Search Results (1,532)

This study investigates how phospholipid headgroups influence passive membrane penetration and structural impact of four nitrogen-, sulfur-, and oxygen-containing heterocycles (NSO-HETs)—N-methyl-2-pyrrolidone (PIR), 1,4-dioxane (DIOX), oxane (OXA), and phenol (PHE). Using all-atom molecular dynamics simulations combined with Accelerated Weight Histogram free energy calculations, the passive transport of NSO-HETs across DPPC, DPPE, DPPA, and DPPG bilayers was characterized. DPPG showed the highest membrane affinity, increasing permeability (logP_memb/bulk) by 27–64% compared to DPPE, associated with the lowest permeability and tightest lipid packing. Free energy barriers are also decreased in DPPG relative to DPPE; PIR’s central barrier dropped from 19.2 kJ/mol (DPPE) to 16.6 kJ/mol (DPPG), while DIOX’s barrier decreased from 7.2 to 5.2 kJ/mol. OXA exhibited the lowest central barriers (1.2–2.2 kJ/mol) and uniquely accumulated at higher concentrations in the bilayer center than in bulk water, with free energy ranging from −3.4 to −5.9 kJ/mol. PHE and OXA caused significant bilayer thinning (up to 11%) and reduced lipid tail order, especially in DPPE and DPPA. Concentration effects were most pronounced in DPPE, where high solute loading disrupted lipid order and altered free energy profiles. These results highlight the crucial role of headgroup identity in modulating NSO-HET membrane permeability and structural changes. Full article

Spin transport behaviors in heavy metal/ferromagnetic insulator (HM/FI) bilayers have attracted considerable attention due to various novel phenomena and applications in spintronic devices. Herein, we investigate the planar Hall effect (PHE) in Pt/Tm₃Fe₅O₁₂ (Pt/TmIG) heterostructures at low temperatures; moment switching in the ferrimagnetic insulator TmIG is detected by using electrical measurements. Double switching hysteresis PHE curves are found in Pt/TmIG bilayers, closely related to the magnetic moment of Tm³⁺ ions, which makes a key contribution to the total magnetic moment of TmIG film at low temperature. More importantly, a magnetoresistance (MR) curve with double switching is found, which has not been reported in this simple HM/FI bilayer, and the sign of this MR effect is sensitive to the angle between the magnetic field and current directions. Our findings of these effects in this HM/rare earth iron garnet (HM/REIG) bilayer provide insights into tuning the spin transport properties of HM/REIG by changing the rare earth. Full article

The C-terminus of the BoNT/A heavy chain (BoNT/AHC) mediates binding to its receptor, SV2, a critical step for toxicity. Antibody inhibition of this interaction enhances neuronal survival. We previously identified a functional anti-BoNT/AHC nanobody, HM. To extend its in vivo half-life, we designed and prepared two Fc-optimized nanoparticles, HM-Fc5 and HM-Fc6. Structural modeling (homology/docking) of the HM Fv-AHC complex predicted that HM engages key AHC residues (Tyr¹¹⁵⁵, Phe¹¹⁶⁰, Ile¹¹⁶¹, Val¹¹⁸⁴, Asn¹¹⁸⁸, Lys¹¹⁸⁹, Glu¹¹⁹⁰), which overlap with the SV2 binding site. This suggests HM’s protective mechanism involves blocking toxin-receptor binding and cellular entry. HM-Fc5 and HM-Fc6 retained the stability and function of the parental HM antibody while exhibiting prolonged in vivo half-life. These optimized nanobodies offer economical candidates potentially enabling longer dosing intervals, beneficial for prophylaxis or chronic disease treatment. Significance Statement: The purpose of the study is to design and prepare two Fc optimized nanoparticles, HM-Fc5 and HM-Fc6, and predict the key residues involved in the interaction between HMs and AHC. The experimental results showed that HM-Fc5 and HM-Fc6 have the same stability as the parent HM antibody but have a longer half-life in vivo. The key residues Tyr¹¹⁵⁵, Phe¹¹⁶⁰, Ile¹¹⁶¹, Val¹¹⁸⁴, Asn¹¹⁸⁸, Lys¹¹⁸⁹, and Glu¹¹⁹⁰ overlap with the SV2 binding site. Our experimental results indicate that these nanobody candidates are not only more economical and convenient, but may also have longer dosing intervals, providing strong evidence and reference for prolonging the in vivo half-life of nanomaterials. Full article

Phenylketonuria (PKU) is a monogenic disorder caused by pathogenic variants in the gene encoding phenylalanine hydroxylase (PAH), an enzyme essential for phenylalanine (Phe) metabolism. It is characterized by elevated Phe levels, leading to a wide spectrum of clinical phenotypes. These phenotypes are characterized by varying Phe accumulation, dietary tolerance, and heterogeneous cognitive and neurological outcomes, but current monitoring methods, focused primarily on blood Phe levels, are limited in capturing this variability. In this study, we applied mass spectrometry-based advanced quantitative amino acid analyses, untargeted metabolomics, and lipidomics analyses. We examined the plasma metabolite and lipid profiles in a total of 73 individuals with various PKU phenotypes against healthy controls to see how the metabolome and lipidome of the patients change in different phenotypes. We investigated whether novel markers could be associated with metabolic control status. By elucidating the metabolic and lipid fingerprints of PKU’s phenotypic variability, our findings may provide novel insights that could inform the refinement of dietary and pharmacological interventions, thereby supporting the development of more personalized treatment strategies. Full article

Under global warming, persistent extreme heat events (PHEs) in China have increased significantly in both frequency and intensity, posing severe threats to agriculture and socioeconomic development. Combining observational analysis (1961–2019) and numerical simulations, this study investigates the distinct impacts of Northwest Pacific (NWP) and North Atlantic (NA) sea surface temperature (SST) anomalies on PHEs over China. Key findings include the following: (1) PHEs exhibit heterogeneous spatial distribution, with the Yangtze-Huai River Valley as the hotspot showing the highest frequency and intensity. A regime shift occurred post-2000, marked by a threefold increase in extreme indices (+3σ to +4σ). (2) Observational analyses reveal significant but independent correlations between PHEs and SST anomalies in the tropical NWP and mid-high latitude NA. (3) Numerical experiments demonstrate that NWP warming triggers a meridional dipole response (warming in southern China vs. cooling in the north) via the Pacific–Japan teleconnection pattern, characterized by an eastward-retreated and southward-shifted sub-tropical high (WPSH) coupled with an intensified South Asian High (SAH). In contrast, NA warming induces uniform warming across eastern China through a Eurasian Rossby wave train that modulates the WPSH northward. (4) Thermodynamically, NWP forcing dominates via asymmetric vertical motion and advection processes, while NA forcing primarily enhances large-scale subsidence and shortwave radiation. This study elucidates region-specific oceanic drivers of extreme heat, advancing mechanistic understanding for improved heatwave predictability. Full article

Background and Aims: Primary biliary cholangitis (PBC) is a chronic autoimmune liver disease frequently associated with fatigue and mild cognitive impairment. Brain-derived neurotrophic factor (BDNF) plays key roles in neuroplasticity, immune regulation, and metabolism. This study aimed to evaluate plasma BDNF levels in early-stage PBC and examine their clinical and biochemical associations. Methods: In this observational study, plasma BDNF, IL-6, and IL-18 concentrations were measured by ELISA in 45 patients with early-stage PBC and 31 age- and sex-matched healthy controls (mean age 60.5 years; 96% women). All participants underwent liver elastography using point shear wave elastography (ElastPQ), Doppler ultrasound, laboratory testing, and assessment of cognitive function (PHES) and fatigue severity (MFIS). Non-invasive fibrosis scores (APRI, FIB-4) were calculated. Results: Median plasma BDNF concentrations were significantly higher in PBC patients than in controls [median: 21.04 ng/mL (IQR: 10.68–38.07) vs. 5.80 ng/mL (IQR: 4.58–7.54); p < 0.0001]. In PBC patients, higher BDNF levels correlated inversely with liver stiffness measured by ElastPQ (R = −0.39, p = 0.0258), spleen dimensions, splenic vein flow volume (R = −0.49, p = 0.0018), suggesting an association with milder liver fibrosis and early hemodynamic alterations. A trend toward association between BDNF and IL-6 levels was observed in multivariate analysis. No significant associations were found between BDNF concentrations and markers of hepatocellular injury, cognitive performance, or fatigue severity. Conclusions: Plasma BDNF concentrations are elevated in early-stage PBC and inversely correlate with liver fibrosis severity. No significant associations were found with hepatocellular injury, cognitive function, or fatigue. These findings suggest that BDNF may play a protective role against hepatic fibrogenesis, or alternatively, that BDNF concentrations may decline with advancing liver disease. Further studies are needed to clarify its significance in PBC. Full article

Background: To identify drug candidates that reduce cellular stress, linear peptides known as endomorphin (EM) analogs containing proline surrogates in position 2 were tested in in vitro injury models induced by corticosterone (CORT). Methods: In this study, neuroblastoma (SH-SY5Y) cells were treated with CORT and synthesized peptides, and then the cell viability and morphology, reactive oxygen species production (ROS), mitochondrial membrane potential (ΔΨm), adenosine triphosphate (ATP), and intracellular calcium ion [Ca²⁺]_i levels were evaluated. We also conducted an in-depth analysis of the apoptosis markers using quantitative real-time PCR (qPCR). Finally, we explore the brain-derived neurotrophic factor (BDNF) expression (qPCR) and protein levels (ELI-SA and Western blot). Results: The strongest neuroprotective effect in the CORT-induced stress model was shown by peptide 3 and peptide 7 (in the following sequence Tyr-Inp-Trp-Phe-NH2 and Tyr-Inp-Phe-Phe-NH2, respectively). These peptides significantly improved cell viability and reduced oxidative stress in CORT-treated cells. Conclusions: Their neuroprotective potential appears linked to anti-apoptotic effects, along with in-creased BDNF expression. Moreover, in the lipopolysaccharide (LPS)- and interferon-γ (IFN-γ)-induced damage model in macrophage RAW 264.7 cells, these two peptides reduced the secretion of inflammatory mediators nitric oxide (NO), tumor necrosis factor-α (TNF-α), and interleukin-6 (IL-6). Peptides exhibiting both neuroprotective and anti-inflammatory properties warrant further investigation as potential therapeutic agents. Full article

The enzyme ABH2, one of nine human DNA dioxygenases of the AlkB family, belongs to the superfamily of Fe(II)/α-ketoglutarate-dependent dioxygenases and plays a crucial role in the direct reversal repair of nonbulky alkyl lesions in DNA nucleobases. ABH2 has broad substrate specificity, directly oxidizing DNA damages such as N¹-methyladenine, N³-methylcytosine, 1,N⁶-ethenoadenine, 3,N⁴-ethenocytosine, and a number of others. In our investigation, we sought to uncover the subtleties of the mechanisms governing substrate specificity in ABH2 by focusing on several critical amino acid residues situated in its active site. To gain insight into the function of this enzyme, we performed a functional mapping of its active site region, concentrating on pivotal residues, participating in forming a damaged binding pocket of the enzyme (Val99 and Ser125), as well as the residues directly involved in interactions with damaged bases, namely Arg110, Phe124, Arg172, and Glu175. To support our experimental data, we conducted a series of molecular dynamics simulations, exploring the interactions between the ABH2 mutant forms, bearing corresponding substitutions and DNA substrates, and harboring various types of methylated bases, specifically N¹-methyladenine or N³-methylcytosine. The comparative studies revealed compelling data indicating that alterations in most of the studied amino acid residues significantly influence both the binding affinity of the enzyme for DNA and its catalytic efficiency. Intriguingly, the findings suggest that the mutations impact the catalytic activity of ABH2 to a greater extent than its ability to associate with DNA strands. Collectively, these results show how changes to the active site affect molecular dynamics and reaction kinetics, improving our understanding of the substrate recognition process in this pivotal enzyme. Full article

The flavor characteristics, perception, and molecular mechanisms of eight menthol isomers were investigated by sensory analysis combined with computational simulations. The sensory analysis results show significant differences in the odor profiles of the different menthol isomers. Among them, L-menthol shows a pleasant, sweet, and mint-like odor with a distinct freshness and no off-flavors, whereas the remaining seven isomers were interspersed with negative odors (musty, herbal, or earthy aromas). L-menthol and D-menthol had the lowest detection thresholds of 5.166 and 4.734 mg/L, respectively. The molecular docking results of the menthol isomers with olfactory receptors (Olfr874, OR8B8, and OR8B12) indicate that hydrogen bonding and hydrophobic interactions were the key binding forces. The binding energy ranged from −7.3 to −5.1 kcal/mol. Residues His-55 (Olfr874), Thr-56 (Olfr874), Leu-55 (OR8B8), Tyr-94 (OR8B8), Thr-57 (OR8B8), Phe-199 (OR8B12), and Ser-248 (OR8B12) with high frequencies particularly contributed to the recognition of menthol isomers. These findings contribute to a deeper understanding of the olfactory perception mechanism of menthol and provide data support for the development and precise application of minty odorants. Full article

The deamidation rate is relatively high for Asn residues with Phe as the C-terminal adjacent residue in γS-crystallin, which is one of the human crystalline lens proteins. However, peptide-based experiments indicated that bulky amino acid residues on the C-terminal side impaired Asn deamination. In this study, we hypothesized that the side chain of Phe affects the Asn deamidation rate and investigated the succinimide formation process using quantum chemical calculations. The B3LYP density functional theory was used to obtain optimized geometries of energy minima and transition states, and MP2 and M06-2X calculations were used to obtain the single-point energy. Activation barriers and rate-determining step changed depending on the orientation of the Phe side chain. In pathways where an interaction occurred between the benzene ring and the amide group of the Asn residue, the activation barrier was lower than in pathways where this interaction did not occur. Since the aromatic ring is oriented toward the Asn side in experimentally determined structures of γS-crystallin, the above interaction is considered to enhance the Asn deamidation. Full article

The design of small-molecule inhibitors targeting proprotein convertase subtilisin/Kein type 9 (PCSK9) remains a forefront challenge in combating atherosclerosis. While various monoclonal antibodies have achieved clinical success, small-molecule inhibitors are hindered by the unique structural features of the PCSK9 binding interface. In this study, a potential small-molecule inhibitor was identified through virtual screening, followed by molecular dynamics (MD) simulations to explore the binding mechanisms between the inhibitor and the PCSK9 protein. Binding free energies were calculated using molecular mechanics/Generalized Born surface area (MM/GBSA) with the interaction entropy (IE) method, and critical hot-spot residues were identified via alanine scanning analysis. Key residues, including ARG237, ILE369, ARG194 and PHE379, were revealed to form critical interactions with inhibitor and play dominant roles during the inhibitor’s binding. In addition, the polarization effect was shown to significantly influence PCSK9–ligand binding. The identified inhibitor exhibited highly similar binding patterns with two known active compounds, providing valuable insights for the rational design and optimization of small-molecule inhibitors targeting PCSK9. This work contributes to the development of more effective treatments for hyperlipidemia and associated cardiovascular diseases. Full article

2-Phenylethanol (2-PE), an aromatic alcohol with a rose-like fragrance, is widely used in the food, pharmaceutical, and high-end cosmetic industries. In this study, a high-yield 2-PE-producing strain was isolated and identified as Saccharomyces cerevisiae based on morphological characterization and taxonomic identification. Fermentation medium components (carbon and nitrogen sources) were optimized through single-factor experiments in shaking flasks, and fermentation medium with 40 g/L glucose, 5 g/L malt extract, 1.75 g/L corn steep liquor, 2.5 g/L yeast extract, 5 g/L malt extract, 1.75 g/L corn steep liquor was considered suitable for 2-PE production. RT-qPCR results indicated that corn steep liquor activates expression of genes related to the shikimate pathway and Ehrlich pathway (pha2, aro4, aro8, and aro9), thereby promoting the synthesis of 2-PE through these pathways. Excess yeast extract inhibited the expression of aro8 and aro9, while enhancing the expression of tdh3 and adh2, thus promoting the de novo synthesis of 2-PE. Furthermore, fermentation in a 5 L bioreactor was applied to investigate the effects of feeding strategies, inoculum proportion, and pH on 2-PE production. With a pH of 5.5 and10% inoculum proportion, the supplementation of the substrate L-Phe led to a 2-PE production of 4.81 g/L after 24 h of fermentation. Finally, in situ product recovery (ISPR) techniques was applied to alleviate 2-PE cytotoxicity, achieving a production of 6.41 g/L. This process offers a promising strategy for producing 2-PE efficiently and naturally, paving the way for further industrial applications in food, pharmaceutical, and cosmetic sectors. Full article

This study used integrated in vitro and in vivo approaches to investigate how the starch source (glutinous rice, indica rice, maize, or high-amylose rice) influences starch digestion kinetics and, consequently, the apparent nutrient utilization and amino acid metabolism in goslings. Four diets were formulated using glutinous rice, indica rice, maize, and high-amylose rice, and in vitro digestion and animal experiments were carried out. The data showed the particle sizes of the four starches: glutinous rice ≈ indica rice < corn < amylose. The glutinous rice starch grain is a porous polyhedron with an angular surface, the corn starch grain is an ellipsoid with a smooth surface, the indica rice starch grain is a polyhedron with a smooth and compact surface, and the high-amylose starch grain is an irregular polyhedron with a smooth surface. Starch digestibility was relatively stable for the indica and corn-based diets, and starch digestibility was higher for the indica rice diet compared to the corn- and high-amylose starch-based diets. The utilization of Asp, Ser, Glu, Gly, and Phe was higher for the glutinous rice diet compared to the maize and high-amylose diets. Furthermore, with this diet, the availability of Thr and Ala was observed to be higher than with the indica rice and high-amylose diets. In conclusion, the particle size and structure of starch from different sources (glutinous rice, indica rice, corn, and high-amylose rice) were different, significantly affecting the starch digestion rate. The glutinous rice diet enables a fast digestion rate for starch, which is rapidly digested in the proximal intestine. The inadequate supply of glucose in the distal intestine enhances the oxidative energy supply from dietary amino acids in that region, thereby improving the apparent digestibility of both starch and crude protein. Full article

Background/Objectives: The INK4 locus at chromosome 9p21.3, encoding CDKN2A, CDKN2B and the long non-coding RNA CDKN2B-AS1 (ANRIL), has been implicated in multiple diseases, including glaucoma and cardiovascular disease. ANRIL plays a critical role in gene regulation, inflammation and cell proliferation, contributing to disease susceptibility through shared molecular mechanisms. This study aims to identify SNPs within the INK4 locus associated with both glaucoma and CVD using the Open Targets Genetics platform and assess their pleiotropic effects. Methods: We utilised the Open Targets Genetics platform to identify SNPs at the INK4 locus associated with glaucoma and CVD. For each SNP, we recorded its genomic location, statistical significance and associated phenotypes. We further analysed the SNPs using the Genome Aggregation Database (gnomAD) to confirm their genomic position. Phenotypic associations were assessed using PheWAS data. Results: We identified 20 GWAS SNPs significantly associated with both glaucoma and CVD. All SNPs were located within intronic regions of the long non-coding RNA ANRIL. Certain SNPs such as rs4977756, rs1333037 and rs1063192 have known pleiotropic effects, influencing retinal ganglion cell survival in glaucoma and vascular smooth muscle cell proliferation in CVD. These SNPs influence shared biological pathways, including inflammation, oxidative stress and epigenetic regulation, and may exert either protective or pathogenic effects. Certain SNPs such as rs7853090 and rs1434537531 remain underexplored, emphasising the need for further research. Conclusions: This study highlights the pleiotropic role of ANRIL in glaucoma and CVD, driven by shared genetic and molecular pathways. While SNPs within ANRIL provide valuable insights into disease mechanisms, these conditions remain complex, influenced by multiple genetic and environmental factors. Targeting ANRIL therapeutically poses challenges due to its non-coding nature, but emerging RNA-based therapies, including antisense oligonucleotides and small-molecule modulators, hold promise. Further research into underexplored SNPs and ANRIL’s regulatory mechanisms is essential for advancing therapeutic development and understanding these multifactorial diseases. 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