Search Results (143)

Nuclear factor erythroid 2-related factor 2 (NRF2) has traditionally been framed as a Kelch-like ECH-associated protein 1 (KEAP1)-regulated stress-response transcription factor, but three observations now require a broader framework: NRF2 turnover is controlled by parallel E3 ligase systems; transcriptional output can be limited by coactivator assembly despite unchanged NRF2 abundance; and NRF2 activation can be beneficial or harmful depending on disease context, as illustrated by lung cancer models in which NRF2 paradoxically promotes metastasis through BTB and CNC homology 1 (BACH1) stabilization. We synthesize these observations into an NRF2 partner-code framework in which NRF2 acts as a context-dependent transcriptional platform assembled through four partly independent modules: a degradation module (KEAP1; β-transducin repeat-containing protein, β-TrCP; HMG-CoA reductase degradation protein 1/synoviolin 1, Hrd1/SYVN1; WD repeat-containing protein 23/DDB1- and CUL4-associated factor 11, WDR23/DCAF11); a cytoplasmic scaffold module (p62/sequestosome 1, p62/SQSTM1; IQ motif-containing GTPase-activating protein 1, IQGAP1; type I phosphatidylinositol 4-phosphate 5-kinase γ/heat shock protein 27, PIPKIγ–HSP27; peptidyl-prolyl cis-trans isomerase NIMA-interacting 1, PIN1; peptidyl-prolyl isomerase A/cyclophilin A, PPIA); a nuclear coactivator module at Neh4/5 (CREB-binding protein/p300, CBP/p300; receptor-associated coactivator 3/steroid receptor coactivator 3, RAC3/SRC-3; protein arginine methyltransferase 1/coactivator-associated arginine methyltransferase 1, PRMT1/CARM1; Mediator complex subunit 16, MED16); and a DNA/chromatin module at Neh1 (small musculoaponeurotic fibrosarcoma [Maf] proteins, BACH1, and chromodomain helicase DNA-binding protein 6, CHD6). Mapping 22 partners onto the Neh-domain architecture identifies approximately 25 pharmacologically addressable interfaces, stratified into four translational tiers. The framework reframes NRF2 pharmacology around one principle: the most actionable target is often a partner rather than NRF2 itself, with disease context dictating the direction of modulation. We close with five testable hypotheses and a partner-code decision matrix linking disease, biomarker, and candidate target. Full article

The Structural Maintenance of Chromosomes complex 5/6 (SMC-5/6) safeguards genome stability by coordinating DNA replication, repair, and chromosome organization. Although prior studies have advanced understanding of SMC-6, a domain-resolved view of its functions in vivo, particularly in multicellular organisms, remains incomplete. Because the non-SMC subunit NSE-1 localizes at the SMC-5/6 head interface and reflects complex integrity, we used NSE-1::GFP nuclear localization as a visual readout in an ethyl methanesulfonate (EMS)-based forward genetic screen in Caenorhabditis elegans (C. elegans). We identified three new smc-6 alleles—smc-6(wsh34), smc-6(wsh35), and smc-6(wsh36) through single-nucleotide polymorphism (SNP) mapping and whole-genome sequencing. smc-6(wsh34) and smc-6(wsh35) affect the N-terminal ATPase domain, whereas smc-6(wsh36) lies in the hinge region. ATPase-domain mutants exhibited reduced fertility, decreased progeny viability, hypersensitivity to methyl methanesulfonate and cisplatin, and strong induction of the pro-apoptotic genes egl-1 and ced-13. In contrast, the hinge mutant exhibited moderate fertility defects and partial sensitivity to DNA damage reagents. Structural modeling suggests that the R103 truncation disrupts the SMC-5/6 head interface, whereas the P514L substitution alters hinge dynamics. Together, these findings reveal a functional hierarchy in SMC-6, with the ATPase domain governing repair-associated energy-dependent processes and the hinge maintaining structural integrity. Full article

The present study aimed to compare the composition structure, interfacial, and antioxidant activities of flaxseed protein isolates (FPIs) in different flaxseed varieties. The results showed that apparently intact protein bodies (PBs) were manifested as densely staining cytoplasmic inclusions with distinct boundaries and varying diameter ranges among different flaxseed varieties. Through alkali extraction with isoelectric precipitation, FPIs exhibited a relatively small and irregular lamellar strip structure with varying sizes and shapes packed with spherical particles in studied flaxseed varieties. The different composition structures of FPIs among studied flaxseed varieties were also obtained, involving the protein subunits’ intrinsic fluorescence properties, secondary structures, and amino acid profiles. These structural differences also led to differential purities, aqueous solubility, dispersion properties, and surface charges. Moreover, the varying emulsifying and foaming properties of FPIs from different flaxseed varieties were also observed due to the formation of coarse lipid droplets (5~40 μm) and foams (20~100 μm) with the specific structure of the oil/gas–water interface and bulk aqueous phase. The retention of phenolic compounds into FPIs still displayed evident variety specificity from 323 to 478 mg/100 g and 210 to 347 mg/100 g, which definitely led to escalated antioxidant activities. Thus, FPIs from Longya 13# and Neiya 9# flaxseed varieties were screened for favorable emulsifying and foaming properties due to the balanced molecular rigidity/unfolding and interfacial adsorption/stabilization behavior. Full article

Insect odorant receptors (ORs) are pivotal molecular interfaces that translate environmental chemical cues into neuronal electrical impulses, thereby governing essential behaviors such as foraging, mating, oviposition, and predator avoidance. The past three years have witnessed a paradigm shift driven by high-resolution cryo-electron microscopy (cryo–EM) structures of OR-odorant receptor co-receptor (Orco) heterocomplexes, which definitively established the 1:3 stoichiometry (one odorant-specific OR subunit and three Orco subunits) of the functional ion channel. These structures have revealed the architecture of the ligand-binding pocket and the conformational dynamics underlying channel gating. This structural framework has illuminated long-standing questions regarding the evolution of ORs from ancestral gustatory receptors and their lineage-specific expansion via a “birth-and-death” model, enabling adaptation to diverse ecological niches. Concurrently, the long-debated signal transduction mechanism has been reconciled by evidence of a unified bimodal system, where OR–Orco complexes function as both direct ligand-gated ion channels and activators of an IP3-dependent metabotropic cascade. Here, we integrate these recent breakthroughs—from atomic-level structures and evolutionary genomics to in vivo functional validation—with classical knowledge of OR expression, localization, and diversity. We further synthesize the emerging field of structure-guided applications, including virtual screening for novel semiochemicals and the development of RNAi- and CRISPR-based strategies for pest management. This comprehensive review provides a framework for understanding the molecular logic of insect olfaction and its exploitation for biotechnological innovation. Full article

Cells rely heavily on DNA repair networks to survive genomic damage. For repairing double-strand breaks, Non-Homologous End Joining (NHEJ) remains the primary pathway, which is largely controlled by the DNA-dependent protein kinase catalytic subunit (DNA-PKcs). Researchers have long studied how phosphorylation drives this kinase. However, recent data point to an important additional layer of control. Drawing on evidence accumulated over the past two decades, we propose a “Spatiotemporal Logic Circuit” model for DNA-PKcs regulation. In this model, SUMO-associated interactions may help stabilize synaptic assembly, HUWE1-mediated neddylation may facilitate kinase activation at Lys4007, and K48-linked ubiquitination—potentially involving RNF144A—may contribute to the turnover of persistent repair complexes. Importantly, we frame these UBL-mediated events within the broader autophosphorylation-driven conformational cycle of DNA-PKcs, which remains central to NHEJ progression. Additionally, we highlight the structural interface where activation and degradation signals may converge and the extraction barrier posed by the massive DNA-PKcs scaffold. From a translational perspective, we argue that the exceptional size of DNA-PKcs (~470 kDa) and its topological entrapment on DNA render it an unusually challenging PROTAC target—one that may require p97/VCP-assisted extraction before proteolysis can proceed. We also highlight the underappreciated risk that E3 ligase loss-of-function, already documented in BET-PROTAC resistance, may similarly undermine DNA-PKcs degrader strategies. Full article

This study aimed to design a multi-epitope vaccine (MEV) against Pasteurella multocida (Pm) using immunoinformatics approaches. Based on four conserved outer membrane proteins (OmpA; OmpH; PlpEand LolA), 15 immunodominant epitopes were identified, including 8 CTL epitopes, 3 HTL epitopes, and 4 B-cell epitopes. A vaccine construct was developed by incorporating RGD and PADRE adjuvant sequences. Computational analyses indicated that the vaccine possesses favorable physicochemical properties and structural stability. The molecular docking and normal mode analyses reveal a potential binding interface between the basis and TLR2/TLR4, with a computed binding energy of −10.1 kcal/mol for TLR4, suggesting a possible preferential interaction. Immune simulation predicted the vaccine could effectively elicit responses from B cells, T cells, and key cytokines such as IFN-γ. Additionally, the vaccine sequence was successfully cloned into the pET-28a (+) expression vector, facilitating future recombinant expression. This study provides a theoretical foundation for developing a safe and effective subunit vaccine against Pm. Full article

Mediator is a central transcriptional coactivator that connects sequence-specific transcription factors with RNA polymerase II to control inducible gene expression in plants. MED16 is a Mediator tail module subunit that functions as a context-dependent integrator, helping coordinate developmental programs with environmental adaptation. This review summarizes current evidence for MED16 function from structural and evolutionary perspectives to physiological outputs, with emphasis on how MED16 interacts with transcription factors and other Mediator subunits to shape RNA polymerase II engagement at target loci. In terms of development, MED16 contributes to organ growth and root system architecture, and comparative studies have revealed that it plays conserved roles in lineage-specific wiring. Under abiotic stress, MED16 supports the efficient activation of stress-inducible transcription, including cold acclimation and nutrient stress responses such as phosphate starvation-dependent root remodeling. In immunity, MED16 modulates salicylic acid- and jasmonate/ethylene-associated defence outputs and can be targeted by plant viruses, which is consistent with its role in antiviral transcriptional responses. Mechanistically, MED16 participates in cooperative and competitive interactions within the Mediator complex that tune hormone-responsive outputs, exemplified by MED25-related competition in abscisic acid signalling. We highlight key limitations and future directions, including the need for mechanistic validation beyond Arabidopsis, clearer models of dosage control in crops, improved understanding of context-dependent tail configurations, and high-resolution mapping of MED16 interaction interfaces. Full article

The Mediator complex is a central regulator of eukaryotic transcription, functioning as a dynamic molecular interface between gene-specific transcription factors and RNA polymerase II (Pol II). Although its overall architecture and general role in transcription have been extensively reviewed, accumulating genetic, genomic, and clinical evidence indicates that individual Mediator subunits make distinct and non-redundant contributions to human physiology and disease. In this review, we move beyond a generic description of Mediator function and present a subunit-resolved synthesis of Mediator biology with an emphasis on disease pathogenesis. A key feature of this review is a comprehensive table integrating disease associations and molecular functions of individual human Mediator subunits, enabling rapid assessment of functional specialization across the complex. We further discuss chromatin-based mechanisms of Mediator action, including cooperation with cohesin and architectural factors to regulate enhancer-promoter communication and higher-order genome organization. By organizing recent structural, mechanistic, and pathological findings into a unified framework, this review highlights how disruption of specific Mediator subunits contributes to cancer, developmental disorders, and metabolic disease, and outlines emerging opportunities for therapeutic intervention. Full article

The present study aims to evaluate the interaction of gliclazide with proteins related to inflammation—{inhibitor of nuclear factor kappa-B kinase subunit beta (IKKα) and NF-kappa-B-inducing kinase (NIK)}; oxidative stress—{kelch domain of Kelch-like ECH-associated protein 1 (KKeap1)} and ER stress—{inositol-requiring enzyme-1alpha (IRE1α)}. X-ray crystal structure of IKKα, (PDB ID: 5EBZ), KKeap1 (PDB ID: 4L7B), NIK (PDB ID: 8YHW) and IRE1α (PDB ID: 4YZ9) were obtained from Protein Data Bank and Open Babel 3.1.1 was used to prepare the ligands. Prior to docking, protein structures were prepared by removing water molecules, adding hydrogen atoms, and optimizing side chain conformations using Maestro (Schrödinger Suite, version 2024-2) along with the OPLS4 force field. Ligand docking was performed using the Glide application. Molecular dynamics simulation was performed with Desmond (Schrödinger Suite) within the Maestro interface for 100 ns for the NPT ensemble at 300 K and 1 atm pressure. Physicochemical and pharmacokinetics properties were analyzed using ADMETlab 3.0 and SwissADME. The binding energies of gliclazide with IKKα, NIK, KKeap1 and IRE1α were −8.3, −7.9, −8.4 and −8.8, respectively. Root mean square displacement (RMSD), root mean square fluctuation (RMSF) and radius of gyration analyses predicted relatively strong and stable interactions between gliclazide and the proteins, with favourable pharmacokinetic properties. It was also observed that CYP3A4 metabolizes gliclazide, in addition to CYP2C9 and CYP2C19. The activity of gliclazide against inflammation, oxidative stress and endoplasmic reticulum stress might be via interaction with these proteins. Full article

CK2α and CK2α’, two paralogous members of the human kinome, are catalytic subunits of protein kinase CK2. Together with the regulatory subunit CK2β, they form heterotetrameric holoenzymes. CK2 is the subject of efforts to develop effective and selective inhibitors. For this, secondary binding sites remote from the canonical ATP/GTP cavity are critical. A crystallographic fragment screening with CK2α’ crystals and an established molecular fragment collection was performed to identify new ligands at known or novel sites. It resulted in fourteen CK2α’/fragment structures. Five fragments were found at the CK2β interface of CK2α’ and three fragments at the established αD pocket, which exhibits subtle differences between CK2α and CK2α’; comparative co-crystallisations with CK2α showed that one of them binds to the αD pocket of CK2α’ exclusively. No fragments bound at the substrate-binding region of CK2α’, but a CK2α’ structure with dp10, a decameric section of the substrate-competitive inhibitor heparin, and the indenoindole-type ATP-competitive inhibitor 4w was determined. A comparison with a published CK2α/dp10 structure revealed features consistent with reports about substrate specificity differences between the isoenzymes: dp10 binds to CK2α’ and CK2α with opposite strand orientations, and the local conformations of the isoenzymes in the helix αD region are significantly different. Full article

Background/Objectives. Antibiotic resistance is an escalating global health concern, highlighting the need for innovative antibacterial strategies beyond traditional drugs. GroEL, a highly conserved bacterial chaperonin essential for protein folding and stress tolerance, represents a promising but underexplored therapeutic target. This study aimed to identify short peptides capable of binding GroEL monomers and potentially altering their function, with the long-term goal of disrupting bacterial survival mechanisms. Methods. A phage display screening of a 12-mer peptide library was performed against purified GroEL monomers, yielding five candidate peptides (G1–G5). Their interactions with GroEL were analyzed through molecular docking and molecular dynamics simulations using three-dimensional GroEL structures (1MNF, 1XCK, 8S32). Stability of binding and interaction profiles were assessed through molecular dynamics-based analyses and MM/GBSA free energy calculations. Results. Peptides G4 and G5 displayed the most stable and energetically favorable interactions, with G4–8S32 showing the strongest binding (−116.68 kcal/mol). These peptides localized near inter-subunit interfaces, suggesting potential interference with GroEL oligomerization or allosteric transitions, which are critical for its biological function. Conclusions. Our findings demonstrate that short peptides can stably bind GroEL and potentially modulate its activity. Peptides G4 and G5 represent at our knowledge the first promising scaffolds for developing a novel class of peptide-based antibacterial agents targeting conserved chaperonin systems. This work introduces a new avenue that warrants further experimental validation. Full article

Tandem white organic light-emitting diodes (OLEDs), formed by stacking red, green, and blue organic electroluminescent units, offer a promising route toward high-resolution microdisplays. However, their performance is constrained by the intrinsically short lifetime of blue OLED sub-units. Replacing the unstable blue OLED with a long-lived GaN-based LED could address this limitation, but practical hybridization remains difficult because of incompatible fabrication routes and significant current imbalance between the inorganic and organic units. Here, we demonstrate the first hybrid GaN–OLED tandem white LEDs enabled by an interface-engineered charge-generation unit (CGU). By introducing an ITO/HAT-CN/LiNH₂-doped Bphen CGU, we simultaneously enhance the work function, strengthen the built-in electric field, and smooth the interfacial morphology. These synergistic effects promote efficient charge generation, yielding near-ideal voltage summation and well-balanced electron–hole injection. As a result, the hybrid tandem device shows a nearly twofold increase in current efficiency (from 28.1 to 58.6 cd A^–1) and significantly reduced spectral shift under varying current densities. We further demonstrate the generality of this approach by integrating the GaN emission with yellow OLEDs to produce stable blue–yellow hybrid white emission. This work establishes an applicable strategy for integrating GaN-LEDs and OLEDs, opening a pathway toward efficient, stable, and compact white light engines for next-generation microdisplay technologies. Full article

Researchers strive to exploit kinetic potentials of multistep reactions by positioning enzymes in a regulated fashion. Therein, the proliferating cell nuclear antigen (PCNA) from Sulfolobus solfataricus is a promising biomolecular tool due to its extraordinary architecture. PCNA is a circular DNA sliding clamp, which can bind and move along DNA and thus, be applied for the immobilization and transport of biomolecules on versatile DNA scaffolds. Additionally, its heterotrimeric character facilitates the colocalization of enzyme cascades with defined stoichiometry. This study provides insights into the in vitro binding behavior of PCNA and its potential as protein scaffold for DNA functionalization and controlled biocatalysis: (1) PCNA was capable of binding circular DNA and wireframe DNA nanostructures. (2) DNA binding was predominantly mediated by the PCNA1 subunit. (3) PCNA assembly around DNA was compromised when cysteines were introduced at the PCNA–PCNA interfaces to stabilize the ring via disulfide bonds. (4) A two-enzyme cascade, comprising a pseudo-monomeric cytochrome P450 BM3 monooxygenase and a monomeric alcohol dehydrogenase (ADH), was successfully fused to PCNA, retaining catalytic activity. (5) When immobilized on DNA, the cascade performance was not assessable, due to nearly complete loss of ADH activity in proximity to DNA. Full article

Mycobacteria possess carbon monoxide dehydrogenase (CO-DH) to utilize CO as an energy source and to resist host defense mechanisms. The expression of the CO-DH gene is regulated by CutR, a LysR-type transcriptional regulator (LTTR) that exhibits unique characteristics, suggesting that it functions as a dimer rather than the typical tetramer. Size-exclusion chromatography revealed that CutR forms a stable dimer. Electrophoretic mobility shift assays demonstrated that dimeric CutR specifically binds to an inverted repeat sequence (IR1) containing T-n12-A motifs located upstream of the cutB gene, which encodes the medium subunit of CO-DH. Crystal structure determination at 1.8 Å resolution revealed that CutR consists of an N-terminal DNA-binding domain with a winged helix-turn-helix motif and a C-terminal ligand-binding domain comprising two regulatory subdomains (RD1 and RD2), forming a unique two-fold symmetrical homodimer. This dimer is stabilized through four interfaces, including an extensive 12-stranded antiparallel β-sheet formed between RD1 subdomains via intertwining C-terminal β11 strands. This represents the first symmetric dimeric LTTR structure with tightly associated ligand-binding domains. The recognition helices are spaced closer together than they are in typical DNA-bound LTTRs, despite binding longer T-n12-A sequences, suggesting that a conformational change is required to enhance DNA-binding affinity. A putative ligand-binding site was identified between the RD1 and RD2 subdomains, where glycerol binding induced local conformational changes. Comparative genomic analysis revealed conservation of CutR and the IR1 sequence across Mycobacterium species, supporting the dimeric regulatory mechanism and providing new insights into LTTR diversity. Full article

Prostate stem cell antigen (PSCA) is a Ly6/uPAR protein that targets neuronal nicotinic acetylcholine receptors (nAChRs). It exists in membrane-tethered and soluble forms, with the latter upregulated in Alzheimer’s disease. We hypothesize that PSCA may be linked to a wider spectrum of neurological diseases and could induce neuroinflammation. Indeed, PSCA expression is significantly upregulated in the brain of patients with multiple sclerosis, Huntington’s disease, Down syndrome, bipolar disorder, and HIV-associated dementia. To investigate PSCA’s structure, pharmacology, and inflammatory function, we produced a correctly folded water-soluble recombinant analog (ws-PSCA). In primary hippocampal neurons and astrocytes, ws-PSCA differently regulates secretion of inflammatory factors and adhesion molecules and induces pro-inflammatory responses by increasing TNFβ secretion. Heteronuclear NMR and ¹⁵N relaxation measurements reveal a classical β-structural three-finger fold with conformationally disordered loops II and III. Positive charge clustering on the molecular surface suggests the functional importance of ionic interactions by these loops. Electrophysiological studies in Xenopus oocytes point on ws-PSCA inhibition of α3β2-, high-, and low-sensitive variants of α4β2- (IC₅₀ ~50, 27, and 15 μM, respectively) but not α4β4-nAChRs, suggesting targeting of the β2 subunit. Ensemble docking and molecular dynamics simulations predict PSCA binding to high-sensitive α4β2-nAChR at α4/β2 and β2/β2 interfaces. Complexes are stabilized by ionic and hydrogen bonds between PSCA’s loops II and III and the primary and complementary receptor subunits, including glycosyl groups. This study gives new structural and functional insights into PSCA’s interaction with molecular targets and provides clues to understand its role in the brain function and mental disorders. Full article