Journal of structural biology最新文献

Cryo-iCLEM: Cryo correlative light and electron microscopy with immersion objectives.

IF 3 3区生物学

Journal of structural biology Pub Date : 2025-02-17 DOI: 10.1016/j.jsb.2025.108179

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

{"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":"https://doi.org/10.1016/j.jsb.2025.108179","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":" ","pages":"108179"},"PeriodicalIF":3.0,"publicationDate":"2025-02-17","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":"","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

IF 3 3区生物学

Journal of structural biology Pub Date : 2025-02-01 DOI: 10.1016/j.jsb.2025.108175

Mahdiyeh Mostafavi , Leila Hassani , Maryam Khoshkam

{"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

Structure and self-association of Arrestin-1

IF 3 3区生物学

Journal of structural biology Pub Date : 2025-01-27 DOI: 10.1016/j.jsb.2025.108173

David Salom , Krzysztof Palczewski

{"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

Outlier removal in cryo-EM via radial profiles

IF 3 3区生物学

Journal of structural biology Pub Date : 2025-01-27 DOI: 10.1016/j.jsb.2025.108172

Lev Kapnulin , Ayelet Heimowitz , Nir Sharon

引用次数: 0

GCTransNet: 3D mitochondrial instance segmentation based on Global Context Vision Transformers

IF 3 3区生物学

Journal of structural biology Pub Date : 2025-01-20 DOI: 10.1016/j.jsb.2025.108170

Chaoyi Chen , Yidan Yan , Jingpeng Wu , Wen-Biao Gan

{"title":"GCTransNet: 3D mitochondrial instance segmentation based on Global Context Vision Transformers","authors":"Chaoyi Chen , Yidan Yan , Jingpeng Wu , Wen-Biao Gan","doi":"10.1016/j.jsb.2025.108170","DOIUrl":"10.1016/j.jsb.2025.108170","url":null,"abstract":"<div><div>Mitochondria are double membrane-bound organelles essential for generating energy in eukaryotic cells. Mitochondria can be readily visualized in 3D using Volume Electron Microscopy (vEM), and accurate image segmentation is vital for quantitative analysis of mitochondrial morphology and function. To address the challenge of segmenting small mitochondrial compartments in vEM images, we propose an automated mitochondrial segmentation method called GCTransNet. This method employs grayscale migration technology to preprocess images, effectively reducing intensity distribution differences across EM images. By utilizing 3D Global Context Vision Transformers (GC-ViT) combined with global context self-attention modules and local self-attention modules, GCTransNet precisely models long-range and short-range spatial interactions. The long-range interactions enable the model to capture the global structural relationships within the mitochondrial segmentation network, while the short-range interactions refine local details and boundaries. In our approach, the encoder of the 3D U-Net network, a classical multi-scale learning architecture that retains high-resolution features through skip connections and combines multi-scale features for precise segmentation, is replaced by a 3D GC-ViT. The GC-ViT leverages shifted window-based self-attention, capturing long-range dependencies and offering improved segmentation accuracy compared to traditional U-Net encoders. In the MitoEM mitochondrial segmentation challenge, GCTransNet achieved state-of-the-art results, demonstrating its superiority in automated mitochondrial segmentation. The code and its documentation are publicly available at <span><span>https://github.com/GanLab123/GCTransNet</span><svg><path></path></svg></span>.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"217 1","pages":"Article 108170"},"PeriodicalIF":3.0,"publicationDate":"2025-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143023913","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

Inter-Domain interactions Slow BoNT/A’s onset of action 域间相互作用减缓BoNT/A的开始行动。

IF 3 3区生物学

Journal of structural biology Pub Date : 2025-01-19 DOI: 10.1016/j.jsb.2025.108171

C.J. Lalaurie , M. Zloh , D.R. Higazi , K.A. Bunting , P.A. Dalby

{"title":"Inter-Domain interactions Slow BoNT/A’s onset of action","authors":"C.J. Lalaurie , M. Zloh , D.R. Higazi , K.A. Bunting , P.A. Dalby","doi":"10.1016/j.jsb.2025.108171","DOIUrl":"10.1016/j.jsb.2025.108171","url":null,"abstract":"<div><div>Despite sharing ∼ 43 % sequence identity and structurally similar individual domains, botulinum neurotoxin (BoNT) serotypes A and E have differences in their properties and domain positioning. BoNT/E has a faster onset of action than BoNT/A. This difference is proposed to be due to conformational differences between BoNT/E and the other BoNT serotypes. Where most serotypes have the light chain (LC) and binding domain (BD) on opposite sides of the translocation domain (TD), BoNT/E forms a more compact shape with direct interactions between residues of the LC and BD. To elucidate the structural basis for the different properties of BoNT/A and BoNT/E, biophysical studies including molecular dynamic (MD) simulations, circular dichroism (CD) and small-angle X-ray scattering (SAXS) were applied to BoNT/A, for comparison against previous work on BoNT/E.</div><div>MD simulationsat six pH values across the toxin’s activation barrier (pH ∼ 5.5), followed by one extra repeat for the pH values below 5.5, revealed a rare event at pH 5 and 5.5 where interactions between a previously identified switch region of BoNT/Aand the BD were lost.This hintedat an increased freedom of movement, thus allowing the region to change from α-helical to a β-hairpin. In good agreement with previous work, CD showed a gradual and small loss of helicity as the pH decreased below pH 5.5, stabilising at pH 4.5. Combined with the relative scarcity of structural changes observed by MD in the switch region required for activity, these results may explain the slower onset of action for BoNT/A compared to BoNT/E.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"217 1","pages":"Article 108171"},"PeriodicalIF":3.0,"publicationDate":"2025-01-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143007389","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

Off-axis electron holography of unstained bacteriophages: Towards electrostatic potential measurement of biological samples 未染色噬菌体的离轴电子全息术：生物样品的静电电位测量。

IF 3 3区生物学

Journal of structural biology Pub Date : 2025-01-14 DOI: 10.1016/j.jsb.2025.108169

Elio Karim , Christophe Gatel , Amélie Leforestier , Stéphanie Balor , Vanessa Soldan , Célia Plisson-Chastang , Pierre-Emmanuel Gleizes , Etienne Snoeck

{"title":"Off-axis electron holography of unstained bacteriophages: Towards electrostatic potential measurement of biological samples","authors":"Elio Karim , Christophe Gatel , Amélie Leforestier , Stéphanie Balor , Vanessa Soldan , Célia Plisson-Chastang , Pierre-Emmanuel Gleizes , Etienne Snoeck","doi":"10.1016/j.jsb.2025.108169","DOIUrl":"10.1016/j.jsb.2025.108169","url":null,"abstract":"<div><div>Transmission electron microscopy, especially at cryogenic temperature, is largely used for studying biological macromolecular complexes. A main difficulty of TEM imaging of biological samples is the weak amplitude contrasts due to electron diffusion on light elements that compose biological organisms. Achieving high-resolution reconstructions implies therefore the acquisition of a huge number of TEM micrographs followed by a time-consuming image analysis. This TEM constraint could be overcome by extracting the phase shift of the electron beam having interacted with a “low contrast” sample. This can be achieved by off-axis electron holography, an electron interferometric technique used in material science, but rarely in biology due to lack of sensitivity. Here, we took advantage of recent technological advances on a dedicated 300 keV TEM to re-evaluate the performance of off-axis holography on unstained T4 and T5 bacteriophages at room temperature and in cryogenic conditions. Our results demonstrate an improvement in contrast and signal-to-noise ratio at both temperatures compared to bright field TEM images, with some limitations in spatial resolution. In addition, we show that the electron beam phase shift gives information on charge variations, paving the way to electrostatic potential studies of biological objects at the nanometer scale.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"217 1","pages":"Article 108169"},"PeriodicalIF":3.0,"publicationDate":"2025-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143007383","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

RosettaHDX: Predicting antibody-antigen interaction from hydrogen-deuterium exchange mass spectrometry data RosettaHDX：从氢-氘交换质谱数据预测抗体-抗原相互作用。

IF 3 3区生物学

Journal of structural biology Pub Date : 2025-01-05 DOI: 10.1016/j.jsb.2025.108166

Minh H. Tran , Cristina E. Martina , Rocco Moretti , Marcus Nagel , Kevin L. Schey , Jens Meiler

{"title":"RosettaHDX: Predicting antibody-antigen interaction from hydrogen-deuterium exchange mass spectrometry data","authors":"Minh H. Tran , Cristina E. Martina , Rocco Moretti , Marcus Nagel , Kevin L. Schey , Jens Meiler","doi":"10.1016/j.jsb.2025.108166","DOIUrl":"10.1016/j.jsb.2025.108166","url":null,"abstract":"<div><div>High-throughput characterization of antibody-antigen complexes at the atomic level is critical for understanding antibody function and enabling therapeutic development. Hydrogen-deuterium exchange mass spectrometry (HDX-MS) enables rapid epitope mapping, but its data are too sparse for independent structure determination. In this study, we introduce RosettaHDX, a hybrid method that combines computational docking with differential HDX-MS data to enhance the accuracy of antibody-antigen complex models beyond what either method can achieve individually. By incorporating HDX data as both distance restraints and a scoring term in the RosettaDock algorithm, RosettaHDX successfully generated near-native models (interface root-mean square deviation ≤ 4 Å) for all 9 benchmark complexes examined, averaging 3.6 times more near-native models than Rosetta alone. Near-native models among the top 10 scoring were identified in 3/9 cases, compared to 1/9 with Rosetta alone. Additionally, we developed a predictive metric based on docking results with HDX restraints to identify allosteric peptides in HDX datasets.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"217 1","pages":"Article 108166"},"PeriodicalIF":3.0,"publicationDate":"2025-01-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143007386","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

Phylogenetic analysis and homology modelling of a new Cry8A crystal protein expressed in a sporulating soil bacterium 一种新的Cry8A晶体蛋白在产孢土壤细菌中表达的系统发育分析和同源性建模。

IF 3 3区生物学

Journal of structural biology Pub Date : 2025-01-05 DOI: 10.1016/j.jsb.2025.108167

José D. Antonino , Shalini Chaudhary , Mark Lubberts , Brendan J. McConkey , Camilla A.S. Valença , Marcus V. de Aragão Batista , Patricia Severino , Marcelo da Costa Mendonça , Eliana B. Souto , Silvio S. Dolabella , Sona Jain

{"title":"Phylogenetic analysis and homology modelling of a new Cry8A crystal protein expressed in a sporulating soil bacterium","authors":"José D. Antonino , Shalini Chaudhary , Mark Lubberts , Brendan J. McConkey , Camilla A.S. Valença , Marcus V. de Aragão Batista , Patricia Severino , Marcelo da Costa Mendonça , Eliana B. Souto , Silvio S. Dolabella , Sona Jain","doi":"10.1016/j.jsb.2025.108167","DOIUrl":"10.1016/j.jsb.2025.108167","url":null,"abstract":"<div><div>Cry proteins, commonly found in Gram-positive soil bacteria, are used worldwide as aerial sprays or in transgenic plants for controlling crop pest populations and insect vectors<em>.</em> Via PCR analysis, a spore producing soil isolate (BV5) was speculated to encode a Cry gene. Partial nucleotide sequence of the amplified PCR fragment showed homology with the Cry8 genes present in GenBank. A full-length Cry gene was cloned, and the predicted protein sequence grouped the newly isolated Cry protein with other Cry8A present in GenBank with a high possibility of it being a new Cry8. SDS-PAGE and MALDI-TOF mass spectrometry confirmed the expression of a single 135 KDa protein matching uniquely to the putative protein sequence of the BV5 Cry gene. However, bioassay against the coleopteran <em>Anthonomus grandis</em> (Coleopterans are a known Cry8A target), showed no activity. Phylogenetic analysis and homology modelling was performed to characterize the protein structure and function. These analyses suggest a series of mutations in one of the variable loops on the surface of the protein.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"217 1","pages":"Article 108167"},"PeriodicalIF":3.0,"publicationDate":"2025-01-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142971462","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

Modelling components of nacre structure in silico: Interactions of a nacre peptide with chitin and an aragonite surface 用硅模拟珍珠层结构的组成部分：珍珠层肽与几丁质和文石表面的相互作用。

IF 3 3区生物学

Journal of structural biology Pub Date : 2024-12-26 DOI: 10.1016/j.jsb.2024.108165

Elena Macias-Sánchez , Yumeida Meruvia-Rojas , Julyan H.E. Cartwright , Antonio G. Checa , C.Ignacio Sainz-Díaz

{"title":"Modelling components of nacre structure in silico: Interactions of a nacre peptide with chitin and an aragonite surface","authors":"Elena Macias-Sánchez , Yumeida Meruvia-Rojas , Julyan H.E. Cartwright , Antonio G. Checa , C.Ignacio Sainz-Díaz","doi":"10.1016/j.jsb.2024.108165","DOIUrl":"10.1016/j.jsb.2024.108165","url":null,"abstract":"<div><div>The nacre formation process is a fascinating phenomenon involving mineral phase transformations, self-assembly processes, and protein–mineral interactions, resulting in a hierarchical structure that exhibits outstanding mechanical properties. However, this process is only partially known, and many aspects of nacre structure are not well understood, especially at the molecular scale. To understand the interplay between components—aragonite, protein and chitin—of the structure of nacre observed experimentally, we investigate the interactions of a peptide that is part of the protein lustrin A, identified in the nacreous layer of the shell of the abalone <em>Haliotis rufescens</em>, with the (001) crystal surface of aragonite and the chitin molecule. We report the results of atomistic molecular-modelling calculations and molecular-dynamics simulations of the peptide interacting with both the aragonite surface and the chitin polymer. The peptide shows an energetically favourable binding to the aragonite surface. The interaction of the carboxylic groups of the glutamic unit with the crystalline surface is essential to reproduce the characteristic elastomeric properties of this peptide in nacre.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"217 1","pages":"Article 108165"},"PeriodicalIF":3.0,"publicationDate":"2024-12-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142895584","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