Pub Date : 2025-09-01Epub 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":"2025-09-01","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 : 2025-09-01Epub Date: 2025-06-22DOI: 10.1016/j.jsb.2025.108226
Roman Ye. Brodskii , Olga V. Vashchenko
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.
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.
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.
{"title":"Preferential binding as a driving mechanism of lipid domains formation","authors":"Roman Ye. Brodskii , 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":"2025-09-01","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}
Pub Date : 2025-09-01Epub 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.
{"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":"10.1016/j.jsb.2025.108228","url":null,"abstract":"<div><div>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. <em>In silico</em> 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.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"217 3","pages":"Article 108228"},"PeriodicalIF":2.7,"publicationDate":"2025-09-01","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}
Pub Date : 2025-09-01Epub 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":"2025-09-01","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 : 2025-09-01Epub 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":"2025-09-01","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 : 2025-09-01Epub Date: 2025-06-18DOI: 10.1016/j.jsb.2025.108227
Danielle Wiles , James Roest , Julian P. Vivan , Travis Beddoe
Cannabis sativa 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 C. sativa products, driving scientific interest in optimising terpene expression profiles and shaping the selective breeding of terpene profiles in C. sativa cultivars. In particular, the monoterpene, terpinolene, is influential in defining the sensory and therapeutic qualities of many C. sativa strains due to its woody, citrus-like aroma. Here we report the 2.5 Å resolution crystal structure of terpinolene synthase (CsTOS) from C. sativa 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 C. sativa industry.
{"title":"The product specificities of terpinolene synthase, from cannabis sativa, reveals the plasticity of the terpene synthase active site","authors":"Danielle Wiles , James Roest , Julian P. Vivan , 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":"2025-09-01","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}
Pub Date : 2025-09-01Epub Date: 2025-05-28DOI: 10.1016/j.jsb.2025.108215
Pauline Roth , Utz H. Ermel , Deborah Moser , Gunnar Arctaedius , Maren Wehrheim , Margot P. Scheffer , Achilleas S. Frangakis
Biomolecular image analysis and data interpretation is significantly improved through the application of advanced visualization techniques. Numerous visualization packages are currently available, spanning a broad spectrum of applications. Recently, we developed a plugin called ArtiaX which extended the capabilities of UCSF ChimeraX to address the specific demands of cryo-electron tomography. Here, we introduce the evolution of ArtiaX, that can now generate models to facilitate particle selection, define camera recording paths, and execute particle selection routines. Diverse models can be generated and populated with putative particle positions and orientations. In addition, models can be used to drive the camera position, thereby simplifying the process of movie creation. The plugin incorporates fundamental image filtering options for the on-the-fly analysis of tomographic data and provides compatibility of particle lists with RELION-5 .star files. Collectively, this update of ArtiaX comprehensively encompasses essential tools for the analysis and visualization of electron tomograms. It retains its hallmark attributes of speed, reliability, and user-friendliness, fostering seamless human–machine interaction.
{"title":"ArtiaX: geometric models, camera paths and image processing tools","authors":"Pauline Roth , Utz H. Ermel , Deborah Moser , Gunnar Arctaedius , Maren Wehrheim , Margot P. Scheffer , Achilleas S. Frangakis","doi":"10.1016/j.jsb.2025.108215","DOIUrl":"10.1016/j.jsb.2025.108215","url":null,"abstract":"<div><div>Biomolecular image analysis and data interpretation is significantly improved through the application of advanced visualization techniques. Numerous visualization packages are currently available, spanning a broad spectrum of applications. Recently, we developed a plugin called ArtiaX which extended the capabilities of UCSF ChimeraX to address the specific demands of cryo-electron tomography. Here, we introduce the evolution of ArtiaX, that can now generate models to facilitate particle selection, define camera recording paths, and execute particle selection routines. Diverse models can be generated and populated with putative particle positions and orientations. In addition, models can be used to drive the camera position, thereby simplifying the process of movie creation. The plugin incorporates fundamental image filtering options for the on-the-fly analysis of tomographic data and provides compatibility of particle lists with RELION-5 .star files. Collectively, this update of ArtiaX comprehensively encompasses essential tools for the analysis and visualization of electron tomograms. It retains its hallmark attributes of speed, reliability, and user-friendliness, fostering seamless human–machine interaction.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"217 3","pages":"Article 108215"},"PeriodicalIF":3.0,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144187251","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}
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.
腺苷酸环化酶9 （AC9）通过产生cAMP来调节许多生理功能，cAMP是调节下游效应物的重要第二信使。AC9的激活受GPCR信号的高度调控。例如，AC9被g - αs结合激活，而g - αs又被gs驱动的gpcr激活。2019年，利用单粒子冷冻电镜（cryo-EM）报道了牛AC9 （bAC9）的结构。然而，人类AC9 （hAC9）的结构迄今尚未报道，尽管它对药物开发有潜在的益处。本文采用单粒子冷冻电镜分析了hAC9和hAC9与Gαs配合物（hAC9-Gαs）的结构。AC9- g - αs的可溶性结构域、AC9- g - αs的跨膜结构域和单独的AC9分别以2.7 Å、3.4 Å和3.2 Å的分辨率进行分析。结果揭示了hAC9的激活机制及其camp生成功能的三个关键方面。首先，在g - αs结合时观察到可溶性结构域的构象变化，导致催化位点广泛开放。其次，我们分析了hac9 - g - αs络合物中c -末端封闭催化位点的确切位置。最后，我们意外地发现了一个细长的密度，表明在TM结构域中有一个单酰基链。与最近关于脂质对AC变构调节的报道一致，这一发现表明TM结构域可能是一个潜在的药物靶点。这些结构上的发现增强了我们对AC9和其他ac的结构和功能的理解，并将为未来ac靶向药物的发现提供基础。
{"title":"Structural insights into human adenylyl cyclase 9 in complex with Gαs by cryo-EM","authors":"Risa Nomura , Shota Suzuki , Koki Nishikawa , Hiroshi Suzuki , 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":"2025-09-01","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}
Pub Date : 2025-09-01Epub Date: 2025-06-23DOI: 10.1016/j.jsb.2025.108229
Mia Argyrou , Eleni Pitsillou , Andrew Hung , Assam El-Osta , Tom C. Karagiannis
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.
{"title":"Insights into the pathogenic mechanisms associated with the SARS-CoV-2 spike protein","authors":"Mia Argyrou , Eleni Pitsillou , Andrew Hung , Assam El-Osta , 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":"2025-09-01","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}
Pub Date : 2025-09-01Epub 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":"2025-09-01","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}
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