Structural insights into the binding mechanism of Clr4 methyltransferase to H3K9 methylated nucleosome.

The establishment and maintenance of heterochromatin, a specific chromatin structure essential for genomic stability and regulation, rely on intricate interactions between chromatin-modifying enzymes and nucleosomal histone proteins. However, the precise trigger for these modifications remains unclear, thus highlighting the need for a deeper understanding of how methyltransferases facilitate histone methylation among others. Here, we investigate the molecular mechanisms underlying heterochromatin assembly by studying the interaction between the H3K9 methyltransferase Clr4 and H3K9-methylated nucleosomes. Using a combination of liquid-state nuclear magnetic resonance spectroscopy and cryo-electron microscopy, we elucidate the structural basis of Clr4 binding to H3K9-methylated nucleosomes. Our results reveal that Clr4 engages with nucleosomes through its chromodomain and disordered regions to promote de novo methylation. This study provides crucial insights into the molecular mechanisms governing heterochromatin formation by highlighting the significance of chromatin-modifying enzymes in genome regulation and disease pathology.

Biomonitoring of PAHs and PCBs in industrial, suburban, and rural areas using snails as sentinel organisms.

There is a worldwide concern about the presence of persistent organic pollutants (POPs) in the environment because of their toxicity, bioaccumulation, and resistance to degradation. Various conventional monitoring techniques have been used to assess their presence in diverse environmental compartments. Most currently available methods, however, have limitations with regards to long-term monitoring. In the present work, juvenile Cornu aspersum (O. F. Müller, 1774) snails were tested in field microcosms as biomonitors for two major classes of organic pollutants, namely, polycyclic aromatic hydrocarbons (PAHs) and polychlorinated biphenyls (PCBs). The study assessed their deployment in one suburban, one rural, and two industrial sites over an 18-week period and monitored for temporal variations of 16 PAHs and 22 PCBs. Sampling was conducted once every 3 weeks. Targeted pollutants were extracted from the caged snails using the QuEChERS extraction procedure and subsequently analyzed using gas chromatography coupled to tandem mass spectrometry (GC-MS/MS). The results showed that the bioaccumulation of specific pollutants was site dependent; significantly higher levels of PCBs were observed at the industrial sites as compared to the suburban and rural ones. PAHs were bioaccumulated by the snails via ingestion of air and soil whereas PCBs were mainly bioaccumulated via soil contact and ingestion. The findings of this study indicate that C. aspersum is a reliable model organism for the biomonitoring of organic pollutants in air and soil compartments and can be used as part of an integrated environmental assessment.

Mass calibrants for positive chemical ionization-high resolution mass spectrometry (CI-HRMS) for the identification of unknown compounds using accurate mass measurements.

Gas Chromatography-Electron Ionization-Mass Spectrometry (GC-EI-MS) is still the most routinely performed method for metabolite profiling as compared to other hyphenated techniques. But when it comes to identification of unknown compounds, information on the molecular weight is not readily available because the molecular ion is not always found with electron ionization (EI). Thus, the use of chemical ionization (CI) is envisaged that commonly produces the molecular ion; in combination with accurate mass measurement, this technique would further allow for calculation of sum formulas of those compounds. However, for proper accuracy of analysis, a mass calibrant is needed. We set out to find a commercially available reference material with mass peaks that would qualify the substance as mass calibrant under CI conditions. Six commercially available mass calibrants, FC 43, PFK, Ultramark 1621, Ultramark 3200F, Triton X-100, and PEG 1000, were tested under CI conditions to understand their fragmentation behavior. Our findings indicate that Ultramark 1621 and PFK best fit the expectations of a mass calibrant for HRMS analysis whereby PFK provided a fragmentation pattern similar to EI outcomes thus enabling the use of mass reference tables commonly provided within commercial mass spectrometers. On the other hand, Ultramark 1621 is a mixture of fluorinated phosphazines that shows stable fragment intensities.

Field evaluation of metal bioaccumulation in the gastropod Helix aspersa at agricultural and industrial sites in Lebanon.

Juvenile Helix aspersa Müller exposed in field microcosms were used to assess the spatial and temporal bioaccumulation of Cd, Cr, Cu, Fe, Mn, Ni, Pb, and Zn at two agricultural and two industrial sites in Lebanon. The study was performed over a 12-week period where caged snails were sampled once every 3 weeks and assessed for metal bioaccumulation and partitioning between soft tissue and shells. Results showed that metal bioaccumulation by snails was site dependent, with Fe and Cd being the greatest and least accumulated metals, respectively. Significant differences between bioaccumulation in each of the matrices (soft tissue and shells) were also observed. Time-dependent bioaccumulation results showed an increasing accumulation trend at both agricultural sites, while a slight decline was observed at the end of the sampling campaign for the industrial sites. The study of the bioaccumulation factors (BAF) revealed that tested H. aspersa were macroconcentrators for Zn and Cd (BAF > 2) and deconcentrators for all other analyzed elements (BAF < 1). The high partitioning factor values obtained for Cu and Zn indicate an affinity of these two elements for the soft tissues of the snails. The results of this field study indicate that H. aspersa are well suited for active biomonitoring and could provide reliable information on metal pollution and bioavailability.

Determination of heavy metals contamination in thyme products by inductively coupled plasma mass spectrometry.

Thyme herbs constitute a major part of the Mediterranean diet and are gaining worldwide popularity. However, their chemical contamination with toxic metals may put consumers at a health risk. The objective of this study was to assess the incidence of Arsenic (As), Cadmium (Cd), Lead (Pb) and Mercury (Hg) in thyme-containing products. Composite samples were collected twice at six-month interval. Samples were digested by microwave digestion oven and analyzed by Inductively Coupled Plasma Mass Spectrometry (ICP-MS). 11%, 22%, and 86% of samples had unacceptable levels of As, Hg and Pb respectively according to the international standards set by Codex Alimentarius and all the samples had acceptable limits of Cd. This study highlighted the importance of monitoring and enforcing regulatory actions related to the contamination of the food chain with heavy metals.

Deciphering the therapeutical potentials of rosmarinic acid.

Lemon balm is herbal tea used for soothing stomach cramps, indigestion, and nausea. Rosmarinic acid (RA) is one of its chemical constituents known for its therapeutic potentials against cancer, inflammatory and neuronal diseases such as the treatment of neurofibromatosis or prevention from Alzheimer's diseases (AD). Despite efforts, recovery and purification of RA in high yields has not been entirely successful. Here, we report its aqueous extraction with optimal conditions and decipher the structure by nuclear magnetic resonance (NMR) spectroscopy. Using various physical-chemical and biological assays, we highlight its anti-aggregation inhibition potentials against the formation of Tau filaments, one of the hallmarks of AD. We then examine its anti-cancer potentials through reduction of the mitochondrial reductase activity in tumor cells and investigate its electrochemical properties by cyclic voltammetry. Our data demonstrates that RA is a prominent biologically active natural product with therapeutic potentials for drug discovery in AD, cancer therapy and inflammatory diseases.

Synthesis of lanthanide tag and experimental studies on paramagnetically induced residual dipolar couplings.

Nuclear Magnetic Resonance (NMR) spectroscopy is an indispensable technique for the structure elucidation of molecules and determination of their characteristic interactions. Residual Dipolar Coupling (RDC) is an NMR parameter that provides global orientation information of molecules but necessitates the use of an anisotropic orientation medium for the partial alignment of the target molecule with respect to the magnetic field. Importantly, anisotropic paramagnetic tags have been successful as orienting media in biomolecular NMR applications but their use in small organic molecules remains imperfect due to challenges in designing functional lanthanide complexes with varying degrees of bonding in the Ln(III) inner coordination sphere. In this study, we propose a strategy for the synthesis of the lanthanide tag 4-mercaptomethylpyridine-2,6-dicarboxylic acid, 4-MMDPA and the measurement of RDCs in a target molecule using several paramagnetic lanthanide complexes.

Derivatization and combination therapy of current COVID-19 therapeutic agents: a review of mechanistic pathways, adverse effects, and binding sites.

Current treatment of patients with coronavirus 2019 (COVID-19) involves repurposed drugs that inhibit viral infection by either binding to their respective targets or via modulating cellular signal transduction. However, there is still a great deal of efficacy enhancement through combination therapy and derivatization. Combination therapy should involve agents with significant activity and different mechanisms of action. The structural map of the interaction between a drug and its target protein will help guide drug discovery for devising safe and effective ways to treat COVID-19. Herein, we report numerous synthetic designs based on enhanced affinity to the viral carbohydrate-rich protein spikes and protein-binding sites of COVID-19.

Disordered region of H3K9 methyltransferase Clr4 binds the nucleosome and contributes to its activity.

Heterochromatin is a distinctive chromatin structure that is essential for chromosome segregation, genome stability and regulation of gene expression. H3K9 methylation (H3K9me), a hallmark of heterochromatin, is deposited by the Su(var)3-9 family of proteins; however, the mechanism by which H3K9 methyltransferases bind and methylate the nucleosome is poorly understood. In this work we determined the interaction of Clr4, the fission yeast H3K9 methyltransferase, with nucleosomes using nuclear magnetic resonance, biochemical and genetic assays. Our study shows that the Clr4 chromodomain binds the H3K9me3 tail and that both, the chromodomain and the disordered region connecting the chromodomain and the SET domain, bind the nucleosome core. We show that interaction of the disordered region with the nucleosome core is independent of H3K9me and contributes to H3K9me in vitro and in vivo. Moreover, we show that those interactions with the nucleosome core are contributing to de novo deposition of H3K9me and to establishment of heterochromatin.

Surfactant adsorption kinetics in microfluidics.

Emulsions are metastable dispersions. Their lifetimes are directly related to the dynamics of surfactants. We design a microfluidic method to measure the kinetics of adsorption of surfactants to the droplet interface, a key process involved in foaming, emulsification, and droplet coarsening. The method is based on the pH decay in the droplet as a direct measurement of the adsorption of a carboxylic acid surfactant to the interface. From the kinetic measurement of the bulk equilibration of the pH, we fully determine the adsorption process of the surfactant. The small droplet size and the convection during the droplet flow ensure that the transport of surfactant through the bulk is not limiting the kinetics of adsorption. To validate our measurements, we show that the adsorption process determines the timescale required to stabilize droplets against coalescence, and we show that the interface should be covered at more than [Formula: see text] to prevent coalescence. We therefore quantitatively link the process of adsorption/desorption, the stabilization of emulsions, and the kinetics of solute partitioning-here through ion exchange-unraveling the timescales governing these processes. Our method can be further generalized to other surfactants, including nonionic surfactants, by making use of fluorophore-surfactant interactions.

Remodeling of the conformational ensemble of the repeat domain of tau by an aggregation enhancer.

Misfolding of the microtubule-associated protein Tau is a hallmark of Alzheimer disease and several other neurodegenerative disorders. Because of the dynamic nature of the Tau protein, little is known about the changes in Tau structure that occur during misfolding. Here we studied the structural consequences upon binding of the repeat domain of Tau, which plays a key role in pathogenic aggregation, to an aggregation enhancer. By combining NMR experiments with molecular simulations we show that binding of the aggregation enhancer polyglutamic acid remodels the conformational ensemble of Tau. Our study thus provides insight into an early event during misfolding of Tau.

The active Hsc70/tau complex can be exploited to enhance tau turnover without damaging microtubule dynamics.

The pathological accumulation of abnormally hyperphosphorylated and aggregated tau, a neuronal microtubule (MT)-associated protein that functions to maintain MT stability, is implicated in a number of hereditary and sporadic neurodegenerative diseases including frontotemporal dementia and Alzheimer's disease. Targeting tau for the treatment of these diseases is an area of intense interest and toward that end, modulation of cellular molecular chaperones is a potential therapeutic target. In particular, the constitutive Hsp70 isoform, Hsc70, seems highly interconnected with tau, preserving tau protein levels and synergizing with it to assemble MTs. But the relationship between tau and Hsc70, as well as the impact of this interaction in neurons and its therapeutic implications remain unknown. Using a human dominant negative Hsc70 that resembles isoform selective inhibition of this important chaperone, we found for the first time that Hsc70 activity is required to stimulate MT assembly in cells and brain. However, surprisingly, active Hsc70 also requires active tau to regulate MT assembly in vivo, suggesting that tau acts in some ways as a co-chaperone for Hsc70 to coordinate MT assembly. This was despite tau binding to Hsc70 as substrate, as determined biochemically. Moreover, we show that while chronic Hsc70 inhibition damaged MT dynamics, intermittent treatment with a small molecule Hsp70 inhibitor lowered tau in brain tissue without disrupting MT integrity. Thus, in tauopathies, where MT injury would be detrimental to neurons, the unique relationship of tau with the Hsc70 machinery can be exploited to deplete tau levels without damaging MT networks.

Hsp90-Tau complex reveals molecular basis for specificity in chaperone action.

Protein folding in the cell relies on the orchestrated action of conserved families of molecular chaperones, the Hsp70 and Hsp90 systems. Hsp70 acts early and Hsp90 late in the folding path, yet the molecular basis of this timing is enigmatic, mainly because the substrate specificity of Hsp90 is poorly understood. Here, we obtained a structural model of Hsp90 in complex with its natural disease-associated substrate, the intrinsically disordered Tau protein. Hsp90 binds to a broad region in Tau that includes the aggregation-prone repeats. Complementarily, a 106-Å-long substrate-binding interface in Hsp90 enables many low-affinity contacts. This allows recognition of scattered hydrophobic residues in late folding intermediates that remain after early burial of the Hsp70 sites. Our model resolves the paradox of how Hsp90 specifically selects for late folding intermediates but also for some intrinsically disordered proteins-through the eyes of Hsp90 they look the same.

Inhibition of tau filament formation by conformational modulation.

Antiaggregation drugs play an important role in therapeutic approaches for Alzheimer's disease. Although a large number of small molecules that inhibit the aggregation of the tau protein have been identified, little is known about their mode of action. Here, we reveal the mechanism and the nature of tau species that are generated by interaction of tau with the organic compound pthalocyanine tetrasulfonate (PcTS). We demonstrate that PcTS interferes with tau filament formation by targeting the protein into soluble oligomers. A combination of NMR spectroscopy, electron paramagnetic resonance, and small-angle X-ray scattering reveals that the soluble tau oligomers contain a dynamic, noncooperatively stabilized core with a diameter of 30-40 nm that is distinct from the core of tau filaments. Our results suggest that specific modulation of the conformation of tau is a viable strategy for reduction of pathogenic tau deposits.

Imbalance of Hsp70 family variants fosters tau accumulation.

Dysfunctional tau accumulation is a major contributing factor in tauopathies, and the heat-shock protein 70 (Hsp70) seems to play an important role in this accumulation. Several reports suggest that Hsp70 proteins can cause tau degradation to be accelerated or slowed, but how these opposing activities are controlled is unclear. Here we demonstrate that highly homologous variants in the Hsp70 family can have opposing effects on tau clearance kinetics. When overexpressed in a tetracycline (Tet)-based protein chase model, constitutive heat shock cognate 70 (Hsc70) and inducible Hsp72 slowed or accelerated tau clearance, respectively. Tau synergized with Hsc70, but not Hsp72, to promote microtubule assembly at nearly twice the rate of either Hsp70 homologue in reconstituted, ATP-regenerating Xenopus extracts supplemented with rhodamine-labeled tubulin and human recombinant Hsp72 and Hsc70. Nuclear magnetic resonance spectroscopy with human recombinant protein revealed that Hsp72 had greater affinity for tau than Hsc70 (I/I0 ratio difference of 0.3), but Hsc70 was 30 times more abundant than Hsp72 in human and mouse brain tissue. This indicates that the predominant Hsp70 variant in the brain is Hsc70, suggesting that the brain environment primarily supports slower tau clearance. Despite its capacity to clear tau, Hsp72 was not induced in the Alzheimer's disease brain, suggesting a mechanism for age-associated onset of the disease. Through the use of chimeras that blended the domains of Hsp72 and Hsc70, we determined that the reason for these differences between Hsc70 and Hsp72 with regard to tau clearance kinetics lies within their C-terminal domains, which are essential for their interactions with substrates and cochaperones. Hsp72 but not Hsc70 in the presence of tau was able to recruit the cochaperone ubiquitin ligase CHIP, which is known to facilitate the ubiquitination of tau, describing a possible mechanism of how the C-termini of these homologous Hsp70 variants can differentially regulate tau triage. Thus, efforts to promote Hsp72 expression and inhibit Hsc70 could be therapeutically relevant for tauopathies.

ß-Sheet core of tau paired helical filaments revealed by solid-state NMR.

One of the hallmarks of Alzheimer's disease is the self-assembly of the microtubule-associated protein tau into fibers termed "paired helical filaments" (PHFs). However, the structural basis of PHF assembly at atomic detail is largely unknown. Here, we applied solid-state nuclear magnetic resonance (ssNMR) spectroscopy to investigate in vitro assembled PHFs from a truncated three-repeat tau isoform (K19) that represents the core of PHFs. We found that the rigid core of the fibrils is formed by amino acids V306 to S324, only 18 out of 99 residues, and comprises three ß-strands connected by two short kinks. The first ß-strand is formed by the well-studied hexapeptide motif VQIVYK that is known to self-aggregate in a steric zipper arrangement. Results on mixed [(15)N:(13)C]-labeled K19 fibrils show that ß-strands are stacked in a parallel, in-register manner. Disulfide bridges formed between C322 residues of different molecules lead to a disturbance of the ß-sheet structure, and polymorphism in ssNMR spectra is observed. In particular, residues K321-S324 exhibit two sets of resonances. Experiments on K19 C322A PHFs further confirm the influence of disulfide bond formation on the core structure. Our structural data are supported by H/D exchange NMR measurements on K19 as well as a truncated four-repeat isoform of tau (K18). Site-directed mutagenesis studies show that single-point mutations within the three different ß-strands result in a significant loss of PHF aggregation efficiency, highlighting the importance of the ß-structure-rich regions for tau aggregation.