Journal of structural biology最新文献

{"title":"Molecular recognition and structural plasticity in amyloid–nucleic acid complexes","authors":"Ritika Kukreja,&nbsp;Michael P. Latham","doi":"10.1016/j.jsb.2025.108233","DOIUrl":"10.1016/j.jsb.2025.108233","url":null,"abstract":"<div><div>Emerging evidence highlights the importance of the interactions between amyloidogenic proteins and nucleic acids in both pathological and functional amyloid systems. Here, we review the current knowledge on the mechanisms by which nucleic acids modulate amyloid assembly and structure, highlighting conserved paradigms that govern these interactions. Drawing from studies of prion protein, amyloid-β, α-synuclein, and functional bacterial amyloids, we describe how nucleic acids act as cofactors in amyloidogenesis and influence the biological roles of these systems. Despite these studies, key questions remain regarding the structural specificity, sequence dependence, and biophysical principles underlying these interactions. Biophysical and structural tools such as NMR spectroscopy and cryo-EM offer exciting opportunities to resolve these gaps and deepen our understanding of how nucleic acids shape amyloid formation, function, and pathology.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"217 3","pages":"Article 108233"},"PeriodicalIF":3.0,"publicationDate":"2025-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144633415","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":"Binding of an N protein peptide to M protein of a bat coronavirus","authors":"Xiaodong Wang,&nbsp;Siqi Yang ,&nbsp;Penghui Yang ,&nbsp;Ziyi Sun,&nbsp;Xiaoming Zhou","doi":"10.1016/j.jsb.2025.108234","DOIUrl":"10.1016/j.jsb.2025.108234","url":null,"abstract":"<div><div>The interaction between the membrane (M) protein and the nucleocapsid (N) protein of coronaviruses plays a crucial role in virus assembly and morphogenesis. Previous studies indicate that one M−N interaction occurs between M protein and the carboxy-terminus of N protein. However, the mechanistic details of M−N interactions remain unclear. Here, we present a complex structure of an N protein carboxy-terminal peptide bound to M protein from <em>Pipistrellus</em> bat coronavirus HKU5. The structure shows that the M−N peptide binding site includes a “horizontal” groove located between the carboxy-terminal domain and the transmembrane domain of M protein. Combined with molecular docking and binding analysis, our results provide structural insight into the binding mechanism between M and N proteins of a coronavirus.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"217 3","pages":"Article 108234"},"PeriodicalIF":3.0,"publicationDate":"2025-07-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144633414","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":"Multiscale visualization of nucleolar chromatin in yeast Saccharomyces cerevisiae.","authors":"Claudie Carron, Sarah Danché, Valdir Gomes Neto, Mickaël Lelek, Nana Kadidia Maiga, Isabelle Léger-Silvestre, Thomas Mangeat, Stéphanie Balor, Carla C Oliveira, Christophe Zimmer, Frédéric Beckouët, Christian Rouvière, Benjamin Albert, Sylvain Cantaloube, Olivier Gadal","doi":"10.1016/j.jsb.2025.108228","DOIUrl":"https://doi.org/10.1016/j.jsb.2025.108228","url":null,"abstract":"<p><p>Spatial organization of chromosomes is crucial for genome stability, transcription, and proper mitotic segregation. By employing a range of imaging technologies, including random illumination microscopy and single molecule localization microscopy (SMLM), we conducted an in-depth exploration of the chromatin organization in budding yeast, with optical resolutions ranging from 250 nm to 50 nm. In silico models based on passively moving polymer chains and local tethering to nuclear landmarks explained much of the experimental data in yeast chromatin. We compared these models with our new imaging data of the nucleoplasmic and nucleolar chromatin. Chromatin fibers observed in the nucleoplasm showed some similarity with model prediction with a resolution of 150 nm. However, we visualized local clustering of chromatin in both the nucleoplasm and nucleolus, rather than the tube-like appearance predicted by polymer chain models. In the nucleolus, local clustering of ribosomal DNA (rDNA) chromatin is consistently observed from 150 nm resolution down to 50 nm. We also observed that actively transcribed rDNA spatially segregates from bulk nucleolar chromatin. Using correlative light and electron microscopy (CLEM), we found that local rDNA clustering is forming a specific nucleolar subdomain visible in transmission electron microscopy, the yeast equivalent of metazoan fibrillar center. We conclude that nucleolar chromatin forms a distinct sub-nucleolar compartment in yeast, supporting the model of a tripartite structural organization of the yeast nucleolus.</p>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":" ","pages":"108228"},"PeriodicalIF":3.0,"publicationDate":"2025-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144584210","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":"Passage of ribosomes through microsprayer increases functional activity – Implications for activity assays in time-resolved cryo-EM","authors":"Priyanka Garg ,&nbsp;Xiangsong Feng ,&nbsp;Swastik De ,&nbsp;Joachim Frank","doi":"10.1016/j.jsb.2025.108232","DOIUrl":"10.1016/j.jsb.2025.108232","url":null,"abstract":"<div><div>This study examines the validity of an assay that is used to report on the retainment of functional competence by ribosomes as they pass a microsprayer. We find a reproducible <em>increase</em>, rather than the expected <em>decrease</em> in GFP production as monitored by fluorescence, which may suggest heterogeneity or partial aggregation of ribosomes in solution. An even larger increase in functional activity is observed when sonication is used, pointing to mechanical agitation as the decisive factor in both scenarios. The results have a bearing on the design and interpretation of validation experiments in time-resolved cryo-EM based on microfluidic chips.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"217 3","pages":"Article 108232"},"PeriodicalIF":3.0,"publicationDate":"2025-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144575723","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":"Crystal structure, enzymatic and thermodynamic properties of the Thermus thermophilus phage Tt72 lytic endopeptidase with unique structural signatures of thermal adaptation","authors":"Sebastian Dorawa ,&nbsp;Katarzyna Biniek-Antosiak ,&nbsp;Magdalena Bejger ,&nbsp;Anna-Karina Kaczorowska ,&nbsp;Karol Ciuchcinski ,&nbsp;Agnieszka Godlewska ,&nbsp;Magdalena Płotka ,&nbsp;Gudmundur O. Hreggvidsson ,&nbsp;Lukasz Dziewit ,&nbsp;Tadeusz Kaczorowski ,&nbsp;Wojciech Rypniewski","doi":"10.1016/j.jsb.2025.108230","DOIUrl":"10.1016/j.jsb.2025.108230","url":null,"abstract":"<div><div>We presents the discovery and molecular characterization of a novel lytic enzyme from the extremophilic <em>Thermus thermophilus</em> MAT72 phage vB_Tt72. The protein of 346-aa (MW = 39,705) functions as phage vB_Tt72 endolysin and shows low sequence identity (&lt;37 %) to members of M23 family of peptidoglycan hydrolases, except for two uncharacterized endopeptidases of <em>T. thermophilus</em> phages: φYS40 (87 %) and φTMA (88 %). The enzyme exhibits lytic activity mainly against bacteria of the genus <em>Thermus</em> and, to a lesser extent, against other Gram-negative and Gram-positive bacteria. The protein is monomeric in solution and is highly thermostable (T_m = 98.3 °C). It retains ∼ 50 % of its lytic activity after 90 min of incubation at 99 °C. Crystallographic analysis, at 2.2 Å resolution, revealed a fold characteristic of M23 metallopeptidases, accounting for 40 % of the structure. The remaining parts of the molecule are folded in a manner that was previously undescribed. The M23 fold contains a Zn²⁺ ion coordinated by a conserved His-Asp-His triad, and two conserved His residues essential for catalysis. The active site is occupied by a phosphate or a sulfate anion, while the substrate-binding groove contains a ligand, which is a fragment of <em>E. coli</em> peptidoglycan. The common sequence-based criteria failed to identify the protein as (hyper)thermophilic. It is likely that the protein’s thermal stability is owed to peculiar features of its three-dimensional structure. Instead of trimmed surface loops, observed in many thermostable proteins, the catalytic domain contains two long loops that interlace and form an α-helical bundle with its own hydrophobic core.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"217 3","pages":"Article 108230"},"PeriodicalIF":3.0,"publicationDate":"2025-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144522821","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":"Insights into the pathogenic mechanisms associated with the SARS-CoV-2 spike protein","authors":"Mia Argyrou ,&nbsp;Eleni Pitsillou ,&nbsp;Andrew Hung ,&nbsp;Assam El-Osta ,&nbsp;Tom C. Karagiannis","doi":"10.1016/j.jsb.2025.108229","DOIUrl":"10.1016/j.jsb.2025.108229","url":null,"abstract":"<div><div>Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the pathogenic agent responsible for the coronavirus disease 2019 (COVID-19) pandemic, uses the trimeric spike protein to gain entry into the host cell. Structural studies have revealed that the spike protein is comprised of the S1 and S2 subunits. The S1 subunit of the spike protein contains the receptor-binding domain (RBD), which binds to the human angiotensin-converting enzyme 2 (ACE2) receptor. The interaction between the RBD and ACE2 facilitates membrane fusion and host cell infection. The SARS-CoV-2 spike protein also contains a unique insertion of four amino acids that results in the 682-RRAR↓S-686 polybasic furin cleavage motif at the boundary of the S1 and S2 subunits. The furin cleavage motif contributes to the high infectivity and transmissibility of SARS-CoV-2. This review provides a comprehensive analysis of the molecular interactions of the spike protein, with a specific focus on the RBD and furin cleavage site. In addition to examining the binding characteristics with ACE2, the interactions with alternative receptors, such as neuropilin-1 (NRP1) and the nicotinic acetylcholine receptors (nAChRs) are highlighted. The ability of the spike protein to bind alternative receptors and host factors has been linked to the pathophysiology of COVID-19 and the persistence of symptoms in the post COVID-19 condition. Furthermore, we examine the impact of spike protein mutations on receptor affinity and disease severity. SARS-CoV-2 continues to evolve, with variants remaining an ongoing threat to public health. Understanding these molecular interactions is critical for the development of novel therapeutic interventions.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"217 3","pages":"Article 108229"},"PeriodicalIF":3.0,"publicationDate":"2025-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144481082","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":"Preferential binding as a driving mechanism of lipid domains formation","authors":"Roman Ye. Brodskii ,&nbsp;Olga V. Vashchenko","doi":"10.1016/j.jsb.2025.108226","DOIUrl":"10.1016/j.jsb.2025.108226","url":null,"abstract":"<div><div>Lipid membranes are uniquely complex biological structures with large and still undisclosed regulatory potential in many living processes caused by versatile changes in their structure while adsorption of various guest molecules (dopants). This work is devoted to exploring spontaneous dopant-driven formation of lipid domains in a monolipid membrane observed experimentally for dopants with bimodal adsorption. The work offers the results obtained for a wide range of different cases exploiting our proposed original simulation method and numerical model. The central idea of the approach is dopant binding ‘like the surroundings’, i.e. preferential binding.</div><div>The value range of the preferential binding extent was determined, where stable domains are formed and their size distribution becomes steady. The density of domain size distribution is power-law, i.e. the domain patterns possesses self-similarity. Outside this range, only one phase dominates if the extent is too large, whereas if it is too small, great dispersion of membrane was observed, so the membrane is physically homogeneous. Various neighboring as well as different methods of calculation of dopant binding probabilities are considered. The results obtained differed quantitatively but not qualitatively. The suggested model and the domain definition are similar to those used in percolation theory. Thus, the results can be applicated to percolation problems.</div><div>Grounding on analysis of literature data on domain patterns formed in various lipid systems, we suggested that the preferential binding mechanism is in line with the mechanism of preferential neighboring which is implicitly assumed in such systems irrespective of their specific nature.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"217 3","pages":"Article 108226"},"PeriodicalIF":3.0,"publicationDate":"2025-06-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144484878","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":"The product specificities of terpinolene synthase, from cannabis sativa, reveals the plasticity of the terpene synthase active site","authors":"Danielle Wiles ,&nbsp;James Roest ,&nbsp;Julian P. Vivan ,&nbsp;Travis Beddoe","doi":"10.1016/j.jsb.2025.108227","DOIUrl":"10.1016/j.jsb.2025.108227","url":null,"abstract":"<div><div><em>Cannabis sativa</em> is a high-value plant renowned for its diverse chemical composition and abundant terpene content, contributing to its unique aroma, flavour, and therapeutic effects. Terpenes significantly influence consumer preference for <em>C. sativa</em> products, driving scientific interest in optimising terpene expression profiles and shaping the selective breeding of terpene profiles in <em>C. sativa</em> cultivars. In particular, the monoterpene, terpinolene, is influential in defining the sensory and therapeutic qualities of many <em>C. sativa</em> strains due to its woody, citrus-like aroma. Here we report the 2.5 Å resolution crystal structure of terpinolene synthase (CsTOS) from C. <em>sativa</em> in its apo form. The structure exhibits the class I monoterpene synthase fold with an open active site conformation. Using site-directed mutagenesis, we identified H618 as a key residues in determining product specificity. Substituting H618 with charged residues resulted in the preferential formation of limonene over terpinolene, highlighting its critical role in stabilising the substrate intermediate. Additionally, novel mutations uncovered an extended epistatic network of residues within 5 Å of the active site, spanning the α-helical bundle of the terpene synthase fold. These interactions contribute to monoterpene formation by modulating substrate positioning and catalytic activity. These insights advance our understanding of monoterpene biosynthesis and enable the targeted engineering of terpene synthases for customised terpene production, offering significant potential for the <em>C. sativa</em> industry.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"217 3","pages":"Article 108227"},"PeriodicalIF":3.0,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144321669","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 human adenylyl cyclase 9 in complex with Gαs by cryo-EM","authors":"Risa Nomura ,&nbsp;Shota Suzuki ,&nbsp;Koki Nishikawa ,&nbsp;Hiroshi Suzuki ,&nbsp;Yoshinori Fujiyoshi","doi":"10.1016/j.jsb.2025.108223","DOIUrl":"10.1016/j.jsb.2025.108223","url":null,"abstract":"<div><div>Adenylyl cyclase 9 (AC9) regulates many physiologic functions through the production of cAMP, an important second messenger that regulates downstream effectors. The activation of AC9 is highly regulated by GPCR signaling. For example, AC9 is activated by the binding of Gαs, which, in turn, is activated by Gs-driven GPCRs. The structure of bovine AC9 (bAC9) was reported in 2019 using single-particle cryo-electron microscopy (cryo-EM). The structure of human AC9 (hAC9), however, has not been reported to date despite its potential benefit for drug development. Here, we analyzed the structures of hAC9 and hAC9 in complex with Gαs (hAC9-Gαs) using single-particle cryo-EM. The soluble domain of AC9-Gαs, the transmembrane (TM) domain of AC9-Gαs, and AC9 alone were analyzed at resolutions of 2.7 Å, 3.4 Å, and 3.2 Å, respectively. The results revealed three key aspects of the activation mechanism of hAC9 and its cAMP-generating function. First, a conformational change of the soluble domain was observed upon Gαs binding, resulting in a widely open catalytic site. Second, we analyzed the exact position of the C-terminus occluding the catalytic site in the hAC9-Gαs complex. Finally, we unexpectedly identified an elongated density suggestive of a single acyl chain in the TM domain. Consistent with recent reports on the allosteric regulation of AC by lipids, this finding suggests that the TM domain could serve as a potential drug target.<!--> <!-->These structural findings enhance our understanding of the structure and function of AC9 and other ACs and will provide a foundation for future AC-target drug discovery.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"217 3","pages":"Article 108223"},"PeriodicalIF":3.0,"publicationDate":"2025-06-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144196126","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 generalist deep-learning volume segmentation tool for volume electron microscopy of biological samples","authors":"Yuyao Huang ,&nbsp;Nickhil Jadav ,&nbsp;Georgia Rutter ,&nbsp;Lech Szymanski ,&nbsp;Mihnea Bostina ,&nbsp;Duane P. Harland","doi":"10.1016/j.jsb.2025.108214","DOIUrl":"10.1016/j.jsb.2025.108214","url":null,"abstract":"<div><div>We present the Volume Segmentation Tool (VST), a deep learning software tool that implements volumetric image segmentation in volume electron microscopy image stack data from a wide range of biological sample types. VST automates the handling of data preprocessing, data augmentation, and network building, as well as the configuration for model training, while adapting to the specific dataset. We have tried to make VST more accessible by designing it to operate entirely on local hardware and have provided a browser-based interface with additional features for visualizations of the networks and augmented datasets. VST can utilise contour map prediction to support instance segmentation on top of semantic segmentation. Through examples from various resin-embedded sample derived transmission electron microscopy and scanning electron microscopy datasets, we demonstrate that VST achieves state of the art performance compared to existing approaches.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"217 3","pages":"Article 108214"},"PeriodicalIF":3.0,"publicationDate":"2025-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144191912","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}