Search Results (1,439)

Human immunodeficiency virus type 2 (HIV-2) is a lentivirus closely related to HIV-1 but exhibits distinct molecular and clinical features that influence viral infectivity and efficacy of antiretroviral therapy. The HIV capsid is a critical structural component with multifaceted roles during infection and mediates some of the observed divergence between HIV-1 and HIV-2. Unlike HIV-1, study of the HIV-2 capsid is limited and standard protocols for the in vitro assembly of HIV-1 capsid protein (CA) lattice structures have not been successfully translated to the HIV-2 context. This work identifies effective approaches for the assembly of the HIV-2 CA lattice and leverages this to biochemically characterize HIV-2 CA assemblies and mutant phenotypes. Our findings elaborate on the sensitivity of HIV-2 CA to chemical conditions and reveal that it assembles into a more varied spectrum of particle morphologies compared to HIV-1. Utilizing these assemblies, we tested the hypothesis that HIV-1 and HIV-2 employ divergent mechanisms to stabilize CA oligomer forms and investigate the effects of non-conserved substitutions at the CA inter-protomer interfaces. This work advances our understanding of the key biochemical determinants of HIV-2 CA assembly that are distinct from HIV-1 and may contribute to their divergent virological properties. Full article

Bispecific peptides represent an emerging therapeutic platform in immunotherapy, offering simultaneous engagement of two distinct molecular targets to enhance specificity, functional synergy, and immune modulation. Their compact structure and modular design enable precise interaction with protein–protein interfaces and shallow binding sites that are otherwise difficult to target. This review summarizes current design strategies of bispecific peptides, including fused, linked, and self-assembled architectures, and elucidates their mechanisms in bridging tumor cells with immune effector cells and blocking immune checkpoint pathways. Recent developments highlight their potential applications not only in oncology but also in autoimmune and infectious diseases. Key translational challenges, including proteolytic stability, immunogenicity, delivery barriers, and manufacturing scalability, are discussed, along with emerging peptide engineering and computational design strategies to address these limitations. Bispecific peptides offer a versatile and adaptable platform poised to advance precision immunotherapy and expand therapeutic options across immune-mediated diseases. Full article

ATPase family AAA domain-containing protein 2 (ATAD2) has been recognized as a key oncogene that regulates chromatin remodeling, transcription, and cancer progression. As a member of the bromodomain (BRD) family, ATAD2 plays a crucial role in epigenetic modifications and is associated with multiple malignancies. Despite being considered an undruggable target in the past, crystallography and computational modeling have significantly accelerated ATAD2 drug discovery and development. This review provides a comprehensive overview of the structural features, functional roles, and biological significance of ATAD2, particularly in the context of cancer. We present an in-depth overview of different molecular strategies reported in the literature to suppress ATAD2 expression, including genetic and pharmacological approaches, and discuss their mechanistic and therapeutic implications. Particular emphasis is given to recent efforts in developing small-molecule inhibitors, detailing their binding interactions, therapeutic potential, and challenges in clinical translation. In addition, we performed alanine scanning calculations on molecular dynamics (MD)-simulated trajectories derived from protein–ligand complexes based on X-ray co-crystal structures containing three distinct ligands with different binding modes. This analysis provided critical insights into the binding interface of BRD-ATAD2, enhancing our understanding of its ligand interactions. Furthermore, we examine the emerging roles of ATAD2 in mediating resistance to cancer therapies, underscoring its potential as a target for overcoming drug resistance. By integrating structural insights, mechanistic studies, drug discovery efforts, and the challenges of developing ATAD2-targeted cancer therapies, this review emphasizes the need for further research to optimize ATAD2 inhibition strategies and explore its full therapeutic potential in oncology. Full article

The parallel global increase in obesity and Alzheimer’s disease (AD) underscores an urgent public health challenge, with converging evidence indicating that metabolic dysfunction strongly contributes to neurodegeneration. Obesity is now recognized not only as a systemic metabolic condition but also as a modifiable risk factor for AD, acting through mechanisms such as chronic low-grade inflammation, insulin resistance, and adipose tissue dysfunction. Among the molecular mediators at this interface, adipokines have emerged as pivotal regulators linking metabolic imbalance to cognitive decline. Adipokines are hormone-like proteins secreted by adipose tissue, including adiponectin, leptin, and resistin, that regulate metabolism, inflammation and can influence brain function. Resistin, frequently elevated in obesity, promotes neuroinflammation, disrupts insulin signaling, and accelerates β-amyloid (Aβ) deposition and tau pathology. Conversely, adiponectin enhances insulin sensitivity, suppresses oxidative stress, and supports mitochondrial and endothelial function, thereby exerting neuroprotective actions. The imbalance between resistin and adiponectin may shift the central nervous system toward a pro-inflammatory and metabolically compromised state that predisposes to neurodegeneration. Beyond their mechanistic relevance, adipokines hold translational promise as biomarkers for early risk stratification and therapeutic monitoring. Importantly, natural compounds, including polyphenols, alkaloids, and terpenoids, have shown the capacity to modulate adipokine signaling, restore metabolic homeostasis, and attenuate AD-related pathology in preclinical models. This positions adipokines not only as pathogenic mediators but also as therapeutic targets at the intersection of diabetes, obesity, and dementia. By integrating mechanistic, clinical, and pharmacological evidence, this review emphasizes adipokine signaling as a novel axis for intervention and highlights natural compound-based strategies as emerging therapeutic approaches in obesity-associated AD. Beyond nutraceuticals, antidiabetic agents also modulate adipokines and AD-relevant pathways. GLP-1 receptor agonists, metformin, and thiazolidinediones tend to increase adiponectin and reduce inflammatory tone, while SGLT2 and DPP-4 inhibitors exert systemic anti-inflammatory and hemodynamic benefits with emerging but still limited cognitive evidence. Together, these drug classes offer mechanistically grounded strategies to target the adipokine–inflammation–metabolism axis in obesity-associated AD. Full article

This study reports the development of a fiber-optic localized surface plasmon resonance (FO-LSPR) sensor incorporating a three-dimensional micropillar array functionalized with gold nanoparticles. The micropillar structures were fabricated on the fiber facet using a single-mask imprint lithography process, followed by nanoparticle immobilization to create a composite plasmonic surface. Compared with flat polymer-coated fibers, the micropillar array markedly increased the effective sensing surface and enhanced light trapping by providing anti-reflective conditions at the interface. Consequently, the sensor demonstrated superior performance in refractive index sensing, yielding a sensitivity of 4.54 with an R² of 0.984, in contrast to 3.13 and 0.979 obtained for the flat counterpart. To validate its biosensing applicability, Interleukin-8 (IL-8), a cancer-associated cytokine, was selected as a model analyte. Direct immunoassays revealed quantitative detection across a broad dynamic range (0.1–1000 pg/mL) with a limit of detection of 0.013 pg/mL, while specificity was confirmed against non-target proteins. The proposed FO-LSPR platform thus offers a cost-effective and reproducible route to overcome the surface-area limitations of conventional designs, providing enhanced sensitivity and stability. These results highlight the potential of the micropillar-based FO-LSPR sensor for practical deployment in point-of-care diagnostics and real-time biomolecular monitoring. Full article

The SETD6 protein lysine methyltransferase monomethylates specific lysine residues in a diverse set of substrates which contain the target lysine residue in a highly variable amino acid sequence context. To investigate the mechanism underlying this multispecificity, we analyzed SETD6 substrate recognition using AlphaFold 3 docking and peptide SPOT array methylation experiments. Structural modeling of the SETD6–E2F1 complex suggested that substrate binding alone is insufficient to restrict SETD6 activity to only one lysine residue, pointing to additional sequence readout at the target site. Methylation of mutational scanning peptide SPOT arrays derived from four different SETD6 substrates (E2F1 K117, H2A.Z K7, RELA K310, and H4 K12) revealed sequence preferences of SETD6 at positions −1, +2, and +3 relative to the target lysine. Notably, glycine or large aliphatic residues were favored at −1, isoleucine/valine at +2, and lysine at +3. These preferences, however, were sequence context dependent and variably exploited among different substrates, indicating conformational variability of the enzyme–substrate interface. Mutation of SETD6 residue L260, which forms a contact with the +2 site in the available SETD6-RELA structure, further demonstrated substrate-specific differences in recognition at the +2/+3 sites. Together, these findings reveal a versatile mode of peptide recognition in which the readout of each substrate position depends on the overall substrate peptide sequence. These findings can explain the multispecificity of SETD6 and similar mechanisms may underlie substrate selection in other protein methyltransferases. Full article

Immune checkpoint inhibitors (ICIs), including PD-L1 inhibitors, have been approved by the FDA for the treatment of cancers; however, only a small number of cancer patients benefit from these ICIs. Furthermore, the development of drug resistance to this type of treatment is often inevitable. The mechanisms of resistance to PD-L1 inhibitors can be attributed, in part, to an incomplete understanding of the regulation of PD-L1 protein expression. In this study, we identified the role of the E3 ligase GP78, also known as the Autocrine Motility Factor Receptor (AMFR), in the regulation of PD-L1 protein levels. We show that GP78 physically interacts with PD-L1, which is confirmed by IP and Western blotting and is supported by molecular modelling using AlphaFold2. Our modeling studies predict that the interface amino acids of the Ig1 domain of PD-L1 interact with the RING domain and a β-hairpin preceding the CUE domain of GP78. The crystal structure of the PD-1/PD-L1 complex reveals that the interaction with PD-1 is mediated by the Ig1 domain of PD-L1. Furthermore, proteasomal degradation of PD-L1 has been observed via GP78-mediated K48-linked ubiquitination, indicating a key regulatory role for GP78 in the downregulation of PD-L1. Because GP78 expression is inversely correlated with PD-L1 levels in cancer, these findings may have clinical implications for predicting tumor immune evasion and patient response to PD-1/PD-L1 blockade therapies. Taken together, these findings identify a previously unknown mechanism by which GP78 targets PD-L1 for ubiquitination and subsequent degradation in cancer cells, and suggest that blocking the interaction between PD-L1 and PD-1 by an E3 ligase is a novel strategy to improve immunotherapies for cancer patients. Full article

Lipid nanoparticles are a clinically validated platform for delivering nucleic acids, but performance is constrained by multiscale physiological barriers spanning circulation, vascular interfaces, extracellular matrices, cellular uptake, and intracellular trafficking. This review links composition–structure–function relationships for ionizable lipids, helper phospholipids, cholesterol, and PEG-lipids to systemic fate, endothelial access, endosomal escape, cytoplasmic stability, and nuclear transport. We outline strategies for tissue and cell targeting, including hepatocyte ligands, immune and tumor selectivity, and selective organ targeting through compositional tuning, together with approaches that modulate escape using pH-responsive chemistries or fusion-active peptides and polymers. We further examine immunomodulatory co-formulation, route and schedule effects on biodistribution and immune programming, and manufacturing and stability levers from microfluidic mixing to lyophilization. Across these themes, we weigh trade-offs between stealth and engagement, potency and tolerability, and potency and manufacturability, noting that only a small fraction of endosomes supports productive release and that protein corona variability and repeat dosing can reshape tropism and clearance. Convergence of standardized assays for true cytosolic delivery, biomarker-guided patient selection, and robust process controls will be required to extend LNP therapeutics beyond the liver while sustaining safety, access, and scale. Full article

Molecularly imprinted polymer (MIP) biosensors offer an attractive strategy for selective biomolecule detection, yet imprinting proteins with structural fidelity remains a major challenge. In this work, we present a rationally designed electrochemical biosensor for matrix metal-loproteinase-8 (MMP-8), a key salivary biomarker of periodontal disease. By integrating graphene oxide (GO) with electropolymerized poly(eriochrome black T, EBT) films on screen-printed carbon electrodes, the partially reduced GO interface enhanced electrical conductivity and facilitated the formation of well-defined poly(EBT) films with re-designed polymerization route, while template extraction generated artificial antibody-like sites capable of specific protein binding. The MIP-based electrodes were comprehensively validated through morphological, spectroscopic, and electrochemical analyses, demonstrating stable and selective recognition of MMP-8 against structurally similar interferents. Complementary density functional theory (DFT) modeling revealed energetically favorable interactions between the EBT monomer and catalytic residues of MMP-8, providing molecular-level insights into imprinting specificity. These experimental and computational findings highlight the importance of rational monomer selection and nanomaterial-assisted polymerization in achieving selective protein imprinting. This work presents a systematic approach that integrates electrochemical engineering, nanomaterial interfaces, and computational validation to address long-standing challenges in protein-based MIP biosensors. By bridging molecular design with practical sensing performance, this study advances the translational potential of MIP-based electrochemical biosensors for point-of-care applications. Full article

Arabinogalactan proteins (AGPs: hydroxyproline-rich glycoproteins) are ubiquitous in plants and play various functions in cases of development and reproduction. In Arabidopsis thaliana some AGPs can work as markers for gametophytic cell differentiation (among others embryological structures they mark generative cell wall and/or plasma membrane, and also sperm cells). However, apart from Arabidopsis, this labeling of generative cell and sperm cells in pollen grains has only been observed in a few flowering plant species belonging to dicotyledons. No such studies are available in monocotyledons. The main aim of our study was to see whether AGPs would be present at the generative cell–vegetative cell interface in different monocotyledons (representatives of Asparagaceae, Amarylidaceae and Liliaceae), and we also wanted to test whether they would be the same AGPs as in dicotyledons. For the study, we selected Gagea lutea (L.) Ker Gawl., Ornithogalum nutans L. and Galanthus nivalis L. species that differ in shape and size of generative cells. Antibodies against arabinogalactan proteins AGPs were used, including JIM8, JIM13, JIM14, MAC207, LM2, LM14, JIM15 and JIM4. The localization of the examined compounds was determined using immunohistochemistry techniques. The key finding was that AGPs (detected with JIM8 and JIM13 antibodies) consistently mark the boundary between the generative cell and the surrounding vegetative cytoplasm, suggesting their association with the generative cell–vegetative cell interface in all species studied. Identifying such molecular markers in male gametophyte may enhance the understanding of gametophytic cell fate, sperm cell identity and the molecular mechanisms underlying fertilization. Such labeling may also be useful in studies on pollen development, species comparisons, or responses to environmental stresses. Full article

The recruitment of peripheral membrane proteins is tightly regulated by membrane lipid composition and local electrostatic microenvironments. Our experimental observations revealed that Vp54, a viral matrix protein, exhibited preferential binding to lipid bilayers enriched in anionic lipids such as phosphatidylglycerol (PG) and phosphatidylserine (PS), compared to neutral phosphatidylcholine/phosphatidylethanolamine liposomes, and this occurred in a curvature-dependent manner. To elucidate the molecular basis of this selective interaction, we performed a series of computational analyses including helical wheel projection, electrostatic potential calculations, electric field lines simulations, and electrostatic force analysis. Our results showed that the membrane-proximal region of Vp54 adopted an amphipathic α-helical structure with a positively charged interface. In membranes containing PG or PS, electrostatic potentials at the interface were significantly more negative, enhancing attraction with Vp54. Field line and force analyses further confirmed that both the presence and spatial clustering of anionic lipids intensify membrane–Vp54 electrostatic interactions. These computational findings align with experimental binding data, jointly demonstrating that membrane lipid composition and organization critically modulate Vp54 recruitment. Together, our findings highlight the importance of electrostatic complementarity and membrane heterogeneity in peripheral protein targeting and provide a framework applicable to broader classes of membrane-binding proteins. Full article

Osteoarthritis involves complex interactions between articular joint tissues and the immune system, which is implicated in molecular trafficking via barrier-function modulating cytokines. The current study aims to test effects of an acute spike in TNF-α or TGF-β on vascular barrier function at multiple length scales, from the heart to tissue compartments of the knee, and cellular inhabitants of those respective compartments, in a spontaneous guinea pig model of osteoarthritis. First we quantified the intensity of a fluorescent-tagged 70 kDa tracer, similar in size to albumin, the most prevalent transporter protein in the blood, in tissue compartments of bone (periosteum, marrow space, compact bone, and epiphyseal bone) and cartilage (superficial cartilage, calcified cartilage, and the interface between, i.e., the epiphyseal line), as well as at sites of tendon attachment to bone (entheses). We then examined tracer presence and intensity in the respective pericellular and extracellular matrix zones of bone and cartilage. Acute exposure to TGF-β reduced barrier function (increased permeability) at nearest vascular interfaces in four of eight tissue compartments studied, compared to TNF-α where one of eight tissue compartments showed significant diminishment in barrier function. The increase in permeability associated with reduced barrier function was observed at both tissue compartment and cellular length scales. The observation of pericellular transport of the albumin-sized molecules to osteocytes contrasts with previous observations of barrier function in healthy, untreated animals and is indicative of increased molecular transport in pericellular regions of musculoskeletal tissues in cytokine-treated animals. Understanding age- and disease-related changes in molecular transport within musculoskeletal structures, such as the knee joint, is crucial for elucidating the etiology and pathogenesis of osteoarthritis. Full article

The urinary bladder is a primary target organ for environmental toxicants such as arsenic. The objects of this study were two-fold. First, we constructed a novel 3D urinary bladder mucosa model (3D-UBMM) composed of an overlying epithelium and a supporting subepithelial layer. Primary human bladder urothelial and fibroblast cells were immortalized by introducing the human CDK4^R24C and TERT genes. The construction of the 3D-UBMM involved incorporating immortalized fibroblast cells into a collagen raft, while immortalized urothelial cells were cultured at the air-liquid interface. This 3D-UBMM closely resembles the human bladder epithelium in terms of morphology and marker protein expression, including uroplakin 1b, P63, and cytokeratin 5. Second, using the 3D-UBMM we investigated the cytotoxicity of sodium arsenite (iAs^III) and dimethylarsenic acid (DMA^V). Exposure to iAs^III and DMA^V resulted in increased urothelial necrosis, increased γ-H2AX-positive cells, and reduced P63-positive cells, all in a dose–response manner. These findings affirm that this novel 3D-UBMM resembles the human bladder epithelium and offers a practical in vitro model for evaluating bladder toxicants and carcinogens, identifying mechanisms of carcinogenesis, and supporting hazard identification and risk assessment. 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

Inherited retinal dystrophies (IRDs) are clinically and genetically heterogeneous disorders. Most IRDs follow a monogenic inheritance pattern. However, an increasing number of unresolved cases suggest the possible contribution of oligogenic or digenic mechanisms. Here, we report two ultra-rare missense variants—AIPL1 R302L and BBS2 P134R—that co-segregate with early-onset nonsyndromic retinal degeneration in affected individuals from a non-consanguineous family. We performed a multi-level computational investigation to assess whether these variants may act through a convergent pathogenic mechanism. Using AlphaFold2-predicted structures, we modeled both wild-type and mutant proteins, introduced point mutations, and performed energy minimization and validation. FoldX, DynaMut2, and DUET all predicted destabilizing effects at the variant sites, corroborated by local disruption of secondary structure and altered surface electrostatics. Comparative docking (via HDOCK and ClusPro) identified a putative interaction interface between the TPR domain of AIPL1 and the β-sheet face of BBS2. This interface was destabilized in the double-mutant model. At the systems level, transcriptomic profiling confirmed co-expression of AIPL1 and BBS2 in human retina and fetal eye, while functional enrichment analysis highlighted overlapping involvement in ciliary and proteostasis pathways. Network propagation suggested that the two proteins may converge on shared interactors relevant to photoreceptor maintenance. Collectively, these in silico results provide structural and systems-level support for a candidate digenic mechanism involving AIPL1 and BBS2. While experimental validation remains necessary, our study proposes a testable mechanistic hypothesis and underscores the value of computational approaches in uncovering complex genetic contributions to IRDs. Full article