Pub Date : 2025-09-12DOI: 10.1016/j.jsb.2025.108247
Stephen A. Zorc , Paola Munoz-Tello , Timothy O’Leary , Xiaoyu Yu , Mithun Nag Karadi Giridhar , Alexander D. Hondros , Althea Hansel-Harris , Stefano Forli , Patrick R. Griffin , Douglas J. Kojetin , Raktim N. Roy , Michalina Janiszewska
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.
{"title":"Structural insights into IMP2 dimerization and RNA binding","authors":"Stephen A. Zorc , Paola Munoz-Tello , Timothy O’Leary , Xiaoyu Yu , Mithun Nag Karadi Giridhar , Alexander D. Hondros , Althea Hansel-Harris , Stefano Forli , Patrick R. Griffin , Douglas J. Kojetin , Raktim N. Roy , 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}
Pub Date : 2025-09-09DOI: 10.1016/j.jsb.2025.108239
Szu-Chi Chung, Po-Cheng Chou
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.
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 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 CRISP, available at https://github.com/phonchi/CryoParticleSegment.
{"title":"CRISP: A modular platform for cryo-EM image segmentation and processing with Conditional Random Field","authors":"Szu-Chi Chung, 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}
Pub Date : 2025-08-15DOI: 10.1016/j.jsb.2025.108238
Yunsheng Liu , Wangsheng Song , Rongde Zhong , Jinfang Zhang , Xianlin Wu , Yanyan Jia , Zengwei Kou
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.
{"title":"Characterization of NMDA receptor Allostery modulation","authors":"Yunsheng Liu , Wangsheng Song , Rongde Zhong , Jinfang Zhang , Xianlin Wu , Yanyan Jia , 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}
Pub Date : 2025-08-13DOI: 10.1016/j.jsb.2025.108237
Nikola Schlosserová , Giulia Chiara Maria Perrone , Jakub Treml , Maria Noemi Sgobba , Lorenzo Guerra , Ciro Leonardo Pierri
Fungal Immunomodulatory Proteins from Ganoderma 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 Clostridium difficile or protective antigen of Anthrax toxin from Bacillus anthracis 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.
{"title":"Sequence/structural/functional relationships between Ganoderma fungal immunomodulatory proteins (gFIPs) and proteins involved in the modulation of immune response","authors":"Nikola Schlosserová , Giulia Chiara Maria Perrone , Jakub Treml , Maria Noemi Sgobba , Lorenzo Guerra , 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}
Pub Date : 2025-08-08DOI: 10.1016/j.jsb.2025.108236
Victor O. Gawriljuk , Rick Oerlemans , Eswar R. Reddem , Robin M. Gierse , Anna K.H. Hirsch , Matthew R. Groves
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-C-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.
类异戊二烯是最大的、功能多样的天然产物之一，在生命所有领域的细胞过程中发挥着重要作用。与人类不同，许多致病生物如细菌和原生动物通过2- c -甲基赤藓糖醇磷酸（MEP）途径产生类异戊二烯前体。1-脱氧-d -木糖5-磷酸合酶（DXPS）是该途径的第一酶和限速酶。尽管DXPS具有重要的生物学意义和作为药物靶点的潜力，但由于其固有的灵活性和结晶困难，对DXPS的结构研究受到限制。最近的进展，包括更多结晶友好结构的发展和单粒子冷冻电子显微镜（cryo-EM）的应用，极大地扩展了我们对DXPS的结构理解。这篇综述提供了一个全面的概述，在过去的几十年里获得的结构见解，重点是DXPS的整体结构，它的催化机制，并在基于结构的药物发现新兴的相关性。
{"title":"1-Deoxy-D-xylulose 5-phosphate synthase: structural perspectives on an essential enzyme in isoprenoid biosynthesis","authors":"Victor O. Gawriljuk , Rick Oerlemans , Eswar R. Reddem , Robin M. Gierse , Anna K.H. Hirsch , 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}
Pub Date : 2025-07-22DOI: 10.1016/j.jsb.2025.108235
Qingrong Xie , Jiuyu Ding , Chunting Fu , Xi Chen , Ziyi Sun , Xiaoming Zhou
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.
{"title":"A structural perspective of transmembrane transport of zinc by ZnT and ZIP transporters","authors":"Qingrong Xie , Jiuyu Ding , Chunting Fu , Xi Chen , Ziyi Sun , 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}
Pub Date : 2025-07-17DOI: 10.1016/j.jsb.2025.108231
Soheil Mojiri , Joseph M. Dobbs , Niko Faul , Thomas P. Burg , Julia Mahamid , Jonas Ries
Cryogenic correlative light and electron microscopy (cryo-CLEM) is an imaging strategy that integrates specific molecular labeling and molecular resolution structural information. However, there is a resolution gap of more than two orders of magnitude between diffraction-limited fluorescence microscopy and electron microscopy (EM). Single-molecule localization microscopy (SMLM) performed at cryogenic temperatures promises to bridge this resolution gap. Nevertheless, the high excitation laser powers required for SMLM risk the devitrification of frozen biological samples, leading to perturbation of their native-like state. Here, we investigate how base cooling temperature, immersion medium, and EM grid support materials influence sample devitrification. Using finite element simulations and experimental validation, we show that a cryo-immersion medium enhances heat dissipation for carbon supports, while metallic supports in a cold nitrogen gas medium tolerate higher laser intensities due to lower base temperatures. Gold supports illuminated at exhibit markedly high laser thresholds, similar to silver-coated grids. Additionally, metallic supports maintain efficient heat dissipation in vacuum-based cryostats. Our findings provide quantitative insights that aid in optimization of cryo-SMLM setups for improved cryo-CLEM imaging.
{"title":"Effects of base temperature, immersion medium, and EM grid material on devitrification thresholds in cryogenic optical super-resolution microscopy","authors":"Soheil Mojiri , Joseph M. Dobbs , Niko Faul , Thomas P. Burg , Julia Mahamid , Jonas Ries","doi":"10.1016/j.jsb.2025.108231","DOIUrl":"10.1016/j.jsb.2025.108231","url":null,"abstract":"<div><div>Cryogenic correlative light and electron microscopy (cryo-CLEM) is an imaging strategy that integrates specific molecular labeling and molecular resolution structural information. However, there is a resolution gap of more than two orders of magnitude between diffraction-limited fluorescence microscopy and electron microscopy (EM). Single-molecule localization microscopy (SMLM) performed at cryogenic temperatures promises to bridge this resolution gap. Nevertheless, the high excitation laser powers required for SMLM risk the devitrification of frozen biological samples, leading to perturbation of their native-like state. Here, we investigate how base cooling temperature, immersion medium, and EM grid support materials influence sample devitrification. Using finite element simulations and experimental validation, we show that a cryo-immersion medium enhances heat dissipation for carbon supports, while metallic supports in a cold nitrogen gas medium tolerate higher laser intensities due to lower base temperatures. Gold supports illuminated at <span><math><mrow><mn>640</mn><mspace></mspace><mi>nm</mi></mrow></math></span> exhibit markedly high laser thresholds, similar to silver-coated grids. Additionally, metallic supports maintain efficient heat dissipation in vacuum-based cryostats. Our findings provide quantitative insights that aid in optimization of cryo-SMLM setups for improved cryo-CLEM imaging.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"217 3","pages":"Article 108231"},"PeriodicalIF":3.0,"publicationDate":"2025-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144665781","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}
Pub Date : 2025-07-14DOI: 10.1016/j.jsb.2025.108233
Ritika Kukreja, Michael P. Latham
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.
{"title":"Molecular recognition and structural plasticity in amyloid–nucleic acid complexes","authors":"Ritika Kukreja, 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}
Pub Date : 2025-07-13DOI: 10.1016/j.jsb.2025.108234
Xiaodong Wang, Siqi Yang , Penghui Yang , Ziyi Sun, Xiaoming Zhou
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 Pipistrellus 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.
{"title":"Binding of an N protein peptide to M protein of a bat coronavirus","authors":"Xiaodong Wang, Siqi Yang , Penghui Yang , Ziyi Sun, 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}
Pub Date : 2025-07-05DOI: 10.1016/j.jsb.2025.108228
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
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.
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