Search Results (2,456)

Large-scale computer simulations were employed to investigate the conformational response of the spike protein components S1 and S2 using a coarse-grained model. Temperature was systematically varied to assess the balance between stabilizing residue–residue interactions and thermal fluctuations. The resulting contact profiles reveal distinct segmental reorganization and self-assembly behaviors between S1 and S2. At lower, thermoresponsive temperatures, pronounced segmental globularization occurs in the N-terminal domain (NTD; M153–K202) and receptor-binding domain (RBD; E406–E471) of S1, whereas S2 exhibits alternating regions of high and low contact density. Increasing temperature reduces this segmental globularization, leaving only minor persistence at elevated temperatures. The temperature dependence of the radius of gyration (R_g) further demonstrates the contrasting thermal behaviors of S1 and S2. For S1, R_g increases continuously and monotonically with temperature, reaching a steady-state value approximately 50% higher than that at low temperature. In contrast, S2 displays a non-monotonic response: R_g initially rises to a maximum nearly sevenfold higher than its low-temperature value, then decreases with further temperature increase. Scaling analysis of the structure factor reveals that the globularity of S1 diminishes significantly upon heating, while S2 becomes modestly more compact yet retains its predominantly fibrous character. Full article

The ongoing evolution of SARS-CoV-2 has given rise to variants with enhanced transmissibility and pathogenicity, many of which harbor mutations in the receptor-binding domain (RBD) of the viral spike protein. These mutations often confer increased viral fitness and immune evasion by modulating interactions with the human ACE2 receptor (hACE2) and escaping neutralizing antibodies. Accurate prediction of the functional consequences of such mutations—particularly their effects on receptor binding and antibody escape—is critical for assessing the public health threat posed by emerging variants. In this study, we apply a Mutation-dependent Biomacromolecular Quantitative Structure–Activity Relationship (MB-QSAR) framework to quantitatively model the biochemical phenotypes of RBD variants. Trained on comprehensive deep mutational scanning (DMS) datasets, our models exhibit strong predictive performance, achieving correlation coefficients (r²) exceeding 0.8 for hACE2 binding affinity and 0.7 for antibody neutralization escape. Importantly, the MB-QSAR approach generalizes well to multi-mutant variants and currently circulating lineages. Structural analysis based on model-derived interaction profiles offers mechanistic insights into key RBD–ACE2 and RBD–antibody interfaces, helping the rational design of broadly protective vaccines and therapeutics. This work establishes MB-QSAR as a rapid, accurate, and interpretable tool for the prediction of protein–protein interaction and forecasting viral adaptation, thereby facilitating early risk assessment of novel SARS-CoV-2 variants. Full article

This study employed a combined computational and experimental approach to investigate the molecular recognition mechanism of 4-methylphenol by human olfactory receptor hOR9Q2. The strategy integrated molecular docking using BIOVIA Discovery Studio, structural modeling of hOR9Q2 based on the AlphaFold2-predicted, molecular dynamics simulations with GROMACS software employing the AMBER14SB force field, and systematic site-directed mutagenesis validation. Computational simulations revealed that the binding cavity formed by transmembrane domains TM3, TM5, and TM6 serves as the key interaction region, with van der Waals, hydrophobic, and Pi-sulfur interactions driving stable binding (ΔG = −40.173 ± 0.34 kJ/mol). Functional characterization identified six critical residues (Cys112, Val158, Met207, Phe251, Leu255, and Tyr259) as essential for receptor activation, while mutations at Ile71 and Ala108 resulted in partial functional impairment. This study reveals the structural basis for hOR9Q2’s selective response to 4-methylphenol, while establishing a computational–experimental framework for precisely locating functional sites on olfactory receptors. These findings elucidate the molecular mechanism of odorant recognition and provide insights for developing odorant prediction models and designing specific olfactory receptor modulators. Full article

Natural peptides derived from plants have been an important source of medical substances for several decades. Due to their mechanism of action, chemical potential, and favourable side effect profile, these peptides represent a safer alternative to synthetic pharmaceutical treatments. In this study, we report the discovery of a natural peptide derived from the Brassica napus (Canola) proteome that exhibits high functional similarity to an artificial intelligence (AI)-generated peptide that is designed to bind to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike 1 (S1) protein receptor-binding domain (RBD) region. The results of a series of experiments including molecular docking simulations, as well as binding and inhibition assays suggest that the natural peptide exhibits functions similar to those of the AI-generated peptide in binding to the RBD region and disrupting its interaction with the human host receptor angiotensin-converting enzyme 2 (ACE2). This study demonstrates the potential of AI-designed peptides to facilitate the identification of natural peptides with similar functional properties. Full article

Alpha7 nicotinic receptors (α7-nAChRs) are implicated in many neurological disorders, but how they fold and assemble is not well understood. Unlike native α7-nAChRs, α7-5HT3 chimeras fold efficiently in HEK cells and do not require chaperones RIC3 or TMEM35A (NACHO) for proper assembly. We investigated the effects of swapping 5HT3 and α7-receptor protein sequences on α7-5HT3R chimera surface expression in mammalian HEK293 or Bosc23 cells, or chimeric receptor function using Xenopus laevis oocytes with or without chaperones. α7-5HT3Rs, consisting of human α7-nAChRs with mouse 5HT3 transmembrane domains (TMs) express without chaperones as measured by cell surface alpha-bungarotoxin binding. However, when subunit TMs from α7-nAChRs and 5HT3Rs were mixed, chaperones were required. Substituting the SAP motif prior to the α7-nAChR “Latch” tail sequence for the 5HT3 C-terminal decreased expression relative to α7-nAChRs with chaperones. Chaperone effects on L264 and G265 mutations in M2 were also investigated. Some constructs that express well in HEK293 or Bosc23 cells are nonfunctional in oocytes with or without NACHO. Our data do not support direct binding of RIC3 or NACHO to the α7-nAChR TM4 (M4) region; instead, they emphasize the functional importance of the conserved SAP motif. Full article

Background/Objectives: Osteoporosis is caused by excessive osteoclast activation via the receptor activator nuclear factor kappa B ligand (RANKL), which is released from osteoblasts or osteocytes. RANKL regulates osteoclast activity by binding to the receptor activator of nuclear factor kappa B (RANK) in the canonical pathway or leucine-rich repeat-containing G protein-coupled receptor 4 (LGR4) in the non-canonical pathway. In this study, we attempted to develop an intact small-fragment protein based on RANKL by removing the RANK-binding site and transforming the amino acid residues at crucial sites to inhibit osteoclast activity and treat osteoporosis. Methods: We expressed a small-fragment variant of RANKL as a soluble glutathione S-transferase (GST) or 6x histidine (His)-tagged fusion protein using a GST- or His-binding domain tag expression vector system. To generate an intact form of small-fragment RANKL, ribosome-inactivating protein–His-fusion RANKL was purified using HisTrap affinity chromatography and treated with tobacco etch virus nuclear inclusion endopeptidase to remove the His-tag fusion protein. Tartrate-resistant acid phosphatase (TRAP) and bone resorption pit formation assays were performed to analyze the inhibitory effects on osteoclast differentiation and activation. Results: The intact forms of 225RANKL295P and 225RANKL295A showed the strongest inhibitory effects on TRAP activity and bone resorption pit formation. Conclusions: Using an optimal construct design, a large and diverse range of small RANKL fragments could be generated. This suggests that the generation of small-fragment RANKL provides a promising avenue for the advancement of novel therapeutic approaches to osteoporosis. Full article

This study investigated the therapeutic potential of a novel probiotic combination consisting of Lactococcus cremoris subsp. cremoris MP01 and Lacticaseibacillus paracasei subsp. paracasei MP02, collectively referred to as LCP, in the treatment of canine atopic dermatitis (CAD). In a 60-day open-label, single-arm trial involving eight dogs, notable clinical improvements were observed following daily LCP treatment, as evidenced by decreasing trends in Canine Atopic Dermatitis Extent and Severity Index and Pruritus Visual Analogue Scale scores, as well as a significant reduction in serum immunoglobulin E levels (p < 0.05). Microbiome and short-chain fatty acid (SCFA) analyses were subsequently conducted in a representative subset of six dogs to explore the effects of LCP on the fecal and skin microbial ecosystems. Concomitant alterations in gut and skin microbiome were observed, including a significant reduction in abundance of Erysipelotrichaceae (p < 0.05) and non-significant decreasing trends in Romboutsia, Escherichia/Shigella spp., and Shigella flexneri, along with a trend toward increased SCFA production. Functional prediction using PICRUSt suggested potential involvement of immune- and infection-related signaling pathways, including those associated with nucleotide-binding oligomerization domain-like receptors, retinoic acid-inducible gene I-like receptors and Shigellosis, supporting the hypothesis that LCP may exert its effects through modulation of the gut–skin axis. These findings support LCP as a safe and promising adjunct therapy for CAD, offering a novel microbiome-targeted approach targeting both clinical symptoms and underlying dysbiosis. Further investigation is warranted to optimize probiotic formulations and better understand the mechanisms underlying microbiome-mediated immune modulation in canine allergy. Full article

Protein–protein docking is a cornerstone of computational structural biology, yet its reliability for large, multimeric assemblies remains uncertain. Standard workflows typically include geometry optimization or molecular dynamics equilibration to relieve local strains and improve input quality, but the extent to which these preparatory steps alter docking outcomes has not been systematically evaluated. Here, we address this question using the mitochondrial chaperonin Hsp60, a dynamic double-ring complex essential for protein folding, and MIX, a kinetoplastid-specific protein with unresolved function, as a stress test system. By comparing docking predictions across minimized, equilibrated, and ensemble-refined structures of Hsp60 in three conformational states (apo, ATP-bound, and ATP–Hsp10), we show that structural relaxation profoundly reshapes the docking landscape. Minimization alone often yielded favorable scores but localized binding, while longer MD trajectories exposed alternative sites, including central cavity, equatorial ATP pocket, and apical domain, each consistent with distinct regulatory hypotheses. These findings reveal that docking outcomes are highly sensitive to receptor preparation, especially in complexes undergoing large conformational transitions. More broadly, our study highlights an underappreciated vulnerability of docking pipelines and calls for ensemble-based and dynamics-aware approaches when predicting interactions in large biomolecular machines. Full article

The COVID-19 pandemic, caused by SARS-CoV-2, has profoundly affected global health and the economy. The emergence of variants with spike mutations, particularly within the receptor-binding domain (RBD), has reduced the efficacy of many neutralizing antibodies (nAbs), and recent variants, including KP.3 and other circulating strains, show partial escape from infection- or vaccine-induced immunity. To overcome this, developing broad-spectrum nAbs that target the conserved S2 subunit of the spike protein is crucial. Unlike the highly mutable RBD, the S2 region remains structurally conserved, providing a promising foundation for universal protection. Deeper insight into S2 structure and function, together with advances in bispecific antibody design, could facilitate the development of next-generation therapeutics resilient to viral evolution. This review examines the structural evolution of the SARS-CoV-2 spike, focusing on the therapeutic potential of S2-targeting antibodies and strategies to overcome antibody resistance. Full article

The γδ T cells belong to a subgroup of T cells known as non-conventional T cells due to their limited T cell receptor (TCR) repertoire and ability to recognize non-peptide antigens. They play a crucial role in combating infections and tumors. Vγ9Vδ2 T cells are typically activated by molecules containing diphosphate groups, collectively known as phosphoantigens (pAgs), through a non-canonical mechanism which involves the intracellular domain of butyrofilin (BTN)3A1 protein. However, no FDA-approved drugs have yet been shown to activate them, and the underlying cellular mechanisms remain unknown. In this study, we combined high-throughput virtual screening of an FDA-approved drug database with in vitro cellular assays to identify potential γδ T cells activators. Our findings demonstrate that Nitazoxanide (NTZ) and Tinidazole induce moderate elicited a statistically significant increase in interferon (IFN)-γ production of Vγ9Vδ2 T cells by their probably interaction with the pAg binding site of BTN3A1. Additionally, NTZ induces expression of CD107a, but only at the highest concentrations tested and promotes the upregulation of HLA-DR in total PBMCs and CD14⁺ monocytes. Blocking BTN3A with a specific antibody led to a marked reduction in all NTZ-induced activations. This work identifies NTZ as a previously unrecognized activator of γδ T cells, highlighting its immunomodulatory potential beyond its known clinical uses. These findings broaden our understanding of γδ T cells pharmacology and suggest new opportunities for drug repurposing and the design of novel chemical scaffolds. Further mechanistic studies will be essential to fully define how NTZ engages the BTN3A–γδ T cells axis. Full article

Dysregulated lipid metabolism is associated with cardiovascular disease, obesity and type 2 diabetes. In the current report, we explore the functional interactions between two important regulators of lipid metabolism, sterol regulatory element-binding protein 1 and 2 (SREBP1/2), and PRDI-BF1 and RIZ homology domain containing 16 (PRDM16). The SREBP family of transcription factors regulate cholesterol and fatty acid synthesis and metabolism, primarily in liver but also in white adipose tissue. PRDM16 is a major regulator of brown adipose tissue (BAT) biogenesis and function as well as an inhibitor of white adipogenesis. We find that PRDM16 interacts with the nuclear forms of SREBP1/2 and inhibits their transcriptional activities. Consequently, inactivation of PRDM16 enhances the expression of well-established SREBP target genes involved in fatty acid and cholesterol synthesis/metabolism. Importantly, PRDM16 inactivation increases the expression of LDL receptor mRNA (1.6-fold) and protein (1.7-fold) and augments the cellular uptake of LDL particles (2.3-fold). Supporting these findings, PRDM16-deficient cells accumulate more neutral lipids in a SREBP1/2-dependent manner. Inactivation of PRDM16 in white and brown preadipocyte cell lines and human adipose-derived stem cells enhances the expression of SREBP target genes. In addition, the expression of adipogenic markers was increased in mature white adipocytes generated from PRDM16-knockdown preadipocytes (1.8- to 3.9-fold). Thus, our study identifies PRDM16 as a novel inhibitor of SREBP-dependent lipid metabolism with implications for adipose biology and metabolic disease. Full article

The SARS-CoV-2 spike protein, through its receptor binding domain (S1-RBD), binds to the angiotensin-converting enzyme 2 (ACE2) receptor on the host cell membrane, leading to viral infection. Several mutations in S1-RBD in SARS-CoV-2 variants are known to enhance infection through an increased affinity for ACE2. While many reports are available describing the SARS-CoV-2 infection mechanism, there is a dearth of studies towards understanding the initial interaction of the S1-RBD with ACE2 on living host cells and the role of endocytosis and cytoskeleton in the process. Here, we reconstituted the interaction between S1-RBD- and ACE2-expressing host cells in a hybrid live cell-supported lipid bilayer (SLB) platform enabling live monitoring of the interaction between S1-RBD on SLBs and the ACE2 receptor on living cells and showed that cells depleted Omicron S1-RBD from SLB corrals, likely through endocytosis. Specifically, interaction of living host cells with S1-RBD-functionalized SLB substrates resulted in the enrichment of S1-RBD and ACE2 at the cell–SLB interface. Interaction of host cells with wild type (WT), Omicron, and Omicron Revertant S1-RBD functionalized on micron-scale SLB corrals, which mimic viral membranes but are flat, also resulted in their enrichment. However, cells interacting with Omicron S1-RBD revealed a depletion of the protein from many corrals, which was generally not observed with the WT S1-RBD and was reduced with the Omicron Revertant, which contains the Q493R mutation reversion, S1-RBD. Further, S1-RBD depletion coincided with the localization of the early endosomal marker EEA1. Importantly, treatment of cells with the clathrin inhibitor, pitstop 2, but not the myosin II inhibitor, blebbistatin, significantly reduced Omicron S1-RBD depletion. Collectively, these observations suggest that the SARS-CoV-2 Omicron variant has evolved, through mutations in its S1-RBD, to take advantage of the cellular endocytic pathway for enhanced infection, which is not observed with the parental SARS-CoV-2 and appears to be lost in the Omicron Revertant variant. Additionally, these results underscore the significance of the hybrid live cell–SLB platform in studying SARS-CoV-2 S1-RBD-ACE2 interaction and the potential impact of mutations in the S1-RBD on adapting to a specific cellular entry mechanism. Full article

Excretory/secretory products from parasites (ESPs) can act as pathogen-associated molecular patterns (PAMPs) to activate innate immunity. Parasites may achieve immune evasion by modulating the interaction between PAMPs and the nucleotide-binding oligomerization domain-like receptor family, pyrin domain-containing three (NLRP3) inflammasome. Previous studies have suggested that some components of ESPs from Clonorchis sinensis (CsESPs) can induce the host’s immune responses, but the components that balance immunopathology and maintain chronic infection in chronic Clonorchis sinensis (C. sinensis) remain unclear. We previously found that the iNOS-interacting protein from C. sinensis (CsNOSIP), a component of CsESP, stimulates macrophages to produce reactive oxygen species (ROS) and nitric oxide (NO), both of which inhibit NLRP3 inflammasome activation. Therefore, this study investigated the effects of CsESP and CsNOSIP on inflammasome activation using RT-PCR, Western blot, and ELISA. This study showed that CsESPs promoted NLRP3 inflammasome activation in RAW264.7 cells, while CsNOSIP inhibited LPS-induced IL-1β secretion through an NLRP3-caspase-1-dependent pathway and reversed the CsESPs-induced activation through the iNOS/NO–NF-κB pathway. These results reveal the antagonistic effects of CsESPs and CsNOSIP in inflammasome regulation, suggesting that this balance contributes to the regulation of the host’s immunity and the promotion of chronic infection of C. sinensis, providing potential targets for prevention and treatment. Full article

Capsicum annuum (pepper) is a globally significant Solanaceous crop vulnerable to devastating pathogens such as Phytophthora capsici. Nucleotide-binding leucine-rich repeat (NLRs) proteins are crucial intracellular immune receptors mediating effector-triggered immunity (ETI). This study presents the comprehensive genome-wide identification and analysis of the NLR gene family in pepper using the high-quality ‘Zhangshugang’ reference genome. We identified 288 high-confidence canonical NLR genes. Chromosomal distribution analysis showed significant clustering, particularly near telomeric regions, with Chr09 harboring the highest density (63 NLRs). Evolutionary analysis demonstrated that tandem duplication is the primary driver of NLR family expansion, accounting for 18.4% of NLR genes (53/288), predominantly on Chr08 and Chr09. Analysis of promoter cis-regulatory elements (CREs) revealed enrichment in defense-related motifs, with 82.6% of promoters (238 genes) containing binding sites for salicylic acid (SA) and/or jasmonic acid (JA) signaling. Transcriptome profiling of Phytophthora capsici-infected resistant (C. annuum cv. CM334) and susceptible (C. annuum cv. NMCA10399) cultivars identified 44 significantly differentially expressed NLR genes, and protein–protein interaction (PPI) network analysis predicted key interactions among them, with Caz01g22900 and Caz09g03820 as potential hubs. This study elucidates the tandem-duplication-driven expansion, domain-specific functional implications, and expression dynamics of the pepper NLR family. It identifies conserved and lineage-specific candidate NLR genes, including Caz03g40070, Caz09g03770, Caz10g20900, and Caz10g21150. These findings provide valuable candidate gene targets for the development of molecular markers for pepper resistance to Phytophthora capsici. Full article

Chemosensory systems are essential in insect behavior, with several key genes associated with these systems emerging as potential targets for pest control. Porphyrophora sophorae (Archangelskaya, 1935), a destructive pest of Chinese licorice (Glycyrrhiza uralensis, Fabaceae), poses a significant threat to the healthy cultivation of licorice. However, the molecular mechanisms underlying its host detection and olfactory recognition remain poorly understood. In this study, we present the first identification of odorant-binding proteins (OBPs) and olfactory receptors (ORs) from the transcriptome of P. sophorae. The identified OBPs contain six conserved cysteine residues, while predictive analysis suggests that PsopOrco may contain six transmembrane domains. Phylogenetic analysis demonstrated that the majority of these olfactory proteins are closely related to OBPs and ORs found in other scale insects. Using RT-qPCR, we assessed the anatomical structures expression of these genes and found that PsopOBP3, PsopOBP6, and PsopOrco were predominantly expressed in the antennae. Additionally, expression levels of OBPs and ORs varied across different tissues, suggesting anatomical structure regulation. These findings expand the gene repertoire of P. sophorae and provide valuable resources for further functional analysis of these key olfactory genes. Full article