Journal of structural biology最新文献

{"title":"Hurdles and advancements in experimental membrane protein structural biology.","authors":"Ruchika Bajaj","doi":"10.1016/j.jsb.2025.108251","DOIUrl":"10.1016/j.jsb.2025.108251","url":null,"abstract":"<p><p>This short review article traces the evolution of membrane protein structural biology over time and describes various challenges faced and overcome by researchers in the field, highlighting some of the major breakthroughs and advancements in the field. It presents a thematic exploration of membrane protein structural biology emphasizing on persistent technical and conceptual challenges from protein expression to structural techniques shaping the field with landmark innovations advancing our ability to determine membrane protein structures. The review specifically focus on a few key areas: sourcing and expressing membrane proteins, developing purification strategies and membrane mimetics, and the emergence of powerful structural tools such as X-ray crystallography, cryo-electron microscopy (cryo-EM) and micro-electron diffraction (MicroED). Each section discusses major advancements addressing long standing bottlenecks and opening avenues to understand structure-function relationships in membrane proteins. Furthermore, it also briefly discusses the impact of important discoveries and future perspectives for the field. The review concludes by discussing current emerging frontiers in the field including in-situ structural methods, AI driven structure prediction and future directions for integrative and dynamic membrane protein research.</p>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":" ","pages":"108251"},"PeriodicalIF":2.7,"publicationDate":"2025-09-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145199956","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mind the corner: Fillets in cryo-FIB lamella preparation to minimise sample loss caused by stress concentration and lamella breakage","authors":"Sergey Gorelick ,&nbsp;Sailakshmi Velamoor ,&nbsp;Patrick Cleeve ,&nbsp;Sylvain Trépout ,&nbsp;Le Ying ,&nbsp;Vivek Naranbhai ,&nbsp;Georg Ramm","doi":"10.1016/j.jsb.2025.108249","DOIUrl":"10.1016/j.jsb.2025.108249","url":null,"abstract":"<div><div>Cryo-FIB milling of biological specimens is a critical and limiting step in the cryo-electron tomography workflow. Preparing electron-transparent cryo-lamellae is a serial, low-throughput process. Even with automation, a skilled operator can typically only produce 15–25 lamellae in a single cryo-FIB session. During sample handling, milling and transfer, the cryo-fixed cells as well as the supporting film layer face various mechanical forces and thermal stresses due to temperature fluctuations. Moreover, after cells are cryo-FIB milled, the resulting thin lamellae continue to endure external forces from mechanical handling and thermal stress. We propose a simple, yet highly effective modification to the standard rectangular milling pattern by implementing “fillets” or corner smoothing providing better mechanical stability. This adjustment helps to avoid sharp corners at the lamella edges, thereby reducing stress concentration. As a result, this modification decreases the likelihood of lamella breakage and improves the overall yield of ready-for-TEM lamellae by over 40 % as verified experimentally.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"217 4","pages":"Article 108249"},"PeriodicalIF":2.7,"publicationDate":"2025-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145119661","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Precise ligand-selective mechanism at the fab domain of a tau-recognizing antibody","authors":"Tomohiro Tsuchida ,&nbsp;Takahiro Tsuchiya ,&nbsp;Katsuhiko Minoura ,&nbsp;Yasuko In ,&nbsp;Katsushiro Miyamoto ,&nbsp;Taizo Taniguchi ,&nbsp;Toshimasa Ishida ,&nbsp;Koji Tomoo","doi":"10.1016/j.jsb.2025.108250","DOIUrl":"10.1016/j.jsb.2025.108250","url":null,"abstract":"<div><div>Insoluble aggregated tau protein in the form of paired helical filaments is a causative agent of the neurofibrillary tangles observed in Alzheimer’s disease (AD). The hexapeptide ²⁷⁵VQIINK²⁸⁰ located in the microtubule-binding domain of tau plays a crucial role in the abnormal aggregation process. Therefore, targeting the VQIINK sequence with a tau aggregation inhibitor may be a promising therapeutic approach for AD. A previous study demonstrated that the Fab domain of the tau antibody (Fab2r3) inhibits tau aggregation by binding to the VQIINK sequence. By determining the three-dimensional structures of the Fab2r3-VQIINK peptide complex and apo Fab2r3, we elucidated the recognition mechanism between Fab2r3 and the VQIINK peptide. However, the basis for the selectivity of Fab2r3 for VQIINK was not completely clear. Therefore, the objective of this report is to investigate the selective binding mechanism of Fab2r3 against VQIINK peptide. Through isothermal titration calorimetry, we show that Ile-4 in the VQIINK peptide is crucial for the selectivity of Fab2r3. X-ray structural analysis of three complexes of Fab2r3 with Ile-4 mutated peptides (VQIVYK, VQILNK, and VQIFNK) suggested that the rigid conformation of a hydrophobic pocket in Fab2r3 plays a vital role in ligand selectivity. These findings may explain the effectiveness of Fab2r3 as a tau aggregation inhibitor.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"217 4","pages":"Article 108250"},"PeriodicalIF":2.7,"publicationDate":"2025-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145125003","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Multi-Technique Investigation to Explore the Structural Integrity and Chemical Complexity of the Brachiopod Lingula anatina (Lamarck, 1801) Shells","authors":"Prabad Pratim Pal,&nbsp;Sourav Bar,&nbsp;Santosh Kumar Bera,&nbsp;Debkumar Sahoo,&nbsp;Sudipta Kumar Ghorai","doi":"10.1016/j.jsb.2025.108248","DOIUrl":"10.1016/j.jsb.2025.108248","url":null,"abstract":"<div><div>The shell of <em>Lingula anatina</em>, a living representative of early brachiopods, exemplifies a unique organophosphatic biomineralization strategy that integrates mineral phases with organic components for structural enhancement. This study employs scanning electron microscopy (SEM), energy-dispersive X-ray spectroscopy (EDS), inductively coupled plasma optical emission spectrometry (ICP-OES), X-ray diffraction (XRD), and Raman spectroscopy to comprehensively analyse the microstructure, composition, and mineralogy of the shell. SEM imaging reveals distinct regional microarchitectures, from compact fibrous laminae to porous, reticulate layers, indicating functional specialization in structural reinforcement and flexibility. Elemental analyses confirm a calcium-phosphate matrix dominated by fluorapatite and enriched with trace elements like Mg, Mn, and Fe. XRD and Raman data validate the coexistence of crystalline fluorapatite and calcite with significant amorphous phases. These findings highlight <em>Lingula’s</em> evolutionary retention of a hierarchical, organic–inorganic composite shell adapted for environmental interaction, structural resilience, and biomineral control.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"217 4","pages":"Article 108248"},"PeriodicalIF":2.7,"publicationDate":"2025-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145069874","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Structural insights into IMP2 dimerization and RNA binding","authors":"Stephen A. Zorc ,&nbsp;Paola Munoz-Tello ,&nbsp;Timothy O’Leary ,&nbsp;Xiaoyu Yu ,&nbsp;Mithun Nag Karadi Giridhar ,&nbsp;Alexander D. Hondros ,&nbsp;Althea Hansel-Harris ,&nbsp;Stefano Forli ,&nbsp;Patrick R. Griffin ,&nbsp;Douglas J. Kojetin ,&nbsp;Raktim N. Roy ,&nbsp;Michalina Janiszewska","doi":"10.1016/j.jsb.2025.108247","DOIUrl":"10.1016/j.jsb.2025.108247","url":null,"abstract":"<div><div>IGF2BP2 (IMP2) is an RNA-binding protein that contributes to tumorigenesis and metabolic disorders. Structural studies focused on individual IMP2 domains have provided important mechanistic insights into IMP2 function; however, structural information on full-length IMP2 is lacking but necessary to understand how to target IMP2 activity in drug discovery. In this study, we investigated the behavior of full-length IMP2 and the influence of RNA binding using biophysical and structural methods including mass photometry, hydrogen–deuterium exchange coupled to mass spectrometry (HDX-MS), and small angle x-ray scattering (SAXS). We found that full-length IMP2 forms multiple oligomeric states but predominantly adopts a dimeric conformation. Molecular models derived from SAXS data suggest the dimer is formed in a head-to-tail orientation by the KH34 and RRM1 domains. Upon RNA binding, IMP2 forms a pseudo-symmetric dimer different from its apo/RNA-free state. We also found that the formation of IMP2 oligomeric species, which includes dimers and higher-order oligomers, is sensitive to ionic strength and RNA binding. Our findings provide the first insight into the structural properties of full-length IMP2, which may lead to novel opportunities for disrupting its function.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"217 4","pages":"Article 108247"},"PeriodicalIF":2.7,"publicationDate":"2025-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145047686","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"CRISP: A modular platform for cryo-EM image segmentation and processing with Conditional Random Field","authors":"Szu-Chi Chung,&nbsp;Po-Cheng Chou","doi":"10.1016/j.jsb.2025.108239","DOIUrl":"10.1016/j.jsb.2025.108239","url":null,"abstract":"<div><div>Distinguishing signal from background in cryogenic electron microscopy (cryo-EM) micrographs is a critical processing step but remains challenging owing to the inherently low signal-to-noise ratio (SNR), contaminants, variable ice thickness, and densely packed particles of heterogeneous sizes. Recent image-segmentation methods provide pixel-level precision and thus offer several advantages over traditional object-detection approaches: segmented-blob mass can be computed to suppress false-positive particles, particle centering can be improved by leveraging the full brightness profile, and irregularly shaped particles can be identified more reliably. However, low SNR makes it difficult to obtain accurate pixel-level annotations for training segmentation models, and, in the absence of systematic evaluation platforms, most segmentation pipelines still rely on ad-hoc design choices.</div><div>Here, we introduce a modular platform that automatically generates high-quality segmentation maps to serve as reference labels. The platform supports flexible combinations of segmentation architectures, feature extractors, and loss functions, and it integrates novel Conditional Random Fields (CRFs) with class-discriminative features to refine coarse predictions into fine-grained segmentations. On synthetic data, models trained with our reference labels achieve pixel-level accuracy, recall, precision, Intersection-over-Union (IoU), and <span><math><msub><mrow><mtext>F</mtext></mrow><mrow><mn>1</mn></mrow></msub></math></span> scores all exceeding 90%. We further show that the resulting segmentations can be used directly for particle picking, yielding higher-resolution 3D density maps from real experimental datasets; these reconstructions match those curated by human experts and surpass the results of existing particle-picking tools. To facilitate further research, we release our methods as the open-source package <em>CRISP</em>, available at <span><span>https://github.com/phonchi/CryoParticleSegment</span><svg><path></path></svg></span>.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"217 4","pages":"Article 108239"},"PeriodicalIF":2.7,"publicationDate":"2025-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145027787","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Characterization of NMDA receptor Allostery modulation","authors":"Yunsheng Liu ,&nbsp;Wangsheng Song ,&nbsp;Rongde Zhong ,&nbsp;Jinfang Zhang ,&nbsp;Xianlin Wu ,&nbsp;Yanyan Jia ,&nbsp;Zengwei Kou","doi":"10.1016/j.jsb.2025.108238","DOIUrl":"10.1016/j.jsb.2025.108238","url":null,"abstract":"<div><div>NMDA receptors are subject to numerous endogenous and exogenous allosteric regulations, which are essential for their complex pathophysiological functions in the brain, and serve as a basis for therapeutic targeting. However, the structural basis of many of these allosteric mechanisms remains unclear. In this study, we first utilized AlphaFold to predict the structural conformations of different NMDA receptor subtypes. Subsequent comparative analyses with experimentally resolved protein structures, coupled with validation using disulfide bond formation, revealed the high precision of these computational predictions. Based on these structures, we systematically investigated the allosteric regulation of NMDA receptors using RoseTTAFold-All-Atom. Our findings elucidated the binding sites of several allosteric modulators across different NMDA receptor subtypes and identified the key amino acids required for binding. These results reveal the structural basis of NMDA receptor allosteric regulation, providing new insights into its physiological and pathological roles, and offering potential avenues for drug development.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"217 3","pages":"Article 108238"},"PeriodicalIF":2.7,"publicationDate":"2025-08-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144866109","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Sequence/structural/functional relationships between Ganoderma fungal immunomodulatory proteins (gFIPs) and proteins involved in the modulation of immune response","authors":"Nikola Schlosserová ,&nbsp;Giulia Chiara Maria Perrone ,&nbsp;Jakub Treml ,&nbsp;Maria Noemi Sgobba ,&nbsp;Lorenzo Guerra ,&nbsp;Ciro Leonardo Pierri","doi":"10.1016/j.jsb.2025.108237","DOIUrl":"10.1016/j.jsb.2025.108237","url":null,"abstract":"<div><div>Fungal Immunomodulatory Proteins from <em>Ganoderma</em> species (gFIPs) have garnered significant interest due to their potential therapeutic applications in modulating immune responses. This study investigates the sequence, structural, and functional relationships of gFIPs with other proteins involved in immune modulation. Utilizing molecular modelling, multiple sequence alignments, and structural superimposition, we analysed two FIP crystallized structures (PDB IDs: 3F3H and 3KCW) alongside homologous sequences from various taxonomic groups. Our results reveal conserved motifs across fungal, bacterial, and human sequences, indicating potential functional similarities. Comparative structural analysis highlights significant conservation in FIP architecture, with variations primarily in the N-terminal regions. Notably, structural alignment with bacterial toxins, such as ADP-ribosylating binary toxin from <em>Clostridium difficile</em> or protective antigen of Anthrax toxin from <em>Bacillus anthracis</em> suggests mechanistic insights into FIP’s immunomodulatory actions. Structural similarities between gFIPs and immune-related proteins, such as bacterial toxin-binding domains, antibody fragments, T-cell receptor components, and immune checkpoint regulators (PD-1) suggest their potential involvement in immune response/inflammation signalling pathways. This comprehensive analysis elucidates the structural basis for the diverse biological activities of gFIPs and underscores their potential as therapeutic agents in immune-related diseases.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"217 3","pages":"Article 108237"},"PeriodicalIF":2.7,"publicationDate":"2025-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144859271","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"1-Deoxy-D-xylulose 5-phosphate synthase: structural perspectives on an essential enzyme in isoprenoid biosynthesis","authors":"Victor O. Gawriljuk ,&nbsp;Rick Oerlemans ,&nbsp;Eswar R. Reddem ,&nbsp;Robin M. Gierse ,&nbsp;Anna K.H. Hirsch ,&nbsp;Matthew R. Groves","doi":"10.1016/j.jsb.2025.108236","DOIUrl":"10.1016/j.jsb.2025.108236","url":null,"abstract":"<div><div>Isoprenoids represent one of the largest and functionally diverse class of natural products, playing essential roles in cellular processes across all domains of life. Unlike humans, many pathogenic organisms such as bacteria and protozoa produce their isoprenoid precursors through the 2-<em>C</em>-methylerythritol phosphate (MEP) pathway. 1-deoxy-D-xylulose 5-phosphate synthase (DXPS) is the first and rate-limiting enzyme of this pathway. Despite its biological importance and potential as a drug target, structural studies on DXPS were limited due to its intrinsic flexibility and difficulties in crystallisation. Recent advances, including the development of more crystallisation-friendly constructs and the application of single-particle cryo-electron microscopy (cryo-EM), have significantly expanded our structural understanding of DXPS. This review provides a comprehensive overview of the structural insights gained over the past decades, focusing on the overall architecture of DXPS, its catalytic mechanism, and emerging relevance in structure-based drug discovery.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"217 3","pages":"Article 108236"},"PeriodicalIF":2.7,"publicationDate":"2025-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144817032","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A structural perspective of transmembrane transport of zinc by ZnT and ZIP transporters","authors":"Qingrong Xie ,&nbsp;Jiuyu Ding ,&nbsp;Chunting Fu ,&nbsp;Xi Chen ,&nbsp;Ziyi Sun ,&nbsp;Xiaoming Zhou","doi":"10.1016/j.jsb.2025.108235","DOIUrl":"10.1016/j.jsb.2025.108235","url":null,"abstract":"<div><div>Being the second most abundant trace metal in cells, zinc plays critical roles in a variety of cellular activities, serving as a structural or enzymatic co-factor, or a signaling molecule. Dysregulation of cellular zinc has been implicated in many pathophysiological conditions including cancer, neurodegenerative diseases and immune system disorders. Therefore, the cellular zinc homeostasis is tightly controlled by various transport proteins. Two solute carrier protein families, ZnT and ZIP transporters, mediate zinc efflux and influx, respectively, and are important players in maintaining the cellular zinc homeostasis. Recent structural advancement of ZnTs and ZIPs has gained new insight into the transport mechanism of zinc by these transporters. In this review, we discuss ZnT and ZIP transporters from a structural perspective to understand the transport mechanism of zinc across biological membranes.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"217 3","pages":"Article 108235"},"PeriodicalIF":3.0,"publicationDate":"2025-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144703772","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}