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
{"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}
F.P. de Isidro-Gómez , J.L. Vilas , J.M. Carazo , C.O.S. Sorzano
{"title":"Automatic detection of alignment errors in cryo-electron tomography","authors":"F.P. de Isidro-Gómez , J.L. Vilas , J.M. Carazo , C.O.S. Sorzano","doi":"10.1016/j.jsb.2024.108153","DOIUrl":"10.1016/j.jsb.2024.108153","url":null,"abstract":"<div><div>Cryo-electron tomography is an imaging technique that allows the study of the three-dimensional structure of a wide range of biological samples, from entire cellular environments to purified specimens. This technique collects a series of images from different views of the specimen by tilting the sample stage in the microscope. Subsequently, this information is combined into a three-dimensional reconstruction. To obtain reliable representations of the specimen of study, it is mandatory to define the acquisition geometry accurately. This is achieved by aligning all tilt images to a standard reference scheme. Errors in this step introduce artifacts into the final reconstructed tomograms, leading to loss of resolution and making them unsuitable for detailed sample analysis. This publication presents algorithms for automatically assessing the alignment quality of the tilt series and their classification based on the residual errors provided by the alignment algorithms. If no alignment information is available, a set of algorithms for calculating the residual vectors focused on fiducial markers is also presented. This software is accessible as part of the Xmipp software package and the Scipion framework.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"217 1","pages":"Article 108153"},"PeriodicalIF":3.0,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142854631","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}
C. Sakr , P. Cook , M. Seiter , C. Hörweg , S. Žák , M. Cordill , M. Burghammer , M. Sztucki , H. Lichtenegger
{"title":"Different strategies towards strength: Unveiling the role of Zn vs Mn/Ca and chitin arrangement in scorpion stingers","authors":"C. Sakr , P. Cook , M. Seiter , C. Hörweg , S. Žák , M. Cordill , M. Burghammer , M. Sztucki , H. Lichtenegger","doi":"10.1016/j.jsb.2025.108174","DOIUrl":"10.1016/j.jsb.2025.108174","url":null,"abstract":"<div><div>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 <em>Centruroides platnicki</em> (PS) and the diplocentrid scorpion <em>Nebo whitei</em> (NS)<em>.</em> 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.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"217 1","pages":"Article 108174"},"PeriodicalIF":3.0,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143074895","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}
Kristina Vogel , Johanna Moeller , Nina G. Bozhanova , Markus Voehler , Anja Penk , Jens Meiler , Clara T. Schoeder
{"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}
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":"2025-03-01","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}
{"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":"2025-03-01","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}
Ida de Vries , Athanassios Adamopoulos , Justina Kazokaitė-Adomaitienė, Tatjana Heidebrecht, Alex Fish, Patrick H.N. Celie, Robbie P. Joosten, Anastassis Perrakis
{"title":"JBP1 and JBP3 have conserved structures but different affinity to base-J","authors":"Ida de Vries , Athanassios Adamopoulos , Justina Kazokaitė-Adomaitienė, Tatjana Heidebrecht, Alex Fish, Patrick H.N. Celie, Robbie P. Joosten, Anastassis Perrakis","doi":"10.1016/j.jsb.2024.108161","DOIUrl":"10.1016/j.jsb.2024.108161","url":null,"abstract":"<div><div>Base-J (β-D-glucopyranosyloxymethyluracil) is an unusual kinetoplastid-specific DNA modification, recognized by base-J containing DNA (J-DNA) binding proteins JBP1 and JBP3. Recognition of J-DNA by both JBP1 and JBP3 takes place by a conserved J-DNA binding domain (JDBD). Here we show that JDBD-JBP3 has about 1,000-fold weaker affinity to base-J than JDBD-JBP1 and discriminates between J-DNA and unmodified DNA with a factor ∼5, whereas JDBD-JBP1 discriminates with a factor ∼10,000. Comparison of the crystal structures of JDBD-JBP3 we present here, with that of the previously characterized JDBD-JBP1, shows a flexible α5-helix that lacks a positively charged patch in JBP3. Mutations removing this positive charge in JDBD-JBP1, resulted in decreased binding affinity relative to wild-type JDBD-JBP1, indicating this patch is involved in DNA binding. We suggest that the α5-helix might rearrange upon JBP1 binding to J-DNA stabilizing the complex. This work contributes to our understanding of how JBPs bind to this unique DNA modification, which may contribute to identifying potential drug targets to end the base-J dependent parasite life cycle.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"217 1","pages":"Article 108161"},"PeriodicalIF":3.0,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142823909","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}
{"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":"2025-03-01","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}
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":"2025-03-01","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}
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":"2025-03-01","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}