Journal of structural biology最新文献_第9页

Cryo-iCLEM: Cryo correlative light and electron microscopy with immersion objectives Cryo- iclem：带浸没物镜的低温相关光学和电子显微镜。

IF 3 3区生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of structural biology

Pub Date : 2025-03-01 DOI: 10.1016/j.jsb.2025.108179

Niko Faul , Shih-Ya Chen , Christian Lamberz , Mark Bruckner , Christian Dienemann , Thomas P. Burg

Correlative light and electron microscopy (CLEM) is a powerful tool for investigating cellular structure and function at the molecular level. However, while electron microscopy is often performed to great advantage at cryogenic temperatures, this is not always the case for light microscopy. One key challenge is the lack of cryo-compatible immersion objectives. In recent years, multiple cryoimmersion light microscopy (cryo-iLM) approaches have been described, but these techniques have never been used in correlative approaches. Here we present a novel workflow for correlative cryoimmersion light microscopy and electron cryomicroscopy (cryo-iCLEM). Cryo-electron tomography conducted before and after cryo-iLM reveals that cryo-iCLEM maintains ultra-thin, electron-transparent samples mechanically intact and does not degrade the ultrastructural preservation achieved through plunge-freezing. For cryo-iLM, the sample is first embedded in a viscous immersion medium at cryogenic temperatures and examined with a custom cryo-immersion objective. After cryo-iLM, the immersion medium is dissolved in liquid ethane, allowing for subsequent cryo-EM imaging. We further show that cryo-iCLEM can be used on FIB-lamellae, demonstrating that mechanically sensitive samples remain undamaged. Embedding the sample in the immersion fluid reduces contamination and thus allows data acquisition over many hours. Samples can therefore be examined in detail with the advantage of low bleaching rates of fluorophores at cryogenic temperatures. In the future, we hope that our approach can help improve the performance of many advanced light microscopy techniques when they are applied in the context of cryo-CLEM.

相关光电子显微镜（CLEM）是在分子水平上研究细胞结构和功能的有力工具。然而，虽然电子显微镜通常在低温下具有很大的优势，但光学显微镜并不总是如此。一个关键的挑战是缺乏与低温兼容的浸入目标。近年来，已有多种低温浸光显微镜（cryo-iLM）方法被描述，但这些技术从未在相关方法中使用。在这里，我们提出了一种新的工作流程，用于相关的冷冻浸泡光学显微镜和电子冷冻显微镜（cryo-iCLEM）。在冷冻- ilm前后进行的冷冻电子断层扫描显示，冷冻- iclem保持了超薄、电子透明的样品的机械完整性，并且不会降低通过浸入式冷冻获得的超微结构保存。对于低温ilm，样品首先在低温下嵌入粘性浸入介质中，并用定制的低温浸入物镜进行检测。在冷冻- ilm后，浸泡介质溶解在液态乙烷中，允许随后的冷冻- em成像。我们进一步表明，cryo-iCLEM可以用于fib片层，表明机械敏感样品保持完好无损。将样品包埋在浸渍液中可以减少污染，因此可以在许多小时内获取数据。因此，可以对样品进行详细检查，其优点是在低温下荧光团的漂白率低。在未来，我们希望我们的方法可以帮助提高许多先进的光学显微镜技术的性能，当他们应用于低温clem的背景下。

{"title":"Cryo-iCLEM: Cryo correlative light and electron microscopy with immersion objectives","authors":"Niko Faul , Shih-Ya Chen , Christian Lamberz , Mark Bruckner , Christian Dienemann , Thomas P. Burg","doi":"10.1016/j.jsb.2025.108179","DOIUrl":"10.1016/j.jsb.2025.108179","url":null,"abstract":"<div><div>Correlative light and electron microscopy (CLEM) is a powerful tool for investigating cellular structure and function at the molecular level. However, while electron microscopy is often performed to great advantage at cryogenic temperatures, this is not always the case for light microscopy. One key challenge is the lack of cryo-compatible immersion objectives. In recent years, multiple cryoimmersion light microscopy (cryo-iLM) approaches have been described, but these techniques have never been used in correlative approaches. Here we present a novel workflow for correlative cryoimmersion light microscopy and electron cryomicroscopy (cryo-iCLEM). Cryo-electron tomography conducted before and after cryo-iLM reveals that cryo-iCLEM maintains ultra-thin, electron-transparent samples mechanically intact and does not degrade the ultrastructural preservation achieved through plunge-freezing. For cryo-iLM, the sample is first embedded in a viscous immersion medium at cryogenic temperatures and examined with a custom cryo-immersion objective. After cryo-iLM, the immersion medium is dissolved in liquid ethane, allowing for subsequent cryo-EM imaging. We further show that cryo-iCLEM can be used on FIB-lamellae, demonstrating that mechanically sensitive samples remain undamaged. Embedding the sample in the immersion fluid reduces contamination and thus allows data acquisition over many hours. Samples can therefore be examined in detail with the advantage of low bleaching rates of fluorophores at cryogenic temperatures. In the future, we hope that our approach can help improve the performance of many advanced light microscopy techniques when they are applied in the context of cryo-CLEM.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"217 1","pages":"Article 108179"},"PeriodicalIF":3.0,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143458330","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Lack of embryonic skeletal muscle in mice leads to abnormal mineral deposition and growth 小鼠胚胎骨骼肌缺乏导致异常的矿物质沉积和生长。

IF 3 3区生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of structural biology

Pub Date : 2025-03-01 DOI: 10.1016/j.jsb.2025.108178

Isabella Silva Barreto , Marianne Liebi , Sophie Le Cann , Saima Ahmed , Leonard C. Nielsen , Tilman A. Grünewald , Hector Dejea , Viviane Lutz-Bueno , Niamh C. Nowlan , Hanna Isaksson

Developing bones can be severely impaired by a range of disorders where muscular loading is abnormal. Recent work has indicated that the effects of absent skeletal muscle on bones are more severe early in development, with rudiment length and mineralization lengths being almost normal in muscle-less limbs just prior to birth. However, the impact of abnormal mechanical loading on the nanoscale structure and composition during prenatal mineralization remains unknown. In this exploratory study, we characterized the mineralization process of humeri from muscle-less limb embryonic mice using a multiscale approach by combining X-ray scattering and fluorescence with infrared and light microscopy to identify potential key aspects of interest for future in-depth investigations. Muscle-less humeri were characterized by initially less mineralized tissue to later catch up with controls, and exhibited continuous growth of mineral particles, which ultimately led to seemingly larger mineral particles than their controls at the end of development. Muscle-less limbs exhibited an abnormal pattern of mineralization, reflected by a more widespread distribution of zinc and homogenous distribution of hydroxyapatite compared to controls, which instead showed trabecular-like structures and zinc localized only to regions of ongoing mineralization. The decrease in collagen content in the hypertrophic zone due to resorption of the cartilage collagen matrix was less distinct in muscle-less limbs compared to controls. Surprisingly, the nanoscale orientation of the mineral particles was unaffected by the lack of skeletal muscle. The identified accelerated progression of ossification in muscle-less limbs at later prenatal stages provides a possible anatomical mechanism underlying their recovery in skeletal development.

在肌肉负荷异常的情况下，发育中的骨骼会受到一系列疾病的严重损害。最近的研究表明，骨骼肌缺失对骨骼的影响在发育早期更为严重，在出生之前，没有肌肉的肢体的基本长度和矿化长度几乎是正常的。然而，在产前矿化过程中，异常机械载荷对纳米级结构和组成的影响尚不清楚。在这项探索性研究中，我们利用多尺度方法，结合x射线散射和荧光、红外和光学显微镜，描述了无肌肉肢体胚胎小鼠肱骨矿化过程，以确定未来深入研究的潜在关键方面。无肌肉肱骨的特点是最初矿化组织较少，后来赶上对照组，并且矿物颗粒持续增长，最终导致在发育结束时矿物颗粒似乎比对照组更大。与对照组相比，无肌肢体表现出异常的矿化模式，锌分布更广泛，羟基磷灰石分布均匀，而对照组则表现出小梁样结构，锌仅局限于正在矿化的区域。与对照组相比，缺乏肌肉的四肢由于软骨胶原基质的吸收而导致的肥厚带胶原含量的减少不那么明显。令人惊讶的是，矿物颗粒的纳米级取向不受骨骼肌缺乏的影响。在产前后期，无肌肉肢体骨化的加速进展提供了一种可能的解剖学机制，其基础是骨骼发育的恢复。

{"title":"Lack of embryonic skeletal muscle in mice leads to abnormal mineral deposition and growth","authors":"Isabella Silva Barreto , Marianne Liebi , Sophie Le Cann , Saima Ahmed , Leonard C. Nielsen , Tilman A. Grünewald , Hector Dejea , Viviane Lutz-Bueno , Niamh C. Nowlan , Hanna Isaksson","doi":"10.1016/j.jsb.2025.108178","DOIUrl":"10.1016/j.jsb.2025.108178","url":null,"abstract":"<div><div>Developing bones can be severely impaired by a range of disorders where muscular loading is abnormal. Recent work has indicated that the effects of absent skeletal muscle on bones are more severe early in development, with rudiment length and mineralization lengths being almost normal in muscle-less limbs just prior to birth. However, the impact of abnormal mechanical loading on the nanoscale structure and composition during prenatal mineralization remains unknown. In this exploratory study, we characterized the mineralization process of humeri from muscle-less limb embryonic mice using a multiscale approach by combining X-ray scattering and fluorescence with infrared and light microscopy to identify potential key aspects of interest for future in-depth investigations. Muscle-less humeri were characterized by initially less mineralized tissue to later catch up with controls, and exhibited continuous growth of mineral particles, which ultimately led to seemingly larger mineral particles than their controls at the end of development. Muscle-less limbs exhibited an abnormal pattern of mineralization, reflected by a more widespread distribution of zinc and homogenous distribution of hydroxyapatite compared to controls, which instead showed trabecular-like structures and zinc localized only to regions of ongoing mineralization. The decrease in collagen content in the hypertrophic zone due to resorption of the cartilage collagen matrix was less distinct in muscle-less limbs compared to controls. Surprisingly, the nanoscale orientation of the mineral particles was unaffected by the lack of skeletal muscle. The identified accelerated progression of ossification in muscle-less limbs at later prenatal stages provides a possible anatomical mechanism underlying their recovery in skeletal development.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"217 1","pages":"Article 108178"},"PeriodicalIF":3.0,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143433421","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Computational Engineering of siderocalin to modulate its binding affinity to the antihypertension drug candesartan 铁苷调节其与抗高血压药物坎地沙坦结合亲和力的计算工程。

IF 3 3区生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of structural biology

Pub Date : 2025-03-01 DOI: 10.1016/j.jsb.2025.108180

Kristina Vogel , Johanna Moeller , Nina G. Bozhanova , Markus Voehler , Anja Penk , Jens Meiler , Clara T. Schoeder

Lipocalin family proteins have been shown to bind a vast array of small molecules and have subsequently been adapted to selectively bind specific ligands. In this study, candesartan, an antihypertension drug, was identified to bind mouse and human siderocalin in biomolecular NMR experiments, allowing for structural insights into the candesartan-siderocalin interaction. The ligand binding site was determined through an integrative structural biology approach using in silico ligand docking guided by NMR experiments. Building on this structurally informed binding model, we used rational protein design to modulate the binding pocket for increased or decreased ligand binding affinity. The predicted mutations were evaluated in vitro using isothermal titration calorimetry. This resulted in a mutant with a 50-fold increase in binding affinity in addition to a second mutant with a five-fold decrease in binding affinity. Thus, siderocalins have potential as a scaffold for creation of various ligand binding-based tools, including drug scavengers.

脂钙蛋白家族蛋白已被证明可以结合大量的小分子，并随后被适应于选择性地结合特定的配体。在这项研究中，坎地沙坦，一种抗高血压药物，在生物分子核磁共振实验中被鉴定为与小鼠和人的铁苷酸结合，允许对坎地沙坦-铁苷酸相互作用的结构见解。通过核磁共振实验指导下的硅配体对接综合结构生物学方法确定配体结合位点。在这个结构知情的结合模型的基础上，我们使用合理的蛋白质设计来调节结合口袋，以增加或减少配体的结合亲和力。预测的突变在体外用等温滴定量热法进行评估。这导致一个突变体的结合亲和力增加了50倍，而另一个突变体的结合亲和力降低了5倍。因此，铁钙蛋白有潜力作为一种支架来创造各种基于配体结合的工具，包括药物清除剂。

{"title":"Computational Engineering of siderocalin to modulate its binding affinity to the antihypertension drug candesartan","authors":"Kristina Vogel , Johanna Moeller , Nina G. Bozhanova , Markus Voehler , Anja Penk , Jens Meiler , Clara T. Schoeder","doi":"10.1016/j.jsb.2025.108180","DOIUrl":"10.1016/j.jsb.2025.108180","url":null,"abstract":"<div><div>Lipocalin family proteins have been shown to bind a vast array of small molecules and have subsequently been adapted to selectively bind specific ligands. In this study, candesartan, an antihypertension drug, was identified to bind mouse and human siderocalin in biomolecular NMR experiments, allowing for structural insights into the candesartan-siderocalin interaction. The ligand binding site was determined through an integrative structural biology approach using <em>in silico</em> ligand docking guided by NMR experiments. Building on this structurally informed binding model, we used rational protein design to modulate the binding pocket for increased or decreased ligand binding affinity. The predicted mutations were evaluated <em>in vitro</em> using isothermal titration calorimetry. This resulted in a mutant with a 50-fold increase in binding affinity in addition to a second mutant with a five-fold decrease in binding affinity. Thus, siderocalins have potential as a scaffold for creation of various ligand binding-based tools, including drug scavengers.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"217 1","pages":"Article 108180"},"PeriodicalIF":3.0,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143468251","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Effects of Gα C-terminal deletion on the intrinsic GDP release/GTPase activity and conformational dynamics Gα C 端缺失对固有 GDP 释放/GTP 酶活性和构象动态的影响

IF 3 3区生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of structural biology

Pub Date : 2025-02-27 DOI: 10.1016/j.jsb.2025.108182

Junyoung Kim, Ka Young Chung

Heterotrimeric G proteins (G proteins) serve as key signaling mediators downstream of G protein-coupled receptors (GPCRs). Comprised of Gα, Gβ, and Gγ subunits, the activation state of Gα, determined by GDP or GTP binding, governs G protein activity. While high-resolution structures of GPCR-G protein complexes have identified the Gα C-terminal 5 residues (i.e., wavy hook) as critical for GPCR binding and coupling selectivity, its influence on Gα’s intrinsic biochemical properties remains unclear. Here, we investigated the role of wavy hook truncation in the intrinsic GDP/GTP turnover rate, GTPase activity, and conformational dynamics of Gαs and Gαi1 using BODIPY-labeled nucleotides and hydrogen/deuterium exchange mass spectrometry (HDX-MS). Truncation of the wavy hook significantly altered the GDP/GTP turnover rate, GTPase activity, and conformational flexibility of Gαs, particularly at the p-loop through α1 region, but had minimal impact on Gαi1. These findings reveal subtype-specific effects of the wavy hook on G protein stability and conformational dynamics, highlighting the importance of structural elements in regulating G protein function and their implications for GPCR signaling studies.

异三聚体G蛋白（G蛋白）是G蛋白偶联受体（gpcr）下游的关键信号介质。由Gα、Gβ和Gγ亚基组成，Gα的激活状态由GDP或GTP结合决定，控制着G蛋白的活性。虽然GPCR- g蛋白复合物的高分辨率结构已经确定了Gα c端5残基（即波浪钩）是GPCR结合和偶联选择性的关键，但其对Gα内在生化特性的影响尚不清楚。本研究利用bodipy标记的核苷酸和氢/氘交换质谱（HDX-MS）研究了波浪钩截断在Gαs和Gαi1的内在GDP/GTP周转率、GTP酶活性和构象动力学中的作用。波浪钩的截断显著改变了g - αs的GDP/GTP周转率、GTP酶活性和构象柔韧性，特别是在p环穿过α1区域，但对g - α1的影响很小。这些发现揭示了波浪钩对G蛋白稳定性和构象动力学的亚型特异性影响，突出了结构元件在调节G蛋白功能中的重要性及其对GPCR信号传导研究的意义。

{"title":"Effects of Gα C-terminal deletion on the intrinsic GDP release/GTPase activity and conformational dynamics","authors":"Junyoung Kim, Ka Young Chung","doi":"10.1016/j.jsb.2025.108182","DOIUrl":"10.1016/j.jsb.2025.108182","url":null,"abstract":"<div><div>Heterotrimeric G proteins (G proteins) serve as key signaling mediators downstream of G protein-coupled receptors (GPCRs). Comprised of Gα, Gβ, and Gγ subunits, the activation state of Gα, determined by GDP or GTP binding, governs G protein activity. While high-resolution structures of GPCR-G protein complexes have identified the Gα C-terminal 5 residues (<em>i.e.,</em> wavy hook) as critical for GPCR binding and coupling selectivity, its influence on Gα’s intrinsic biochemical properties remains unclear. Here, we investigated the role of wavy hook truncation in the intrinsic GDP/GTP turnover rate, GTPase activity, and conformational dynamics of Gαs and Gαi1 using BODIPY-labeled nucleotides and hydrogen/deuterium exchange mass spectrometry (HDX-MS). Truncation of the wavy hook significantly altered the GDP/GTP turnover rate, GTPase activity, and conformational flexibility of Gαs, particularly at the p-loop through α1 region, but had minimal impact on Gαi1. These findings reveal subtype-specific effects of the wavy hook on G protein stability and conformational dynamics, highlighting the importance of structural elements in regulating G protein function and their implications for GPCR signaling studies.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"217 2","pages":"Article 108182"},"PeriodicalIF":3.0,"publicationDate":"2025-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143537316","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}

引用次数: 0

Three-dimensional reconstruction of Magnetofaba australis strain IT-1: Magnetosome chain position with respect to flagella australis Magnetofaba菌株IT-1的三维重建：磁小体链在鞭毛上的位置。

IF 3 3区生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of structural biology

Pub Date : 2025-02-26 DOI: 10.1016/j.jsb.2025.108181

Eduardo Monteiro , Anderson S. Cabral , Viviana Morillo , Daniel Acosta-Avalos , Ulysses Lins , Fernanda Abreu

Magnetotactic bacteria (MTB) are a broad and diverse group of Gram-negative prokaryotes that biomineralize magnetosomes, organelles composed of a magnetic nanocrystal of magnetite (Fe₃O₄) or greigite (Fe₃S₄) and enveloped by a biological membrane. Magnetosomes are arranged in one or more chains intracellularly, which impart a magnetic moment to the cell. These structures permit a passive orientation of the MTB with the geomagnetic field lines (GML), which, when associated with swimming propelled by flagella, originate a phenomenon called magneto-aerotaxis, an important life strategy in a chemical stratified environment. There is a classical model based on elongated cells as vibrios and rods that tries to explain the magneto-aerotaxis. Still, this model raises questions when applied to other morphologies other than elongated cells. Here, we observe the spatial disposition of magnetosomes, motility behavior, and influence of magneto-aerotaxis in Magnetofaba australis strain IT-1, an MTB that achieves high swimming speeds and has some peculiarity in its motility. The three-dimensional reconstruction showed that Mf. australis strain IT-1′s magnetosome chain is misaligned with the swimming axis, which makes it impossible to use the classical model to explain magneto-aerotaxis in this MTB. Despite this, Mf. australis strain IT-1 was capable of swimming aligned to the GML. Also, this work studied the influence of the magnetosome and magneto-aerotaxis between populations of Mf. australis strain IT-1 with and without magnetosomes. Our results indicated that the magnetosome presence not only positively influences the movement in Mf. australis strain IT-1 but also can positively impact population growth in these MTB.

磁小体是由磁铁矿（Fe3O4）或灰铁矿（Fe3S4）的磁性纳米晶体组成的细胞器，由生物膜包裹。磁小体在细胞内排列成一条或多条链，给细胞带来磁矩。这些结构可使 MTB 与地磁场线（GML）被动定向，当与鞭毛推动的游动联系在一起时，就会产生一种称为磁气动的现象，这是在化学分层环境中的一种重要的生命策略。有一种基于拉长细胞（如振子和棒状细胞）的经典模型，试图解释磁气浮现象。然而，当这一模型应用于拉长细胞以外的其他形态时，就会产生问题。在此，我们观察了Magnetofaba australis菌株IT-1中磁小体的空间分布、运动行为以及磁气浮的影响。三维重建结果表明，Mf. australis strain IT-1 的磁小体链与游动轴错位，因此无法用经典模型来解释这种 MTB 的磁气动现象。尽管如此，Mf. australis 菌株 IT-1 仍能对准 GML 游动。此外，这项工作还研究了有磁小体和无磁小体的 Mf. australis 菌株 IT-1 群体之间磁小体和磁气浮的影响。我们的研究结果表明，磁小体的存在不仅会积极影响 Mf.australis 菌株 IT-1 的运动，还会对这些 MTB 的种群增长产生积极影响。

{"title":"Three-dimensional reconstruction of Magnetofaba australis strain IT-1: Magnetosome chain position with respect to flagella","authors":"Eduardo Monteiro , Anderson S. Cabral , Viviana Morillo , Daniel Acosta-Avalos , Ulysses Lins , Fernanda Abreu","doi":"10.1016/j.jsb.2025.108181","DOIUrl":"10.1016/j.jsb.2025.108181","url":null,"abstract":"<div><div>Magnetotactic bacteria (MTB) are a broad and diverse group of Gram-negative prokaryotes that biomineralize magnetosomes, organelles composed of a magnetic nanocrystal of magnetite (Fe<sub>3</sub>O<sub>4</sub>) or greigite (Fe<sub>3</sub>S<sub>4</sub>) and enveloped by a biological membrane. Magnetosomes are arranged in one or more chains intracellularly, which impart a magnetic moment to the cell. These structures permit a passive orientation of the MTB with the geomagnetic field lines (GML), which, when associated with swimming propelled by flagella, originate a phenomenon called magneto-aerotaxis, an important life strategy in a chemical stratified environment. There is a classical model based on elongated cells as vibrios and rods that tries to explain the magneto-aerotaxis. Still, this model raises questions when applied to other morphologies other than elongated cells. Here, we observe the spatial disposition of magnetosomes, motility behavior, and influence of magneto-aerotaxis in <em>Magnetofaba australis</em> strain IT-1, an MTB that achieves high swimming speeds and has some peculiarity in its motility. The three-dimensional reconstruction showed that <em>Mf. australis</em> strain IT-1′s magnetosome chain is misaligned with the swimming axis, which makes it impossible to use the classical model to explain magneto-aerotaxis in this MTB. Despite this, <em>Mf. australis</em> strain IT-1 was capable of swimming aligned to the GML. Also, this work studied the influence of the magnetosome and magneto-aerotaxis between populations of <em>Mf. australis</em> strain IT-1 with and without magnetosomes. Our results indicated that the magnetosome presence not only positively influences the movement in <em>Mf.australis</em> strain IT-1 but also can positively impact population growth in these MTB.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"217 2","pages":"Article 108181"},"PeriodicalIF":3.0,"publicationDate":"2025-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143531298","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}

引用次数: 0

Computational identification of B and T-cell epitopes for designing a multi-epitope vaccine against SARS-CoV-2 spike glycoprotein 设计抗SARS-CoV-2刺突糖蛋白多表位疫苗的B细胞和t细胞表位的计算鉴定

IF 3 3区生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of structural biology

Pub Date : 2025-02-11 DOI: 10.1016/j.jsb.2025.108177

Truc Ly Nguyen , Thong Ba Nguyen , Heebal Kim

Although the peak of the COVID-19 pandemic has passed, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to pose a significant global threat and remains a public health concern. Given the ongoing risk and the substantial loss of life caused by the virus, continuous research into vaccine development is essential. This study employs immunoinformatics approaches to identify T-cell and B-cell epitopes for designing a multi-epitope peptide vaccine candidate targeting the Omicron variant. The proposed vaccine construct comprises 1435 amino acids, including eight linear B lymphocyte, seven cytotoxic T lymphocyte, and five helper T lymphocyte epitopes, along with appropriate adjuvants and linkers. The evaluation of the vaccine revealed high antigenicity, non-allergenicity, non-toxicity, and favorable physicochemical properties. To further assess its efficacy, molecular docking studies were performed to investigate interactions between the vaccine and key immune components, including Toll-like receptors and major histocompatibility complex molecules. Stability of these interactions was confirmed using molecular dynamics simulations in triplicate, conducted over 100 ns using GROMACS 2023 to compute key metrics, such as root mean square deviation, root mean square fluctuation, solvent-accessible surface area, and radius of gyration. The results demonstrate that the multi-epitope vaccine has the potential to elicit strong immune responses against the Omicron variant, providing a promising foundation for further experimental validation and clinical development in COVID-19 vaccine research.

虽然COVID-19大流行的高峰已经过去，但严重急性呼吸综合征冠状病毒2型（SARS-CoV-2）继续构成重大全球威胁，仍然是一个公共卫生问题。鉴于该病毒造成的持续风险和大量生命损失，对疫苗开发的持续研究至关重要。本研究采用免疫信息学方法鉴定t细胞和b细胞表位，设计针对Omicron变异的多表位肽候选疫苗。所提出的疫苗结构包括1435个氨基酸，包括8个线性B淋巴细胞、7个细胞毒性T淋巴细胞和5个辅助T淋巴细胞表位，以及适当的佐剂和连接体。该疫苗具有高抗原性、无致敏性、无毒性和良好的理化性质。为了进一步评估其有效性，进行了分子对接研究，以研究疫苗与关键免疫成分（包括toll样受体和主要组织相容性复合体分子）之间的相互作用。使用GROMACS 2023进行了超过100 ns的三次分子动力学模拟，确认了这些相互作用的稳定性，并计算了关键指标，如均方根偏差、均方根波动、溶剂可及表面积和旋转半径。结果表明，该多表位疫苗有可能引发针对Omicron变体的强免疫应答，为进一步的实验验证和COVID-19疫苗研究提供了有希望的基础。

{"title":"Computational identification of B and T-cell epitopes for designing a multi-epitope vaccine against SARS-CoV-2 spike glycoprotein","authors":"Truc Ly Nguyen , Thong Ba Nguyen , Heebal Kim","doi":"10.1016/j.jsb.2025.108177","DOIUrl":"10.1016/j.jsb.2025.108177","url":null,"abstract":"<div><div>Although the peak of the COVID-19 pandemic has passed, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to pose a significant global threat and remains a public health concern. Given the ongoing risk and the substantial loss of life caused by the virus, continuous research into vaccine development is essential. This study employs immunoinformatics approaches to identify T-cell and B-cell epitopes for designing a multi-epitope peptide vaccine candidate targeting the Omicron variant. The proposed vaccine construct comprises 1435 amino acids, including eight linear B lymphocyte, seven cytotoxic T lymphocyte, and five helper T lymphocyte epitopes, along with appropriate adjuvants and linkers. The evaluation of the vaccine revealed high antigenicity, non-allergenicity, non-toxicity, and favorable physicochemical properties. To further assess its efficacy, molecular docking studies were performed to investigate interactions between the vaccine and key immune components, including Toll-like receptors and major histocompatibility complex molecules. Stability of these interactions was confirmed using molecular dynamics simulations in triplicate, conducted over 100 ns using GROMACS 2023 to compute key metrics, such as root mean square deviation, root mean square fluctuation, solvent-accessible surface area, and radius of gyration. The results demonstrate that the multi-epitope vaccine has the potential to elicit strong immune responses against the Omicron variant, providing a promising foundation for further experimental validation and clinical development in COVID-19 vaccine research.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"217 2","pages":"Article 108177"},"PeriodicalIF":3.0,"publicationDate":"2025-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143414501","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}

引用次数: 0

A computational approach to predict the effects of missense mutations on protein amyloidogenicity: A case study in hereditary transthyretin cardiomyopathy 预测错义突变对蛋白淀粉样变性影响的计算方法：遗传性转甲状腺素型心肌病的案例研究

IF 3 3区生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of structural biology

Pub Date : 2025-02-09 DOI: 10.1016/j.jsb.2025.108176

Ivan A. Pyankov , Valentin Gonay , Yaroslav A. Stepanov , Pavel Shestun , Anna A. Kostareva , Mayya V. Uspenskaya , Michael G. Petukhov , Andrey V. Kajava

With many amyloidosis-associated missense mutations still unidentified and early diagnostic methods largely unavailable, there is an urgent need for a reliable computational approach to predict hereditary amyloidoses from gene sequencing data. Progress has been made in predicting amyloidosis-triggering sequences within intrinsically disordered regions. However, some diseases are caused by mutations in amyloidogenic regions within structured domains that must unfold for amyloid formation. Accurate prediction of amyloidogenic regions requires tools for detecting amyloidogenicity and assessing mutation effects on protein stability. We developed datasets of mutations linked to hereditary ATTR cardiomyopathy and others likely unrelated, evaluating TTR mutants with amyloidogenicity and stability predictors. Notably, the stability predictors consistently indicated that ATTR-related mutations tend to destabilize the TTR structure more than non-ATTR-associated mutations. Using these datasets and newly generated mutation features, we developed a machine learning model SDAM-TTR to predict mutations leading to ATTR cardiomyopathy.

由于许多淀粉样变性相关的错义突变仍未被发现，而且早期诊断方法在很大程度上是不可用的，因此迫切需要一种可靠的计算方法来从基因测序数据中预测遗传性淀粉样变性。在预测内在紊乱区域内淀粉样变性触发序列方面取得了进展。然而，一些疾病是由淀粉样蛋白形成必须展开的结构域内淀粉样蛋白发生区域的突变引起的。准确预测淀粉样变性区域需要检测淀粉样变性和评估突变对蛋白质稳定性的影响的工具。我们开发了与遗传性ATTR心肌病和其他可能不相关的TTR突变相关的数据集，用淀粉样变性和稳定性预测因子评估TTR突变。值得注意的是，稳定性预测因子一致表明，attr相关突变比非attr相关突变更容易破坏TTR结构的稳定性。利用这些数据集和新生成的突变特征，我们开发了一个机器学习模型SDAM-TTR来预测导致ATTR心肌病的突变。

{"title":"A computational approach to predict the effects of missense mutations on protein amyloidogenicity: A case study in hereditary transthyretin cardiomyopathy","authors":"Ivan A. Pyankov , Valentin Gonay , Yaroslav A. Stepanov , Pavel Shestun , Anna A. Kostareva , Mayya V. Uspenskaya , Michael G. Petukhov , Andrey V. Kajava","doi":"10.1016/j.jsb.2025.108176","DOIUrl":"10.1016/j.jsb.2025.108176","url":null,"abstract":"<div><div>With many amyloidosis-associated missense mutations still unidentified and early diagnostic methods largely unavailable, there is an urgent need for a reliable computational approach to predict hereditary amyloidoses from gene sequencing data. Progress has been made in predicting amyloidosis-triggering sequences within intrinsically disordered regions. However, some diseases are caused by mutations in amyloidogenic regions within structured domains that must unfold for amyloid formation. Accurate prediction of amyloidogenic regions requires tools for detecting amyloidogenicity and assessing mutation effects on protein stability. We developed datasets of mutations linked to hereditary ATTR cardiomyopathy and others likely unrelated, evaluating TTR mutants with amyloidogenicity and stability predictors. Notably, the stability predictors consistently indicated that ATTR-related mutations tend to destabilize the TTR structure more than non-ATTR-associated mutations. Using these datasets and newly generated mutation features, we developed a machine learning model SDAM-TTR to predict mutations leading to ATTR cardiomyopathy.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"217 1","pages":"Article 108176"},"PeriodicalIF":3.0,"publicationDate":"2025-02-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143395698","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}

引用次数: 0

Interaction of berberine with different forms of DNA in human telomeric region 小檗碱与人类端粒区不同形式DNA的相互作用。

IF 3 3区生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of structural biology

Pub Date : 2025-02-01 DOI: 10.1016/j.jsb.2025.108175

Mahdiyeh Mostafavi , Leila Hassani , Maryam Khoshkam

Guanine-rich oligonucleotide sequences have the potential to form four-stranded structure known as G-quadruplex. These structures are frequently observed in crucial regions of the human genome, including promoter and telomeric regions. Due to their involvement in regulating gene expression and cell division, G-quadruplexes have emerged as promising targets for anticancer drugs. This study investigated interaction of berberine with different forms of DNA within human telomeric region. The results of absorption and fluorescence spectroscopy indicated that conformation of DNA plays an important role in the mode of binding. Circular dichroism suggested that berberine promotes compaction of the unstable quadruplex structure formed under non-saline conditions. Furthermore, interaction of berberine with the stable structures of G-quadruplex resulted in a change in their compactness without altering the type of DNA structure. 3D fluorescence spectra analysis by chemometrics methods showed formation of two distinct species probably attributed to the self-association and specific binding of berberin to the different forms of DNA. It can be also concluded that berberine forms a more stable complex with the human telomeric hybride type G-quadruplex structure compared with the basket type. In conclusion, the findings imply that the successful design of drugs targeting DNA within the human telomere region necessitates careful consideration of the diverse forms of DNA.

富含鸟嘌呤的寡核苷酸序列具有形成四链结构的潜力，称为g -四重体。这些结构经常在人类基因组的关键区域观察到，包括启动子和端粒区域。由于它们参与调节基因表达和细胞分裂，g -四重体已成为抗癌药物的有希望的靶点。本研究探讨了小檗碱与人类端粒区三种不同形式的DNA的相互作用。吸收光谱和荧光光谱结果表明，DNA的构象对其结合方式起重要作用。圆二色性表明，小檗碱促进了非盐条件下形成的不稳定四重结构的压实。此外，小檗碱与g -四重体稳定结构的相互作用导致其致密性的改变，而不改变DNA结构的类型。化学计量学方法的三维荧光光谱分析显示，两种不同物种的形成可能是由于小檗碱与不同形式的DNA的自结合和特异性结合。与篮型相比，小檗碱与人类端粒杂交型g -四重体结构形成更稳定的配合物。总之，研究结果表明，成功设计针对人类端粒区域内DNA的药物需要仔细考虑DNA的不同形式。

{"title":"Interaction of berberine with different forms of DNA in human telomeric region","authors":"Mahdiyeh Mostafavi , Leila Hassani , Maryam Khoshkam","doi":"10.1016/j.jsb.2025.108175","DOIUrl":"10.1016/j.jsb.2025.108175","url":null,"abstract":"<div><div>Guanine-rich oligonucleotide sequences have the potential to form four-stranded structure known as G-quadruplex. These structures are frequently observed in crucial regions of the human genome, including promoter and telomeric regions. Due to their involvement in regulating gene expression and cell division, G-quadruplexes have emerged as promising targets for anticancer drugs. This study investigated interaction of berberine with different forms of DNA within human telomeric region. The results of absorption and fluorescence spectroscopy indicated that conformation of DNA plays an important role in the mode of binding. Circular dichroism suggested that berberine promotes compaction of the unstable quadruplex structure formed under non-saline conditions. Furthermore, interaction of berberine with the stable structures of G-quadruplex resulted in a change in their compactness without altering the type of DNA structure. 3D fluorescence spectra analysis by chemometrics methods showed formation of two distinct species probably attributed to the self-association and specific binding of berberin to the different forms of DNA. It can be also concluded that berberine forms a more stable complex with the human telomeric hybride type G-quadruplex structure compared with the basket type. In conclusion, the findings imply that the successful design of drugs targeting DNA within the human telomere region necessitates careful consideration of the diverse forms of DNA.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"217 1","pages":"Article 108175"},"PeriodicalIF":3.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143122992","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}

引用次数: 0

Different strategies towards strength: Unveiling the role of Zn vs Mn/Ca and chitin arrangement in scorpion stingers 不同的强度策略：揭示Zn对Mn/Ca和几丁质排列在蝎子毒刺中的作用。

IF 3 3区生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of structural biology

Pub Date : 2025-01-30 DOI: 10.1016/j.jsb.2025.108174

C. Sakr , P. Cook , M. Seiter , C. Hörweg , S. Žák , M. Cordill , M. Burghammer , M. Sztucki , H. Lichtenegger

Arthropods and especially scorpions often use metal ions to harden their cuticle. In this study we analyse the chitin fibre arrangement, metal content and distribution and mechanical properties of the stingers of two scorpions: the buthid scorpion Centruroides platnicki (PS) and the diplocentrid scorpion Nebo whitei (NS). Results show that both scorpions incorporate the same elements, Zn, Mn and Ca, but in different locations in the stinger cuticle. While NS uses Zn ions as hardening agent in the epicuticle, PS uses Mn/Ca ions. Interestingly, Zn ions were also found in PS but had no impact on the enhancement of the mechanical properties of the stinger. The use of different metal ions in biological materials is likely to enable precise adjustments of material properties to suit not only mechanical but biological functions as well.

节肢动物，尤其是蝎子经常使用金属离子来硬化它们的角质层。本研究分析了两种蝎子：半蝎（Centruroides platnicki， PS）和双心蝎（Nebo whitei， NS）毒刺的几丁质纤维排列、金属含量、分布和力学性能。结果表明，两种蝎子在毒刺角质层中含有相同的元素Zn、Mn和Ca，但在不同的位置。NS采用Zn离子作为表皮硬化剂，PS采用Mn/Ca离子作为表皮硬化剂。有趣的是，PS中也存在Zn离子，但对推力杆力学性能的增强没有影响。在生物材料中使用不同的金属离子可能使材料特性的精确调整不仅适合机械功能，也适合生物功能。

引用次数: 0

Structure and self-association of Arrestin-1 Arrestin-1的结构与自结合。

IF 3 3区生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of structural biology

Pub Date : 2025-01-27 DOI: 10.1016/j.jsb.2025.108173

David Salom , Krzysztof Palczewski

Arrestins halt cell signaling by binding to phosphorylated activated G protein-coupled receptors. Arrestin-1 binds to rhodopsin, arrestin-4 binds to cone opsins, and arrestins-2,3 bind to the rest of GPCRs. In addition, it has been reported that arrestin-1 is functionally expressed in mouse cone photoreceptors. The structural characterization of arrestins was spearheaded by the elucidation of the crystal structure of bovine arrestin-1. Further progress in arrestin structural biology showed that the general fold of the four vertebrate arrestin subtypes is conserved and that self-association seems to play important physiological roles. In solution, mammalian arrestin-1 has been proposed to exist in a species-dependent equilibrium between monomers, dimers, and tetramers, the activated monomer being the form that binds to photo-activated phosphorylated rhodopsin. However, the nature and function of the oligomers of the different arrestin subtypes are still under debate. This article reviews several structural aspects of arrestin-1 in light of two recent crystal structures of Xenopus arrestin-1, which have provided insights on the structure, self-association, activation, and evolution of arrestins in general, and of arrestin-1 in particular.

阻滞蛋白通过与磷酸化激活的G蛋白偶联受体结合而停止细胞信号传导。捕集蛋白1与视紫红质结合，捕集蛋白4与视锥蛋白结合，捕集蛋白2,3与其他gpcr结合。此外，有报道称在小鼠视锥细胞光感受器中有功能表达的arrestin-1。阻滞蛋白的结构表征是由阐明牛阻滞蛋白-1的晶体结构率先。拦阻蛋白结构生物学的进一步进展表明，四种脊椎动物拦阻蛋白亚型的一般折叠是保守的，并且自关联似乎起着重要的生理作用。在溶液中，哺乳动物的arrestin-1被认为存在于单体、二聚体和四聚体之间的物种依赖平衡中，被激活的单体是与光活化磷酸化视紫红质结合的形式。然而，不同抑制蛋白亚型的低聚物的性质和功能仍在争论中。本文结合Xenopus arrestin-1最近的两种晶体结构，综述了arrestin-1的几个结构方面，为arrestin-1的结构、自结合、激活和进化提供了一些见解。

{"title":"Structure and self-association of Arrestin-1","authors":"David Salom , Krzysztof Palczewski","doi":"10.1016/j.jsb.2025.108173","DOIUrl":"10.1016/j.jsb.2025.108173","url":null,"abstract":"<div><div>Arrestins halt cell signaling by binding to phosphorylated activated G protein-coupled receptors. Arrestin-1 binds to rhodopsin, arrestin-4 binds to cone opsins, and arrestins-2,3 bind to the rest of GPCRs. In addition, it has been reported that arrestin-1 is functionally expressed in mouse cone photoreceptors. The structural characterization of arrestins was spearheaded by the elucidation of the crystal structure of bovine arrestin-1. Further progress in arrestin structural biology showed that the general fold of the four vertebrate arrestin subtypes is conserved and that self-association seems to play important physiological roles. In solution, mammalian arrestin-1 has been proposed to exist in a species-dependent equilibrium between monomers, dimers, and tetramers, the activated monomer being the form that binds to photo-activated phosphorylated rhodopsin. However, the nature and function of the oligomers of the different arrestin subtypes are still under debate. This article reviews several structural aspects of arrestin-1 in light of two recent crystal structures of <em>Xenopus</em> arrestin-1, which have provided insights on the structure, self-association, activation, and evolution of arrestins in general, and of arrestin-1 in particular.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"217 1","pages":"Article 108173"},"PeriodicalIF":3.0,"publicationDate":"2025-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143066417","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}

引用次数: 0