Search Results (425)

Background: snoRNAs have traditionally been known for their role as guides in post-transcriptional rRNA modifications. Previously, our research group identified several RNAs that may bind to PIP2 with LIPRNA-seq. Among them, snR191 stood out due to its potential specific interaction with this lipid, distinguishing itself from other snoRNAs. However, a detailed study is needed to define the molecular interactions between RNA and lipids, which remain unknown but may serve as a mechanism for transport or liquid–liquid phase separation. This study aimed to determine the interaction between a snoRNA called snR191 and PIP2. Method: A novel methodology for RNA-PIP2 interaction was carried out. Total RNA from Saccharomyces cerevisiae was incubated with PIP2-bound nitrocellulose membranes and RT-PCR reactions. We performed the prediction of snR191-PIP2 interaction by molecular docking and in silico mutations of snoR191. Results: From LIPRNA-seq analysis, we identified that PIP2-bound RNAs were significantly enriched in diverse biological processes, including transmembrane transport and redox functions. Our RNA-PIP2 interaction approach was successful. We demonstrated that snR191 specifically interacts with PIP2 in vitro. The elimination of DNA ensured that the interaction assay was RNA-specific, strengthening the robustness of the experiment. PIP2 was docked to snR191 in a stem–loop–stem motif. Six hydrogen bonds across four nucleotides mediated the PIP2-snR191 interaction. Finally, mutations in snR191 affected the structural folding. Conclusions: In this study, we demonstrate the effectiveness of a new methodology for determining RNA–lipid interactions, providing strong evidence for the specific interaction between snR191 and PIP2. Integrating biochemical and computational approaches has allowed us to understand the binding of these biomolecules. Therefore, this work significantly broadens our understanding of snR191-PIP2 interactions and opens new perspectives for further research. Full article

Relaxation behavior of water confined in reverse micelles under temperature-induced micelle clustering is undertaken using broadband dielectric spectroscopy in frequency range 1 Hz–20 GHz. All microemulsion systems with sufficiently noticeable micelle water pool (water/surfactant molar ratio W > 10) depict three relaxation processes, in low, high and microwave frequencies, anchoring with relaxation of shell (bound) water, orientation of surfactant anions at water-surfactant interface and relaxation of bulk water confined in reverse micelles. The analysis of dielectric relaxation processes in AOT-based w/o microemulsions under temperature induced clustering of reverse micelles were made according to structural information obtained in NMR and conductometry experiments. The “wait and switch” relaxation mechanism was applied for the explanation of results for water in the bound and bulk states under spatial limitation in reverse micelles. It was shown that surfactant layer predominantly influences the bound water. The properties of water close to AOT interface are determined by strong interactions between water and ionic AOT molecules, which perturb water H-bonding network. The decrease in micelle size causes a weakening of hydrogen bonds, deformation of its steric network and reduction in co-operative relaxation effects. Full article

Fish gelatin (FG) has garnered significant attention as an alternative to mammalian gelatin, primarily attributed to its distinct advantages. These include the absence of epidemic transmission risks and the lack of religious restrictions, making it a more universally acceptable and safer option. However, its application is limited due to shortcomings such as insufficient gel properties (such as rheological properties, gel strength, etc.). In this study, flaxseed gum (FFG) of 0–1.2% w/v was used to modify FG. The rheological properties, structural characteristics, and chemical bond changes of FG before and after modification were systematically analyzed using instruments such as a rheometer, infrared spectrometer, and Zeta potential analyzer. The results revealed that an appropriate amount of FFG could increase the gel strength of FG, but excessive FFG (>0.4%) reduced its gel strength. Moreover, FFG could increase the gelation transition temperature and apparent viscosity of the composite gel. FTIR confirmed that FFG and FG were bound through hydrogen bonding, β-sheet structure formation, and multi-electrolyte complexation. The ESEM showed that FFG promoted the formation of a denser network structure of FG. This study laid a theoretical foundation for the application and development of FG in the field of high-gel foods. Full article

Water within coal reservoirs exerts dual effects on methane adsorption–desorption by competing for adsorption sites and reducing permeability. The bound water effect, caused by coal wettability, significantly constrains coalbed methane (CBM) production, rendering investigations into coal wettability crucial for efficient CBM development. Compared with other geological formations, coals are characterized by a highly developed microporous structure, making the CO₂ sequestration mechanism in coal seams closely linked to the microscale interactions among gas, water, and coal matrixes. However, the intrinsic mechanisms remain poorly understood. In this study, molecular dynamics simulations are employed to investigate the wettability behaviors of CO₂, CH₄, and water on different coal matrix surfaces under varying temperature and pressure conditions, for coal macromolecules representative of four coal ranks. The study reveals the evolution of water wettability in response to CO₂ and CH₄ injection, identifies wettability differences among coal ranks, and analyzes the microscopic mechanisms governing wettability. The results show the following: (1) The contact angle increases with gas pressure, and the variation in wettability is more pronounced in CO₂ environments than in CH₄. As pressure increases, the number of hydrogen bonds decreases, while the peak gas density of CH₄ and CO₂ increases, leading to larger contact angles. (2) Simulations under different temperatures for the four coal ranks indicate that temperature has minimal influence on low-rank Hegu coal, whereas for higher-rank coals, gas adsorption on the coal surface increases, resulting in reduced wettability. Interfacial tension analysis further suggests that higher temperatures reduce water surface tension, cause dispersion of water molecules, and consequently improve wettability. Understanding the wettability variations among different coal ranks under variable pressure–temperature conditions provides a fundamental model and theoretical basis for investigating deep coal seam gas–water interactions and CO₂ geological sequestration mechanisms. These findings have significant implications for the advancement of CO₂-ECBM technology. Full article

Prion diseases such as chronic wasting disease involve the conformational conversion of the cellular prion protein (PrP^C) into its misfolded, β-rich isoform (PrP^Sc). While chemical denaturants such as guanidine hydrochloride (GdnHCl) and urea are commonly used to study this process in vitro, their distinct molecular effects on native and misfolded PrP conformers remain incompletely understood. In this study, we employed 500 ns all-atom molecular dynamics simulations and essential collective dynamics analysis to investigate the differential effects of GdnHCl and urea on a composite PrP^C/PrP^Sc system, where white-tailed deer PrP^C interfaces with a corresponding PrP^Sc conformer. GdnHCl was found to preserve interfacial alignment and enhance β-sheet retention in PrP^Sc, while urea promoted partial β-strand dissolution and interfacial destabilization. Both denaturants formed transient contacts with PrP, but urea displaced water hydrogen bonds more extensively. Remarkably, we also observed long-range dynamical coupling across the PrP^C/PrP^Sc interface and between transiently bound solutes and distal protein regions. These findings highlight distinct, denaturant-specific mechanisms of protein destabilization and suggest that localized interactions may propagate non-locally via mechanical or steric pathways. Our results provide molecular-scale insights relevant to prion conversion mechanisms and inform experimental strategies using GdnHCl and urea to modulate misfolding processes in vitro. Full article

The ionotropic γ-aminobutyric acid (GABA) receptor (GABAR) is a key target for the development of antiparasitic agents, particularly against ectoparasites, such as fleas and ticks. Binding stability and selectivity of sarolaner enantiomers for Ctenocephalides felis RDL receptors (RDLR) were investigated in the current study. Wild-type (WT) C. felis RDLR and its A285S mutant were constructed using homology-based, fragment-based threading and AI-driven approaches, of which, SWISS-MODEL generated the most reliable structures. Molecular docking showed that the sarolaner S-enantiomer had higher binding affinity for both receptors than the R-enantiomer, primarily due to hydrogen bonding with Ile256, π–π stacking with Phe326, and hydrophobic interactions with Ile267 and Ile268. Molecular dynamics simulations confirmed the binding stability of the S-enantiomer-receptor complex in which key residues maintained interactions throughout the trajectories. Binding free energy analysis supported these results and highlighted the role of nonpolar interactions in binding stability. The A285S mutation had minimal impact on the binding pocket, and the S-enantiomer remained selective for and bound to the mutant receptor. Insights into the insecticidal mechanism of sarolaner enantiomers are given, and the current findings may inform the development of veterinary drugs from novel isoxazoline-based NAMs targeting insect GABARs. Full article

Streptococcus pneumoniae (S. pneumoniae) Sortase A (SrtA) anchors virulence proteins to the surface of the cell wall by recognizing and cleaving the LPXTG motif. These toxins help bacteria adhere to and colonize host cells, promote biofilm formation, and trigger host inflammatory responses. Therefore, SrtA is an ideal target for the development of new preparations for S. pneumoniae. In this study, we found that phloretin (pht) and phlorizin (phz) exhibited excellent affinities for SrtA based on virtual screening experiments. We analyzed the interactive mechanism between pht, phz, and alnusone (aln, a reported S. pneumoniae SrtA inhibitor) and SrtA based on molecular dynamics simulation experiments. The results showed that these inhibitors bound to the active pocket of SrtA, and the root mean square deviation (RMSD) and distance analyses showed that these compounds and SrtA maintained stable configuration and binding during the assay. The binding free energy analysis showed that both electrostatic forces (ele), van der Waals forces (vdw), and hydrogen bonds (Hbonds) promoted the binding between pht, phz, and SrtA; however, for the binding of aln and SrtA, the vdw force was much stronger than ele, and Hbonds were not found. The binding free energy decomposition showed that HIS141, ILE143, and PHE119 contributed more energy to promote pht and SrtA binding; ARG215, ASP188, and LEU210 contributed more energy to promote phz and SrtA binding; and HIS141, ASP209, and ARG215 contributed more energy to promote aln and SrtA binding. Finally, the transpeptidase activity of SrtA decreased significantly when treated with different concentrations of pht, phz, or aln, which inhibited S. pneumoniae biofilm formation and adhesion to A549 cells without affecting normal bacterial growth. These results suggest that pht, phtz, and aln are potential materials for the development of novel inhibitors against S. pneumoniae infection. Full article

Acetone carboxylase (AC) from Xanthobacter autotrophicus is a 360 KDa α₂β₂γ₂ heterohexamer that catalyzes the ATP-dependent formation of phosphorylated acetone and bicarbonate intermediates that react at Mn(II) metal active sites to form acetoacetate. Structural models of X. autotrophicus AC (XaAC) with and without nucleotides reveal that the binding and phosphorylation of the two substrates occurs ~40 Å from the Mn(II) active sites where acetoacetate is formed. Based on the crystal structures, a significant conformational change was proposed to open and close a tunnel that facilitates the passage of reaction intermediates between the sites for nucleotide binding and phosphorylation of substrates and Mn(II) sites of acetoacetate formation. We have employed electron paramagnetic resonance (EPR), kinetic assays, and hydrogen/deuterium exchange mass spectrometry (HDX-MS) of poised ligand-bound states and site-specific amino acid variants to complete an in-depth analysis of Mn(II) coordination and allosteric communication throughout the catalytic cycle. In contrast with the established paradigms for carboxylation, our analyses of XaAC suggested a carboxylate shift that couples both local and long-range structural transitions. Shifts in the coordination mode of a single carboxylic acid residue (αE89) mediate both catalysis proximal to a Mn(II) center and communication with an ATP active site in a separate subunit of a 180 kDa α₂β₂γ₂ complex at a distance of 40 Å. This work demonstrates the power of combining structural models from X-ray crystallography with solution-phase spectroscopy and biophysical techniques to elucidate functional aspects of a multi-subunit enzyme. Full article

The isotopic shift of the bound-electron g factor in highly charged ions (HCI) provides a sensitive probe for testing physics beyond the Standard Model, particularly through interactions mediated by a hypothetical scalar boson. In this study, we analyze the sensitivity of this method within the Higgs portal framework, focusing on the uncertainties introduced by quantum electrodynamics corrections, including finite nuclear size, nuclear recoil, and nuclear polarization effects. All calculations are performed for the ground-state $1s$ configuration of hydrogen-like HCI, where theoretical predictions are most accurate. Using selected isotope pairs (e.g., ${\mathrm{He}}^{4/6}$, ${\mathrm{Ne}}^{20/22}$, ${\mathrm{Ca}}^{40/48}$, ${\mathrm{Sn}}^{120/132}$, ${\mathrm{Th}}^{230/232}$), we demonstrate that the dominant source of uncertainty arises from finite nuclear size corrections, which currently limit the precision of new physics searches. Our results indicate that the sensitivity of this method decreases with increasing atomic number. These findings highlight the necessity of improved nuclear radius measurements and the development of alternative approaches, such as the special differences method, to enable virtually the detection of fifth-force interactions. Full article

Microbial transglutaminase (mTG) is most frequently utilized in order to increase the gelling properties of soybean protein isolate (SPI), but there are still some limitations of mTG-based hydrogel fabrication technology. Therefore, we aimed to develop a dual modification technique based on enzyme plus organic acid treatment to fabricate SPI hydrogels with high gel strength and stability. Our results showed that mTG plus glucose-δ-lactone (GDL), lactobionic acid (LBA) or maltobionic acid (MBA) treatment could significantly improve the gel strength, textural properties, and water-holding capacity of SPI hydrogels. Also, the addition of these organic acids remarkably reduced the surface hydrophobicity (H₀) and intrinsic fluorescence as well as increased the storage modulus (G′), loss modulus (G″) values, average particle size, and the absolute value of zeta potential of samples. GDL, LBA, or MBA greatly increased the β-sheet level and decreased the α-helix level in hydrogels, as well as dissociated 11S subunits of SPI into 7S subunits. Notably, covalent interactions, hydrogen bonding, and hydrophobic interactions of three organic acids with SPI, as well as the effects of organic acids on the interactions among the intramolecular and intermolecular forces of SPI molecules, contributed to their promoting effects on the formation of hydrogels. The LF-NMR and SEM analyses confirmed the effects of GDL, LBA, and MBA on converting the free water into immobilized and bound water as well as forming a dense stacked aggregate structure. Therefore, GDL, LBA, and MBA are promising agents to be combined with mTG in the fabrication of SPI hydrogels with high gel strength and stability. Full article

Formononetin is widely used in anti-tumor research, but its poor water solubility leads to low absorption and poor utilization efficiency in vivo, limiting further development. The triphenylphosphine cation was partially attached to the 7-position hydroxyl group of formononetin to specifically target it into the mitochondria of tumor cells to enhance the anti-tumor effect. Detailed structural characterization via ¹H-NMR and ¹³C-NMR analysis confirmed the physical properties and chemical structures of 21 newly synthesized derivatives. The effects of these derivatives on tumor cells were assessed by in vitro and computational methods. MTT results from four tumor cell lines showed that formononetin derivatives containing triphenylphosphine had stronger anti-tumor activity than formononetin and exhibited more cytotoxic effects in cancer cells than in normal cells. In particular, the final product 2c (IC₅₀ = 12.19 ± 1.52 μM) showed more potent anti-tumor activity against A549 cells. It was also superior to formononetin and 5-FU. To identify the potential biological targets, the core-expressed gene SHMT2 in lung cancer mitochondria was screened using network pharmacology technology, and molecular docking analysis confirmed the stable binding of the end products to the amino acid residues of the core genes through the formation of hydrogen bonds and via other interactions. In addition, molecular docking simulations further confirmed that the end product exhibited excellent stability when bound to SHMT2. These results suggest that triphenylphosphine-containing formononetin derivatives are worthy of further exploration in the search for novel drug candidates for the treatment of cancer. Full article

An outstanding adsorbent, such as the metal–organic framework (MOF) MIL-101 (Cr), was employed to study the adsorption of two dyes, namely reactive red 2 (RR2) and reactive blue 19 (RB19). Experimental adsorption data were retrieved at T = 25, 35 and 45 °C and analyzed to define the adsorption mechanism of these dyes. A modeling approach based on a double-layer model derived from statistical physics was used. The maximum adsorption capacity (MAC) was found to be 875, 954 and 1002 mg/g for RR2 and 971, 1093 and 1148 mg/g for RB19, at T = 25, 35 and 45 °C, respectively. These values indicate that MIL-101 (Cr) exhibits outstanding performance in removing potential water pollutants such as the RR2 and RB19 dyes. The possible orientations of the RR2 and RB19 dyes upon adsorption were determined by analyzing the number of dye molecules bound per MIL-101 (Cr) active sites during the adsorption process. It was found that the RR2 dye was removed via a mixed parallel and non-parallel orientation on MIL-101 (Cr), while RB19 was removed via an inclined orientation at higher temperatures. The adsorption mechanism suggested that MIL-101 (Cr) site density was reduced due to an exothermic effect, which decreases the number of active sites participating in dye adsorption, even though the reduction in water adsorption may be attributed to the overall endothermic behavior. From the adsorption energy (AE) and the chemical structure of MIL-101 (Cr) and both dyes, it was concluded that hydrogen bonds, Van der Waals forces and π-π stacking are involved in the dye removal process. This research provides new physical insights into the adsorption mechanism of two relevant dyes on an outstanding adsorbent such as the MIL-101 (Cr) MOF. Full article

Background: Alzheimer’s disease (AD) is a multifactorial neurodegenerative disorder characterised by the accumulation of neurotoxic substances in the brain, ultimately leading to progressive cognitive decline. The complex aetiology and involvement of multiple molecular targets in AD pathogenesis have made discovering effective therapeutic agents particularly challenging. Targeting multiple proteins simultaneously with a single therapeutic agent may offer a promising strategy to address the disease’s multifaceted nature. Methods: This study employed advanced computational methodologies to perform multitargeted molecular docking of FDA-approved drugs against four key AD-associated proteins implicated in disease progression. Among the screened compounds, Rebamipide—a drug conventionally used for treating gastrointestinal disorders—demonstrated notable binding affinities across all targets. Pharmacokinetic predictions, interaction fingerprinting, WaterMap analysis, density functional theory (DFT) calculations, and 100 ns MD simulations were performed for each protein–ligand complex to evaluate its multitarget potential. Results: Rebamipide bound effectively to the NR1 ligand-binding core, suggesting modulation of glutamatergic signalling while reducing β-secretase production and regulating neurotransmitter homeostasis through inhibiting monoamine oxidase-A. Furthermore, Rebamipide enhanced cholinergic neurotransmission by inhibiting human acetylcholinesterase, potentially improving cognitive function. Pharmacokinetic analyses confirmed favourable drug-like properties. Molecular interaction fingerprints revealed consistent hydrogen bonding, hydrophobic contacts, and π-π stacking interactions. WaterMap analysis indicated thermodynamically favourable water displacement upon binding, enhancing ligand affinity. DFT analysis of Rebamipide showed a 4.24 eV HOMO-LUMO gap, with ESP values ranging from −6.63 × 10⁻² to +6.63 × 10⁻² A.U., indicating reactive sites. TDDFT predicted strong UV absorption at 314 nm with a peak intensity of ~6500 L mol⁻¹ cm⁻¹. MD simulations over 100 ns demonstrated minimal structural deviations and stable ligand–protein complexes, reinforcing its multitarget efficacy. Conclusions: The comprehensive in silico investigation highlights Rebamipide as a promising multitargeted therapeutic candidate for Alzheimer’s disease. Its ability to modulate multiple pathogenic pathways simultaneously underscores its potential utility; however, these computational findings warrant further experimental validation to confirm its efficacy and therapeutic relevance in AD. Full article

Tomato (Solanum lycopersicum) is highly susceptible to both high and low temperatures, which threaten its growth, yield, and quality. Ascorbate peroxidase (APX) plays a pivotal role in plant responses to abiotic stresses. In this study, we unveil the positive involvement of heat- and cold-induced SlAPX2 in bolstering tomato resilience to temperature extremes. Knockout of SlAPX2 using the CRISPR/Cas9 technique exacerbated oxidative stress under heat and cold conditions, as evidenced by reduced Fv/Fm and increased electrolyte leakage (REL), malondialdehyde (MDA) content, and hydrogen peroxide (H₂O₂) levels. Furthermore, SlAPX2 expression was modulated by abscisic acid (ABA), and the transcription factor ABF4 in the ABA signaling pathway positively regulated SlAPX2 transcription. Using yeast one-hybrid (Y1H) and dual luciferase (LUC) assays, we found that ABF4 directly bound to the SlAPX2 promoter, thereby activating its transcription. Additionally, silencing of SlABF4 compromised tomato’s tolerance to heat or cold. Collectively, these findings reveal a regulatory module, SlABF4–SlAPX2, that enhances tomato tolerance to temperature extremes by detoxifying excessive reactive oxygen species (ROS). This study advances our understanding of ABA-mediated stress responses and highlights the SlABF4–SlAPX2 module as a promising target for breeding temperature-resilient tomato cultivars. Full article

In this study, complexes of pregelatinized Chinese yam starch with ferulic acid (PCYS+FA) were prepared using a boiling water bath, with varying levels of Chinese yam starch (CYS) and ferulic acid (FA). The investigation focused on the effects of FA addition (3%, 9%, and 15%) on the physicochemical properties and structure of PCYS+FA complexes. The solubility, swelling, and water-holding capacity of PCYS+FA were compared with those of CYS, with the solubility and swelling showing a gradual enhancement with increasing FA content. The incorporation of FA reduced the thermal stability of CYS, decreasing the initial degradation temperature from 245.94 °C (CYS) to 228.17 °C (PCYS+15%FA). Infrared spectroscopy revealed that CYS and FA were bound through non-covalent intramolecular hydrogen bonding. Furthermore, X-ray diffractograms showed that FA and CYS formed a V-type complex, in which the crystallinity of PCYS reached a minimum of 3.72%, and the degree of molecular ordering was reduced. Scanning electron microscopy analysis demonstrated that FA adhered to the surface of starch granules, resulting in the formation of pores that facilitated the entry of FA molecules into the internal crystal region of starch, allowing them to interact with starch molecules. Full article