Search Results (414)

Although the SARS-CoV-2 pandemic no longer poses a global emergency, the virus continues to diversify and acquire immunoevasive properties. Understanding the molecular pathways that shape SARS-CoV-2 pathogenesis has become essential. In this paper, we summarize the most recent current evidence on how the spike protein structurally evolves, on changes in key non-structural proteins, such as nsp14, and on host factors, such as TMPRSS2 and neuropilin-1. These changes, together, shape viral entry, replication fidelity and interferon antagonism. Given the emerging Omicron variants of SARS-CoV-2, recent articles in the literature, cryo-EM analyses, and artificial intelligence-assisted mutational modeling were analyzed to infer and contextualize mutation-driven mechanisms. It is through these changes that the virus adapts and evolves, such as optimizing angiotensin-converting enzyme binding, modifying antigenic surfaces, and accumulating mutations that affect CD8⁺ T-cell recognition. Multi-omics data studies further support SARS-CoV-2 pathogenesis through convergent evidence linking viral adaptation to host immune and metabolic reprogramming, as occurs in myocarditis, liver injury, and acute kidney injury. By integrating proteomic, transcriptomic, and structural findings, this work presents how the virus persists and dictates disease severity through interferon antagonism (ORF6, ORF9b, and nsp1), adaptive immune evasion, and metabolic rewiring. All these insights underscore the need for next-generation interventions that provide a multidimensional framework for understanding the evolution of SARS-CoV-2 and guiding future antiviral strategies. Full article

The function of the highly conserved GTPase LepA, a homolog of elongation factor EF-G, remains unknown in translation. However, there is biochemical data that it implicates in the 30S ribosomal subunit biogenesis. Here, using cryo-electron microscopy, we characterized 30S subunits isolated from an Escherichia coli strain with a deleted lepA gene. The cryo-EM maps for ∆lepA 30S particles were divided into classes corresponding to consecutive assembly intermediates: from particles characterized by unformed helices h44/h45 of the central decoding center (CDR) and highly flexible head, through intermediates with a distorted CDR and a partial stabilization of the head, to near-mature 30S subunits with correctly docked h44 in the CDR, accessible 3′ end of 16S rRNA for translation but significant flexibility in head domain. Cryo-EM analysis of ΔlepA 30S intermediates revealed that they predominantly proceed to nearly mature functional state and exhibit suboptimal flexibility in the head domain. This finding suggests that LepA likely contributes to the final proper stabilization of the 3′ domain of the 30S subunit during ribosome assembly. Full article

Background: The global incidence of multidrug-resistant and extensively drug-resistant tuberculosis continues to rise. The ribosome serves as a target for multiple antimicrobials, making functional research on it hold great significance. Methods: Using homologous recombination combined with a multiple serine integrase-mediated site-specific recombination system, we replaced the two endogenous rRNA operons in Mycobacterium smegmatis MC² 155 with a single copy of the single rRNA operon from Mycobacterium tuberculosis H37Rv, constructing the M. smegmatis BRkoA strain. We assessed growth kinetics at 37 °C, cold sensitivity at lower temperatures, transcriptional levels by RT-qPCR, 70S ribosome integrity through cryo-EM, and antimicrobial susceptibility by microdilution assays. Results: The BRkoA strain was successfully constructed. It exhibited markedly slower growth compared to the wild-type strain. Cold-sensitivity assays indicated potential ribosome assembly defects, while transcriptional analysis suggested altered rRNA processing and modification. Cryo-EM analysis further demonstrated the absence of specific ribosomal proteins in the BRkoA 70S ribosome. Moreover, BRkoA displayed reduced susceptibility tendency to several ribosome-targeting antibiotics, including kanamycin, amikacin, paromomycin, gentamicin, and linezolid. Conclusions: Replacement of the two endogenous rrn operons in M. smegmatis with a single copy of the single M. tuberculosis rrn operon using a serine integrase-mediated recombination system caused growth impairment and decreased sensitivity tendency to several ribosome-targeting antimicrobials. These findings suggest that ribosome structural variation contributes to intrinsic drug resistance mechanisms. Full article

The National Institute of Standards and Technology (NIST) is developing analytical methods to characterize extracellular vesicles (EVs) to support the urgent need for standardized EV reference materials (RMs). This study used orthogonal techniques, cryogenic electron microscopy (Cryo-EM), particle tracking analysis (PTA), asymmetrical flow field-flow fractionation (AF⁴), and microfluidic resistive pulse sensing (MRPS), to evaluate particle size distributions (PSDs) and particle number concentrations (PNCs) of human mesenchymal stem cells (MSCs) and LNCaP prostate cancer cell EVs. Proteomic profiles were assessed by mass spectrometry (MS), and microRNA (miRNA) content of LNCaP EVs was evaluated by small RNA-seq at two independent laboratories. A commercial green fluorescent protein exosome served as a control, except in Cryo-EM, proteomic, and miRNA analyses. Cryo-EM, regarded as the gold standard for morphological resolution, served as PSD reference. PSDs from all methods skewed larger than Cryo-EM, with MRPS closest, AF⁴ most divergent, and PTA intermediate with broader distributions. All techniques reported broad PSDs (30 nm to >350 nm) with PNCs decreasing with increasing particle size, except for AF⁴. Quantitative discrepancies in PNCs reached up to two orders of magnitude across methods and cell sources. MS identified global and EV-specific proteins, including syntenin-1 and tetraspanins CD9, CD63, and CD81. RNA-seq revealed notable inter-laboratory variation. These findings highlight the variability across measurement platforms and emphasize the need for reproducible methods to support NIST’s mission of developing reliable EV reference materials. Full article

Volume electron microscopy (Volume-EM) has transformed structural cell biology by enabling nanometre-resolution imaging across cellular and tissue scales. Serial-section TEM, Serial Block-Face Scanning Electron Microscopy (SBF-SEM), Focused Ion Beam Scanning Electron Microscopy (FIB-SEM) and multi-beam SEM now routinely generate terabyte-scale volumes that capture organelles, synapses and neural circuits in three dimensions, while cryogenic Volume-EM extends this landscape by preserving vitrified, fully hydrated specimens in a near-native state. Together, these room-temperature and cryogenic modalities define a continuum of approaches that trade off volume, resolution, throughput and structural fidelity, and increasingly interface with correlative light microscopy and cryo-electron tomography. In parallel, advances in computation have turned Volume-EM into a data-intensive discipline. Multistage preprocessing pipelines for alignment, denoising, stitching and intensity normalisation feed into automated segmentation frameworks that combine convolutional neural networks, affinity-based supervoxel agglomeration, flood-filling networks and, more recently, diffusion-based generative restoration. Weakly supervised and self-supervised learning, multi-task objectives and human-AI co-training mitigate the scarcity of dense ground truth, while distributed storage and streaming inference architectures support segmentation and proofreading at the terascale and beyond. Open resources such as COSEM, MICRONS, OpenOrganelle and EMPIAR provide benchmark datasets, interoperable file formats and reference workflows that anchor method development and cross-laboratory comparison. In this review, we first outline the physical principles and imaging modes of conventional and cryogenic Volume-EM, then describe current best practices in data acquisition and preprocessing, and finally survey the emerging ecosystem of AI-driven segmentation and analysis. We highlight how cryo-Volume-EM expands the field towards native-state structural biology, and how multimodal integration with light microscopy, cryo-electron tomography (cryo-ET) and spatial omics is pushing Volume-EM from descriptive imaging towards predictive, mechanistic, cross-scale models of cell physiology, disease ultrastructure and neural circuit function. Full article

One of the most important events in the pathogenesis of Parkinson’s disease and related disorders is the formation of abnormal fibrils via the aggregation of α-synuclein (α-syn) with β-sheet-rich organization. The use of Cryo-EM has uncovered different polymorphs of the fibrils, each having unique structural interfaces, which has made the design of inhibitors even more challenging. Here, a structure-guided framework incorporating AI-assisted peptide generation was set up with the objective of targeting the conserved β-sheet motifs that are present in various forms of α-syn fibrils. The ProteinMPNN, then, AlphaFold-Multimer, and PepMLM were employed to create short peptides that would interfere with the growth of the fibrils. The two selected candidates, T1 and S1, showed a significant inhibition of α-syn fibrillation, as measured by a decrease in the ThT fluorescence and the generation of either amorphous or fragmented aggregates. The inhibitory potency of the peptides was in line with the predicted interface energies. This research work illustrates that the integration of cryo-EM structural knowledge with the computational design method leads to the quick discovery of the wide-spectrum peptide inhibitors, which is a good strategy for the precision treatment of neurodegenerative diseases. Full article

Toxins as channel probes, small guanidinium alkaloids, such as tetrodotoxin and saxitoxin, canonical pore occlusion in voltage-gated Na⁺ channels. Cystine-rich peptides from spiders, scorpions, cone snails, and sea anemones, which act as pore blockers or gating modifiers targeting voltage-sensing domains. Recent structural and electrophysiological studies have identified specific binding sites on ion channels, including the S5–S6 pore loops, outer vestibule and turret regions, and S3–S4 “paddle” motifs in NaV, Kv, and CaV channels. These discrete binding epitopes are recognized by different peptide toxins, enabling isoform- and state-specific modulation; for example, μ-conotoxins bind the NaV pore, whereas charybdotoxin and agitoxin target the Kv outer vestibule. Beyond mechanistic insights, peptide toxins inspire translational strategies, including emerging therapies for retinal degenerative diseases. Photopharmacology using chemical photoswitches allows reversible, light-controlled modulation of ion channels in retinal ganglion cells without genetic manipulation or cell transplantation. Although BENAQ was discovered by small-molecule screening rather than toxin-guided design, its ion channel control demonstrates the potential of toxin-based molecular determinants for engineering synthetic compounds. This review thus integrates structural, functional, and translational perspectives, emphasizing the versatility of animal-derived peptide toxins as molecular probes and as blueprints for precision ion channel modulation in health and disease. Full article

The application of cryo-electron microscopy (cryo-EM) in membrane protein structural biology has catalyzed unprecedented advances in our understanding of fundamental biological processes and transformed drug discovery paradigms. This review briefly describes the biological achievements enabled using cryo-EM techniques, including single particle analysis (SPA), micro-electron diffraction (microED), and subtomogram averaging (STA), in elucidating the structures and functions of membrane proteins, ion channels, transporters, and viral glycoproteins. We highlight how these structural insights have revealed druggable sites, enabled structure-based drug design, and provided mechanistic understanding of disease processes. Key biological targets include G protein-coupled receptors (GPCRs), ion channels implicated in neurological disorders, respiratory chain complexes, viral entry machinery, and membrane transporters. The integration of cryo-EM with computational drug design has already yielded clinical candidates and approved therapeutics, marking a new era in membrane protein pharmacology. Full article

The study of gene expression regulation systems, transcriptional, post-transcriptional, and translational processes require in-depth knowledge of the structure and dynamics of protein–DNA and protein–RNA complexes. Furthermore, the discovery of the multiple roles played by different types of RNA, including within extracellular vesicles, has raised new questions about the systems responsible for stabilizing and transporting these RNAs. Over the years, numerous experimental approaches have been developed for the study of complexes between proteins and nucleic acids, both in terms of the type and degree of accuracy of the information they are able to provide. Furthermore, some techniques have proven suitable for monitoring dynamic processes, while others provide very high-resolution data. Finally, the different methods also differ in their applicability directly to the study of complexes within their biological environment, while others can only be used on purified samples. The purpose of this review is to provide an overview of many of these approaches, accompanied by some examples of recent applications, to highlight their strengths and limitations. Full article

Sweet taste receptors (STRs) are class C G protein-coupled receptors (GPCRs) that function as heterodimers of TAS1R2 and TAS1R3. These receptors possess multiple binding sites and can be activated by a wide range of sweet-tasting compounds. Interestingly, TAS1R2 alone or even its extracellular domain-truncated form (TAS1R2-TMD), can act as a functional receptor. Previous studies demonstrated that the sweetener S819 and the sweet inhibitor amiloride act through the transmembrane domain (TMD) of TAS1R2; however, the molecular mechanisms underlying these ligand-specific effects remain unclear, largely due to the historical lack of experimentally determined full-length STR structures. Recent breakthroughs in cryo-EM structural determination of the full-length TAS1R2/TAS1R3 complex now offer an unprecedented opportunity to elucidate receptor activation mechanisms at atomic resolution. In this study, we investigated ligand-induced conformational dynamics of hTAS1R2-TMD using microsecond-scale molecular dynamics (MD) simulations on three systems: hTAS1R2-TMD/S819 (agonist-bound), hTAS1R2-TMD/amiloride (antagonist-bound), and hTAS1R2-TMD (apo). Comparative analyses revealed that agonist and antagonist binding distinctly modulate key structural switches, including the conserved ionic lock (E6.35-R3.50), which stabilizes the inactive state and disrupts upon activation. Notably, we identified a novel salt bridge (D7.32-R3.32) that forms preferentially in the active state, potentially serving as a unique molecular switch for TAS1R2. Additional analyses uncovered ligand-specific rearrangements in hydrogen-bonding and hydrophobic interaction networks. These results provide atomistic insights into how agonists and antagonists differentially modulate TAS1R2 activation and lay a structural foundation for designing novel sweeteners and taste modulators. Full article

The global rise in resistance to first-line antifungal agents highlights the urgent need for new therapeutic strategies. Glycosylphosphatidylinositol (GPI)-anchored protein biosynthesis is an attractive target. The GPI mannosyltransferase I (GPI-MT-I), composed of Gpi14 and Pbn1, catalyzes the essential first mannose transfer from dolichol-phosphomannose (Dol-P-Man) to the GPI precursor. This initial mannosylation is critical for fungal cell wall integrity, yet the molecular basis of GPI-MT-I assembly and substrate recognition remains poorly understood. Here, we present the cryo-EM structure of Candida glabrata GPI-MT-I in complex with Dol-P-Man, revealing how Gpi14 and Pbn1 form a stable complex and engage the mannose donor. An AlphaFold3-predicted acceptor-bound model further defines the structural basis of acceptor substrate recognition and suggests a plausible catalytic mechanism. Comparison with structural homologs highlights a distinct mode of substrate engagement by GPI-MT-I. Together, these findings establish a mechanistic framework for GPI-MT-I function with broader implications for the GPI-MT family. Full article

Alzheimer’s disease (AD), the leading cause of dementia, is defined by two pathological hallmarks, amyloid-β (Aβ) plaques and hyperphosphorylated tau tangles—both now structurally resolved at near-atomic precision thanks to cryo-EM. Despite decades of research, effective disease-modifying therapies remain elusive, underscoring the need for innovative interdisciplinary approaches. This review synthesizes recent advances in structural biology and nanotechnology, highlighting their synergistic potential in revolutionizing AD diagnosis and treatment. Cryo-EM and NMR have revolutionized our understanding of Aβ/tau polymorphs, revealing structural vulnerabilities ripe for therapeutic targeting—yet clinical translation remains bottlenecked by the blood–brain barrier (BBB). Concurrently, nanotechnology offers groundbreaking tools, including nanoparticle-based drug delivery systems for blood–brain barrier (BBB) penetration, quantum dot biosensors for early Aβ detection, and CRISPR-nano platforms for APOE4 gene editing. We discuss how integrating these disciplines addresses critical challenges in AD management—from early biomarker detection to precision therapeutics—and outline future directions for translating these innovations into clinical practice. Full article

Our understanding of Ghrelin, an endogenous ligand of the growth hormone secretagogue receptor 1a (GHSR1a), has expanded from considering it to be a “hunger hormone” to a pleiotropic regulator of whole-body physiology. This review synthesizes the current advances spanning ghrelin biogenesis, signaling, and systems biology. Physiologically, preproghrelin processing and O-acylation by ghrelin O-acyltransferase (GOAT) generate acyl-ghrelin, a high-potency GHSR1a agonist; des-acyl ghrelin predominates in circulation and exerts context-dependent, GHSR1a-independent, or low-potency effects, while truncated “mini-ghrelins” can act as competitive antagonists. The emergence of synthetic ligands, agonists, antagonists, and reverse-agonists has provided the necessary tools to decipher GHSR1a activity. Recent cryo-EM structures of GHSR1a with peptide and small-molecule ligands reveal a bipartite binding pocket and provide a framework for biased signaling, constitutive activity, and receptor partner selectivity. Beyond the regulation of feeding and growth-hormone release, ghrelin modulates glucose homeostasis, gastric secretion and motility, cardiovascular tone, bone remodeling, renal hemodynamics, and innate immunity. Ghrelin broadly dampens pro-inflammatory responses and promotes reparative macrophage phenotypes. In the emerging scholarship on ghrelin’s activity in the central nervous system, ghrelin has been found to influence neuroprotection, stress reactivity, and sleep architecture, and has also been implicated in depression, Alzheimer’s disease, and substance-abuse disorders. Practical and transitional aspects are also highlighted in the literature: approaches for ghrelin stabilization; recent GHSR1a agonists/antagonists and inverse agonists findings; LEAP-2-based strategies; and emerging GOAT inhibitors. Together, structural insights and pathway selectivity position the ghrelin system as a druggable axis for the management of inflammatory diseases, neuropsychiatric and addiction conditions, and for obesity treatment in the post-GLP-1 receptor agonist era. Full article

Polymyxin antibiotics are often the last line of defense against multidrug-resistant Gram-negative pathogens. A key resistance mechanism involves the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) to lipid A, mediated by the bifunctional enzyme ArnA. However, the evolutionary rationale and structural basis for ArnA’s domain fusion, hexameric assembly, and catalytic coordination remain mechanistically unresolved. Here, we integrate evolutionary genomics, high-resolution cryo-electron microscopy (cryo-EM), and computational protein design to provide a comprehensive mechanistic analysis of ArnA. Our evolutionary analysis reveals that the dehydrogenase (DH) and formyltransferase (TF) domains evolved independently and were selectively fused in Gammaproteobacteria, suggesting an adaptive advantage. A 2.89 Å cryo-EM structure of apo-ArnA resolves the flexible interdomain linker and reveals a DH-driven hexameric architecture essential for enzymatic activity. 3D variability analysis captures intrinsic conformational dynamics, indicating a molecular switch that may coordinate sequential catalysis and substrate channeling. Structure-based peptide inhibitors targeting the hexamerization and predicted ArnA–ArnB interaction interfaces were computationally designed, offering a novel strategy for disrupting L-Ara4N biosynthesis. These findings illuminate a previously uncharacterized structural mechanism of antimicrobial resistance and lay the groundwork for therapeutic intervention. Full article

Metal anodes promise improvements in energy density and cost; however, their performance is determined within the first several nanometers at the interface. This review reports on how polymer-based artificial solid electrolyte interphases (SEIs) are engineered to stabilize Li and aqueous-Zn anodes, and how these designs are now evaluated against operando readouts rather than post-mortem snapshots. We group the related molecular strategies into three classes: (i) side-chain/ionomer chemistry (salt-philic, fluorinated, zwitterionic) to increase cation selectivity and manage local solvation; (ii) dynamic or covalently cross-linked networks to absorb microcracks and maintain coverage during plating/stripping; and (iii) polymer–ceramic hybrids that balance modulus, wetting, and ionic transport characteristics. We then benchmark these choices against metal-specific constraints—high reductive potential and inactive Li accumulation for Li, and pH, water activity, corrosion, and hydrogen evolution reaction (HER) for Zn—showing why a universal preparation method is unlikely. A central element is a system of design parameters and operando metrics that links material parameters to readouts collected under bias, including the nucleation overpotential (η_nuc), interfacial impedance (charge transfer resistance (R_ct)/SEI resistance (R_SEI)), morphology/roughness statistics from liquid-cell or cryogenic electron microscopy (Cryo-EM), stack swelling, and (for Li) inactive-Li inventory. By contrast, planar plating/stripping and HER suppression are primary success metrics for Zn. Finally, we outline parameters affecting these systems, including the use of lean electrolytes, the N/P ratio, high areal capacity/current density, and pouch-cell pressure uniformity, and discuss closed-loop workflows that couple molecular design with multimodal operando diagnostics. In this view, polymer artificial SEIs evolve from curated “recipes” into predictive, transferable interfaces, paving a path from coin-cell to prototype-level Li- and Zn-metal batteries. Full article