 75 %. The intermediate methyl imidate appeared a key intermediate which also reacted with d-cysteine to give the corresponding d-luciferin substrate rendering this a highly attractive method for synthesizing glycosyl luciferins in good yields.

In-depth occlusion of dentine tubules via the application of (poly-L-aspartic acid)­strontium and phosphate/fluoride to treat dentine hypersensitivity.

Dentine hypersensitivity (DH) is a common oral health issue and occlusion of the exposed dentinal tubules (DTs) is regarded as the most effective therapeutic treatment nowadays. However, it is still difficult to develop easy and effective strategies for deep occlusion of DTs. In this study, we develop a strategy for occluding DTs deeply and compactly via simple application of occlusion media including (poly-L-aspartic acid)­strontium (PAsp­strontium) and phosphate/fluoride. The bonding of strontium ions to poly-L-aspartic acid formed a positively charged PAsp­strontium complexes. After application of 15 min each, the PAsp­strontium and phosphate/fluoride rapidly penetrated into the DTs in turn via the electrostatic interaction, then occluded the DTs with crystals up to a depth of 150 µm. The occlusion within DTs was resistant to abrasive and acidic challenges. The occlusion media performed better than commercial desensitizers Duraphat and Gluma. Moreover, this strategy possessed sufficient biocompatible and excellent performance in vivo. The application of occlusion media would shed light on in the management of DH.

Facile preparation, characterization and application of novel sugarcane bagasse-derived nanoceria-biochar for defluoridation of drinking water: kinetics, thermodynamics, reusability and mechanism.

Although expensive, rare-earth oxides are well known for being powerful defluoridation agents. Being costlier, cerium is used as a hybrid adsorbent in conjunction with a prudent and environmentally benign substance like biochar. The novel CeO2/BC (surface area 260.05 m2/g) composite was shaped using the facile chemical precipitation technique without any cross-linkers. Surface properties of synthesised CeO2/BC were investigated using powder XRD, FTIR, BET, pH point of zero charge and SEM. According to XRD analysis, immobilized Ce is primarily in form of CeO2, while pristine biochar is in an amorphous state. Batch mode adsorption tests were carried out with different solution pH, F- initial concentration, adsorbent dosage and contact time and counter anions. CeO2/BC can be used in a varied pH range (2-10) but shows maximum removal at pH 4. The Langmuir adsorption isotherm and a pseudo-second-order kinetic model are best fitted to support the adsorption process with a maximum Langmuir adsorption capacity of 16.14 mg/g (F- concentration 5 to 40 mg/L). The removal phenomenon is non-spontaneous in nature. The plausible mechanism of fluoride uptake was explained using XPS and pHPZC, and it was demonstrated that the fluoride was mainly removed by ion exchange and electrostatic attraction. The adsorbent could be successfully used up to fourth cycle after regenerating.

Adsorption removal of fluoride from polluted drinking waters using Mn-Al-La oxide.

Trimetal oxides have received high attention in treatment of fluoride-polluted drinking waters. In this study, Mn-Al-La (MAL) oxide with a mole ratio of 2:1:1 was successively prepared and characterized by XRD, FTIR, XPS, and TEM. It exhibited as cotton-like assemblages (500-800 nm of axial lengths), and BET specific surface area was 52 m2/g. It was used to study fluoride adsorptions in aqueous solutions by batch experiments, under different adsorbent/adsorbate levels, times, temperatures, pH and coexisting anions, and treat simulated groundwater (with 2.85 mg/L fluoride and pH 7.0) by batch and column tests. Adsorption data well fitted to pseudo-second-order rate model (R2 = 0.996-0.999), and Langmuir (R2 = 0.962 - 0.997) and Freundlich (R2 = 0.964-0.989) isothermal models. Their maximum adsorption capacities could reach 45-113 mg/g. Only H2PO4- anions had a restrictive impact at pH 7.0, and there was a good removal ability at pH 3-9. Adsorption processes were spontaneous, endothermic, and random. Adsorption mechanisms were electrostatic interaction and ligand exchange at pH 7.0. Adsorption capacity could reach 73% of initial value at pH 7.0, after three cycles. All application data on the polluted groundwater treatments show MAL oxide is a potential adsorbent for fluoride removals.

Lanthanide Contraction in LnF3 (Ln = Ce-Lu) and Its Chemical and Structural Consequences: Part 1: Location of YF3 in the LnF3 Series According to Its Chemical and Structural Characteristics.

A lanthanide contraction(LC) of 14 lanthanides (Ln) from 58Ce to 71Lu consists of the interaction of Ln nucleus with 4f-electrons. Rare earth elements (REEs-R) include Sc, Y, La, and 14 Ln. They are located in 4-6th periods of the subgroup of group III. The electronic structure divides R into short (d- Sc, Y, La) and long (14 f-elements Ce-Lu) homologous series. The most important chemical consequence of LC is the creation of a new conglomerate of 16 RF3 by mixing fluorides of d- (Y, La) and f-elements. This determines the location of YF3 among LnF3. The location of YF3 depends on the structural (formula volumes-Vform) and thermochemical (temperatures and heats of phase transformations, phase diagrams) properties. The location of YF3 between HoF3 and ErF3 was determined by Vform at a standard pressure (Pst) and temperature (Tst). The location of YF3 according to heats of phase transformations ΔHfus and ΔHtrans is in a dimorphic structural subgroup (SSGr) D (Ln = Er-Lu), but without the exact "pseudo ZY". According to the temperatures of phase transformations (Ttrans) in LnF3 (Ln = Dy-Lu), YF3 is located in the SSGr D between ErF3 and TmF3. The ErF3-YF3 and YF3-TmF3 phase diagrams show it to be between ErF3 and TmF3. The crystals of five ß-LnF3 (Ln = Ho-Lu) and ß-YF3 were obtained in identical conditions and their crystal structures were studied. Vform (at Pst and Tst) with "pseudo" atomic numberZY = 67.42 was calculated from the unit cell parameters, which were defined with ±5 × 10-4 Å accuracy. It determines the location of YF3 between HoF3 and ErF3.

One-pot synthesis of versatile sphere-like nano adsorbent MnAl2O4 (MAO): an optical and magnetic material for efficient fluoride removal and latent finger print detection.

Spherically shaped trimetallic MnAl2O4 (MAO) nanoadsorbent was prepared in an one-pot synthesis process for the removal of excess fluoride from water. The adsorbent was characterized by thermogravimetric analysis (TGA), X-ray diffraction study (XRD), Fourier transform infrared spectroscopy (FTIR), field emission scanning electron microscopy (FESEM), etc. The adsorption property for fluoride on the MAO was analyzed by batch experiments varying the adsorbent dose, pH, contact time, and initial fluoride concentration. The results showed that the fluoride uptake behavior of the samples could precisely be fitted by the Freundlich model, and the maximum adsorption capacity was estimated to be 39.21 mg/g at room temperature. The pseudo-second-order models accurately described the adsorption kinetics data. The regenerated sample showed excellent reusability along with high removal capacity on real water sample also. The underlying fluoride adsorption mechanism via ion-exchange and electrostatic interaction was established from X-ray photoelectron spectroscopy (XPS) and zeta potential studies. The sample showed excellent luminescence with blue emission with a band gap of 2.6 eV. The materials also showed good elastic behavior exhibiting the Poisson's ratio (σ) 0.32 and excellent latent figure print detection capacity distinguishing the clearly the ridge and furrow regions under UV light. The magnetic behavior was also found to be in long range with antiferromagnetic characteristics.

3D flower-like zirconium magnesium oxide nanocomposite for efficient fluoride removal.

A 3D flower-shaped bimetallic nanocomposite zirconium magnesium oxide (ZMO) was prepared first time by the controlled solution combustion method using triethanolamine (TEA) as a fuel and chelating agent. The composite material was used to remove excess fluoride via adsorption. The thermal stability of the adsorbent was characterized by thermogravimetric analysis (TGA). Fourier transform infrared spectroscopy (FTIR), field emission scanning electron microscopy (FESEM), energy-dispersive X-ray (EDX), and X-ray diffraction (XRD) were used to characterize the adsorbent. The surface charge of the nano adsorbent was determined by Zeta Sizer. The surface area and pore volume of the adsorbent were determined by Brunauer-Emmett-Teller (BET) isotherm and Barrett-Joyner-Halenda (BJH) methods. The adsorption behavior of fluoride was studied systematically varying the pH, contact time, adsorbent dose, and initial fluoride concentration. The adsorption followed the Langmuir isotherm model with a maximum adsorption capacity of 42.14 mg/g. The pseudo-second-order kinetic model was confirmed by the adsorption study. The maximum adsorption efficiency was in the 6-10 pH range. The reaction mechanism was mainly based on ion exchange between hydroxy and fluoride ions which was proven by X-ray photoelectron spectroscopy (XPS). Real water tests indicated that ZMO could be used as a potential defluoridation agent for fluoride containing groundwater treatment.

Discovering covalent inhibitors of protein-protein interactions from trillions of sulfur(VI) fluoride exchange-modified oligonucleotides.

Molecules that covalently engage target proteins are widely used as activity-based probes and covalent drugs. The performance of these covalent inhibitors is, however, often compromised by the paradox of efficacy and risk, which demands a balance between reactivity and selectivity. The challenge is more evident when targeting protein-protein interactions owing to their low ligandability and undefined reactivity. Here we report sulfur(VI) fluoride exchange (SuFEx) in vitro selection, a general platform for high-throughput discovery of covalent inhibitors from trillions of SuFEx-modified oligonucleotides. With SuFEx in vitro selection, we identified covalent inhibitors that cross-link distinct residues of the SARS-CoV-2 spike protein at its protein-protein interaction interface with the human angiotensin-converting enzyme 2. A separate suite of covalent inhibitors was isolated for the human complement C5 protein. In both cases, we observed a clear disconnection between binding affinity and cross-linking reactivity, indicating that direct search for the aimed reactivity-as enabled by SuFEx in vitro selection-is vital for discovering covalent inhibitors of high selectivity and potency.