Pub Date : 2026-01-11DOI: 10.1016/j.jsb.2026.108290
Kanda M Borgognoni, Bradley F Guilliams, Zachary J Butz, Christopher J Ackerson
Cloneable contrast in biological microscopy is exemplified by Green Fluorescent Protein (GFP) in fluorescence microscopy. There are no similarly useful cloneable contrast agents that function in biological electron microscopy. This paper reports a cloneable Selenium NanoParticle (cSeNP) that produces molecular contrast in imaging modalities including cellular electron microscopy, fluorescence microscopy, and X-ray computed tomography. This set of imaging modalities can image all biologically relevant length scales, from subcellular structure to whole organisms. The cSeNP is a ∼5 nm diameter Selenium nanoparticle that is made and conjugated by a protein. Because the cSeNP is electron dense compared to biological molecules, it has high contrast in biological electron microscopy. DNA encoding the cSeNP protein was concatenated to DNA encoding FtsZ, the procaryotic analog of tubulin. FtsZ is membrane associated throughout the cell cycle and localizes to the cleavage furrow of dividing cells. Escherichia coli cells expressing FtsZ-cSeNP fusion proteins were examined by transmission electron tomography and fluorescence light microscopy. These experiments show cSeNP decorated FtsZ filaments and/or cSeNPs in locations that correlate to known FtsZ locations, with less than 5% of cSeNPs in unexpected locations. X-ray imaging shows contrast attributable to cSeNPs is distinguishable from background in E. coli. The cSeNP, therefore, represents a cloneable imaging contrast agent that facilitates location and correlation of proteins-of-interest across all biological length scales. This is especially useful in biological electron microscopy, where larger-area imaging modalities such as fluorescence microscopy are employed to identify sub-areas containing a protein-of-interest to prepare for electron microscopy study.
{"title":"Cloneable contrast across all biological length scales.","authors":"Kanda M Borgognoni, Bradley F Guilliams, Zachary J Butz, Christopher J Ackerson","doi":"10.1016/j.jsb.2026.108290","DOIUrl":"https://doi.org/10.1016/j.jsb.2026.108290","url":null,"abstract":"<p><p>Cloneable contrast in biological microscopy is exemplified by Green Fluorescent Protein (GFP) in fluorescence microscopy. There are no similarly useful cloneable contrast agents that function in biological electron microscopy. This paper reports a cloneable Selenium NanoParticle (cSeNP) that produces molecular contrast in imaging modalities including cellular electron microscopy, fluorescence microscopy, and X-ray computed tomography. This set of imaging modalities can image all biologically relevant length scales, from subcellular structure to whole organisms. The cSeNP is a ∼5 nm diameter Selenium nanoparticle that is made and conjugated by a protein. Because the cSeNP is electron dense compared to biological molecules, it has high contrast in biological electron microscopy. DNA encoding the cSeNP protein was concatenated to DNA encoding FtsZ, the procaryotic analog of tubulin. FtsZ is membrane associated throughout the cell cycle and localizes to the cleavage furrow of dividing cells. Escherichia coli cells expressing FtsZ-cSeNP fusion proteins were examined by transmission electron tomography and fluorescence light microscopy. These experiments show cSeNP decorated FtsZ filaments and/or cSeNPs in locations that correlate to known FtsZ locations, with less than 5% of cSeNPs in unexpected locations. X-ray imaging shows contrast attributable to cSeNPs is distinguishable from background in E. coli. The cSeNP, therefore, represents a cloneable imaging contrast agent that facilitates location and correlation of proteins-of-interest across all biological length scales. This is especially useful in biological electron microscopy, where larger-area imaging modalities such as fluorescence microscopy are employed to identify sub-areas containing a protein-of-interest to prepare for electron microscopy study.</p>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":" ","pages":"108290"},"PeriodicalIF":2.7,"publicationDate":"2026-01-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145966383","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 : 2026-01-08DOI: 10.1016/j.jsb.2026.108289
Pierre-Yves Collart-Dutilleul , T. Cloitre , D. Carayon , A. Slimani , H. Salehi , H. Tassery , F. Cuisinier , A. Desoutter
The dentin–enamel junction (DEJ) plays a critical role in tooth biomechanics, acting as a tough, crack-deflecting interface between the brittle enamel and the more resilient dentin. Although previous studies have described the DEJ using histology and electron microscopy techniques, the three-dimensional (3D) distribution and structural heterogeneity of scallop patterns along the DEJ remain poorly understood. Here, we combined high-resolution X-ray microcomputed tomography (µCT) with multiphoton microscopy (MPM) to investigate scallop morphology, spatial distribution, and collagen fiber organization across human teeth.
Non-carious human teeth (n = 35) were scanned at 5 µm resolution, allowing 3D reconstruction of the DEJ surface. Scallop size, distribution, and root mean square (RMS) roughness were quantified across mesial, distal, buccal, and lingual faces of incisors, canines, premolars, and molars. MPM with second harmonic generation (SHG) provided complementary imaging of collagen fiber presence within scallop structures.
Scallop size depended primarily on location but also on tooth type: the largest scallops (>150 µm) were concentrated on mesial and distal faces at interproximal contact areas, while molars lacked large scallops entirely. RMS roughness confirmed significant topographic heterogeneity between regions. SHG imaging showed high collagen density at scallop peaks.
These findings provide the first whole-tooth 3D mapping of scallop patterns, supporting the hypothesis that scalloped DEJ structures enhance crack resistance and mechanical resilience. Further studies using higher-resolution imaging and comparative models across species may clarify the developmental and functional origins of these unique microstructures.
{"title":"Distribution and size of scallop patterns at the human dentin enamel junction revealed with micro tomography","authors":"Pierre-Yves Collart-Dutilleul , T. Cloitre , D. Carayon , A. Slimani , H. Salehi , H. Tassery , F. Cuisinier , A. Desoutter","doi":"10.1016/j.jsb.2026.108289","DOIUrl":"10.1016/j.jsb.2026.108289","url":null,"abstract":"<div><div>The dentin–enamel junction (DEJ) plays a critical role in tooth biomechanics, acting as a tough, crack-deflecting interface between the brittle enamel and the more resilient dentin. Although previous studies have described the DEJ using histology and electron microscopy techniques, the three-dimensional (3D) distribution and structural heterogeneity of scallop patterns along the DEJ remain poorly understood. Here, we combined high-resolution X-ray microcomputed tomography (µCT) with multiphoton microscopy (MPM) to investigate scallop morphology, spatial distribution, and collagen fiber organization across human teeth.</div><div>Non-carious human teeth (n = 35) were scanned at 5 µm resolution, allowing 3D reconstruction of the DEJ surface. Scallop size, distribution, and root mean square (RMS) roughness were quantified across mesial, distal, buccal, and lingual faces of incisors, canines, premolars, and molars. MPM with second harmonic generation (SHG) provided complementary imaging of collagen fiber presence within scallop structures.</div><div>Scallop size depended primarily on location but also on tooth type: the largest scallops (>150 µm) were concentrated on mesial and distal faces at interproximal contact areas, while molars lacked large scallops entirely. RMS roughness confirmed significant topographic heterogeneity between regions. SHG imaging showed high collagen density at scallop peaks.</div><div>These findings provide the first whole-tooth 3D mapping of scallop patterns, supporting the hypothesis that scalloped DEJ structures enhance crack resistance and mechanical resilience. Further studies using higher-resolution imaging and comparative models across species may clarify the developmental and functional origins of these unique microstructures.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"218 1","pages":"Article 108289"},"PeriodicalIF":2.7,"publicationDate":"2026-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145939562","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 : 2026-01-08DOI: 10.1016/j.jsb.2026.108291
Arun Yadav , Anshu Singh , Aneesh Deshmukh , Pushkar Bharadwaj , Anuj Baliyan , Kate White , Jitin Singla
Mitochondrial morphology is central to cellular function, yet large-scale quantification is limited by the lack of high-resolution whole-cell imaging and efficient segmentation tools. Soft X-ray tomography (SXT) provides native-state 3D whole-cells images, but organelle segmentation remains a bottleneck. We present MitoXRNet, a data- and parameter-efficient 3D deep learning model for mitochondria and nucleus segmentation in SXT tomograms. Using multi-axis 3D slicing, Sobel filter-based boundary enhancement, and a combined Binary-Cross-Entropy and Robust-Dice loss, MitoXRNet achieves a 73.8% Dice score on INS-1E cells with only 1.4 M parameters, outperforming existing methods. A larger 22.6 M variant generalized well to unseen data. Automated segmentation enabled quantitative analysis of mitochondrial remodeling under metabolic stimuli: glucose increased mitochondrial volume and matrix density, while GIP and GKA increased mitochondria number, reduced volume, and elevated density, indicating smaller, denser, more dynamic populations. MitoXRNet provides a scalable framework for high-throughput morphological and biophysical profiling of organelles in native-state SXT data.
{"title":"Robust mitochondria segmentation and morphological profiling using soft X-ray tomography","authors":"Arun Yadav , Anshu Singh , Aneesh Deshmukh , Pushkar Bharadwaj , Anuj Baliyan , Kate White , Jitin Singla","doi":"10.1016/j.jsb.2026.108291","DOIUrl":"10.1016/j.jsb.2026.108291","url":null,"abstract":"<div><div>Mitochondrial morphology is central to cellular function, yet large-scale quantification is limited by the lack of high-resolution whole-cell imaging and efficient segmentation tools. Soft X-ray tomography (SXT) provides native-state 3D whole-cells images, but organelle segmentation remains a bottleneck. We present MitoXRNet, a data- and parameter-efficient 3D deep learning model for mitochondria and nucleus segmentation in SXT tomograms. Using multi-axis 3D slicing, Sobel filter-based boundary enhancement, and a combined Binary-Cross-Entropy and Robust-Dice loss, MitoXRNet achieves a 73.8% Dice score on INS-1E cells with only 1.4 M parameters, outperforming existing methods. A larger 22.6 M variant generalized well to unseen data. Automated segmentation enabled quantitative analysis of mitochondrial remodeling under metabolic stimuli: glucose increased mitochondrial volume and matrix density, while GIP and GKA increased mitochondria number, reduced volume, and elevated density, indicating smaller, denser, more dynamic populations. MitoXRNet provides a scalable framework for high-throughput morphological and biophysical profiling of organelles in native-state SXT data.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"218 1","pages":"Article 108291"},"PeriodicalIF":2.7,"publicationDate":"2026-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145949009","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 : 2026-01-05DOI: 10.1016/j.jsb.2026.108285
George P Lisi
{"title":"Disorder, dynamics, and regulation of proteins and nucleic acids.","authors":"George P Lisi","doi":"10.1016/j.jsb.2026.108285","DOIUrl":"10.1016/j.jsb.2026.108285","url":null,"abstract":"","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":" ","pages":"108285"},"PeriodicalIF":2.7,"publicationDate":"2026-01-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145917846","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}
AstaPs are water-soluble, photooxidative stress-inducible astaxanthin (AXT)-binding proteins found only in Scenedesmaceae microalgae, where they play a central role in survival under severe photooxidative stress. Here, we focused on the unique function of AstaP-pink1, which converts orange AXT into a pink form and generates a UVA absorption spectrum upon protein binding. AstaP-pink1 was expressed in genetically engineered Escherichia coli strains capable of synthesizing AXT. The host strain harboring pAC-Asta produced adonixanthin, AXT, and zeaxanthin in an approximate ratio of 5:3:2, whereas the strain carrying pMF573 predominantly produced AXT (∼90 % of total carotenoid). Co-expression of the gene encoding AstaP-pink1 in these strains resulted in moderate and selective AXT binding, accompanied by a spectral red shift and UVA absorption, thereby generating pink coloration. Crystal structure analysis of AXT-bound recombinant AstaP-pink1 (rAstaP-pink1) revealed both similarities and differences in AXT binding compared with rAstaP-orange1. Density functional theory (DFT) calculations based on the crystal structure suggested that the larger red shift than that of AstaP-orange1 and the distinct UVA absorption are derived from the conformation of AXT that is compelled by binding to AstaP-pink1. This study suggests that AXT binding by AstaP-pink1 not only facilitates the water solubilization of AXT but also generates the observed spectral properties.
{"title":"Structural basis for spectral red shift and UVA absorption in the microalgal water-soluble astaxanthin-binding protein AstaP-pink1","authors":"Tamaki Mitsui , Yasuhito Shomura , Maiko Furubayashi , Ryuichi Kato , Shinichi Takaichi , Shinji Kawasaki","doi":"10.1016/j.jsb.2026.108288","DOIUrl":"10.1016/j.jsb.2026.108288","url":null,"abstract":"<div><div>AstaPs are water-soluble, photooxidative stress-inducible astaxanthin (AXT)-binding proteins found only in Scenedesmaceae microalgae, where they play a central role in survival under severe photooxidative stress. Here, we focused on the unique function of AstaP-pink1, which converts orange AXT into a pink form and generates a UVA absorption spectrum upon protein binding. AstaP-pink1 was expressed in genetically engineered <em>Escherichia coli</em> strains capable of synthesizing AXT. The host strain harboring pAC-Asta produced adonixanthin, AXT, and zeaxanthin in an approximate ratio of 5:3:2, whereas the strain carrying pMF573 predominantly produced AXT (∼90 % of total carotenoid). Co-expression of the gene encoding AstaP-pink1 in these strains resulted in moderate and selective AXT binding, accompanied by a spectral red shift and UVA absorption, thereby generating pink coloration. Crystal structure analysis of AXT-bound recombinant AstaP-pink1 (rAstaP-pink1) revealed both similarities and differences in AXT binding compared with rAstaP-orange1. Density functional theory (DFT) calculations based on the crystal structure suggested that the larger red shift than that of AstaP-orange1 and the distinct UVA absorption are derived from the conformation of AXT that is compelled by binding to AstaP-pink1. This study suggests that AXT binding by AstaP-pink1 not only facilitates the water solubilization of AXT but also generates the observed spectral properties.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"218 1","pages":"Article 108288"},"PeriodicalIF":2.7,"publicationDate":"2026-01-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145917910","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 : 2026-01-03DOI: 10.1016/j.jsb.2026.108287
Samina Kazi, Ezeogo Obaji, Johan Pääkkönen, Carlos Vela-Rodríguez, Bianca Sammer, Philomena Schmid, Albert Galera-Prat, Lari Lehtiö, Renata Prunskaite-Hyyryläinen
Studies in immortalized human mitotic cells demonstrated that MRN Complex Interacting Protein (MRNIP) plays a critical role in genome stability, replication fork protection, and the detection of DNA double-strand breaks via liquid-liquid phase separation. Our earlier work in mice identified its essential role in meiosis during spermatogenesis, namely, meiotic sex chromosome inactivation, highlighting its critical importance for male fertility. Apart from that, MRNIP is a poorly characterized protein with little to no data-based evidence of its biophysical and biochemical properties. In this study, we provide experimental evidence confirming that the N-terminal domain is indeed folded and contains a zinc-ribbon motif. We demonstrate that MRNIP binds a Zn2+ ion at this site, which plays a structural role in stabilizing the folded domain. Together with structural similarity observed across species, these findings support the conserved nature of the N-terminal domain of MRNIP. Our experimental data confirms that the C-terminal region is disordered. Furthermore, we show that both the N- and C-terminal regions exhibit binding specificity for DNA rather than RNA, under low-salt conditions, suggesting low-affinity interactions, whereas no DNA or RNA binding was observed under physiological salt conditions. Our findings provide insight into the biophysical and biochemical properties of MRNIP and offer a foundation for advancing structural and functional studies of MRNIP.
{"title":"Biophysical characterization of zinc and DNA binding properties of MRN complex interacting protein.","authors":"Samina Kazi, Ezeogo Obaji, Johan Pääkkönen, Carlos Vela-Rodríguez, Bianca Sammer, Philomena Schmid, Albert Galera-Prat, Lari Lehtiö, Renata Prunskaite-Hyyryläinen","doi":"10.1016/j.jsb.2026.108287","DOIUrl":"https://doi.org/10.1016/j.jsb.2026.108287","url":null,"abstract":"<p><p>Studies in immortalized human mitotic cells demonstrated that MRN Complex Interacting Protein (MRNIP) plays a critical role in genome stability, replication fork protection, and the detection of DNA double-strand breaks via liquid-liquid phase separation. Our earlier work in mice identified its essential role in meiosis during spermatogenesis, namely, meiotic sex chromosome inactivation, highlighting its critical importance for male fertility. Apart from that, MRNIP is a poorly characterized protein with little to no data-based evidence of its biophysical and biochemical properties. In this study, we provide experimental evidence confirming that the N-terminal domain is indeed folded and contains a zinc-ribbon motif. We demonstrate that MRNIP binds a Zn<sup>2+</sup> ion at this site, which plays a structural role in stabilizing the folded domain. Together with structural similarity observed across species, these findings support the conserved nature of the N-terminal domain of MRNIP. Our experimental data confirms that the C-terminal region is disordered. Furthermore, we show that both the N- and C-terminal regions exhibit binding specificity for DNA rather than RNA, under low-salt conditions, suggesting low-affinity interactions, whereas no DNA or RNA binding was observed under physiological salt conditions. Our findings provide insight into the biophysical and biochemical properties of MRNIP and offer a foundation for advancing structural and functional studies of MRNIP.</p>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":" ","pages":"108287"},"PeriodicalIF":2.7,"publicationDate":"2026-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145906240","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}
The advent of direct electron detectors (DEDs) has driven a major breakthrough in cryo-electron microscopy (cryo-EM), particularly in single-particle analysis (SPA), establishing DEDs as essential tools for achieving near-atomic resolution. In this study, we re-evaluated the performance of the TVIPS TemCam-XF416, an indirect scintillator-coupled CMOS camera (scintillator camera). Using a JEOL CRYOARM 300II, we performed SPA on two well-established benchmark specimens, β-galactosidase and apoferritin, at a 300 kV acceleration voltage. The resulting reconstructions reached resolutions of 2.6 Å and 2.1 Å, respectively. Notably, the apoferritin map clearly resolves the central holes of aromatic side chains—a level of detail previously considered exclusive to DEDs. These results were achieved by implementing the latest standard reconstruction workflows, including motion correction and contrast transfer function refinement, underscoring the critical role of computational methods in attaining high-resolution structures. While scintillator cameras inherently exhibit a lower signal-to-noise ratio than DEDs, our findings with XF416 demonstrate that, with appropriate data collection and processing, such cameras can deliver near-atomic resolution structures. This work establishes a crucial technical benchmark for the scintillator camera evaluated in this study on a high-end 300 kV cryo-EM platform, demonstrating its capability to achieve resolutions suitable for many structural biology applications and providing an updated perspective on its performance capabilities.
{"title":"High-Resolution single particle analysis using a scintillator camera XF416 on CRYOARM300II at 300 kV","authors":"Shinji Aramaki , Tomohito Tanihara , Yuya Yoshida , Naoya Matsunaga , Shigehiro Ohdo , Kouta Mayanagi","doi":"10.1016/j.jsb.2026.108286","DOIUrl":"10.1016/j.jsb.2026.108286","url":null,"abstract":"<div><div>The advent of direct electron detectors (DEDs) has driven a major breakthrough in cryo-electron microscopy (cryo-EM), particularly in single-particle analysis (SPA), establishing DEDs as essential tools for achieving near-atomic resolution. In this study, we re-evaluated the performance of the TVIPS TemCam-XF416, an indirect scintillator-coupled CMOS camera (scintillator camera). Using a JEOL CRYOARM 300II, we performed SPA on two well-established benchmark specimens, β-galactosidase and apoferritin, at a 300 kV acceleration voltage. The resulting reconstructions reached resolutions of 2.6 Å and 2.1 Å, respectively. Notably, the apoferritin map clearly resolves the central holes of aromatic side chains—a level of detail previously considered exclusive to DEDs. These results were achieved by implementing the latest standard reconstruction workflows, including motion correction and contrast transfer function refinement, underscoring the critical role of computational methods in attaining high-resolution structures. While scintillator cameras inherently exhibit a lower signal-to-noise ratio than DEDs, our findings with XF416 demonstrate that, with appropriate data collection and processing, such cameras can deliver near-atomic resolution structures. This work establishes a crucial technical benchmark for the scintillator camera evaluated in this study on a high-end 300 kV cryo-EM platform, demonstrating its capability to achieve resolutions suitable for many structural biology applications and providing an updated perspective on its performance capabilities.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"218 1","pages":"Article 108286"},"PeriodicalIF":2.7,"publicationDate":"2026-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145906274","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 : 2026-01-02DOI: 10.1016/j.jsb.2025.108284
Tayyaba Rabnawaz , Nathanael Leung , Leonard C. Nielsen , Robert A. Harper , Richard M. Shelton , Gabriel Landini , Tim Snow , Andy Smith , Nick Terrill , Marianne Liebi , Tan Sui
Dental caries, one of the most prevalent non-communicable diseases worldwide, is characterised by the progressive deterioration of the structure and mechanical properties of dental hard tissues. In human teeth, dentine is the most abundant mineralised tissue, forming the primary support material. To assess changes in the mechanical properties of dentine caused by dental caries and acid erosion, it is crucial to understand the relationship between organic and inorganic dentine components and their organisation into a 3D anisotropic structure at the nanoscale. Over the past 20 years, alterations in dentine structure caused by caries and artificial demineralisation have been reported using conventional microscopy techniques. However, due to the limited spatial resolution of these techniques, the 3D structural organisation including orientation and degree of alignment of mineralised collagen fibrils at the nanoscale, has not been fully explored. This study investigated alterations in the 3D structure of normal, carious and artificially demineralised dentine using SAXS tensor tomography (SASTT). This technique enabled the observation of differences in the local orientation of organic and inorganic components, as well as variations in local scattering intensity, resulting from natural caries and artificial demineralisation. In comparison to normal dentine, caries caused minor orientational differences of both components but had a major impact on the local X-ray scattering intensity. After artificial demineralisation of the dentine, most of the mineral was lost in the outer layers, resulting in a greater reduction in scattering intensity than that caused by caries.
Significance
The remarkable mechanical properties of human dentine arise from its complex hierarchical 3D structure. In this article, we have investigated the 3D structural alterations in dentine, caused by caries and artificial demineralisation. For this detailed investigation, SAXS tensor tomography (SASTT) has been implemented on the I22 beamline at Diamond Light Source, UK. SASTT is a technique that can probe the nanostructure of dentine, yielding orientation and degree of alignment of the mineralised collagen fibrils, while also providing a 3D reciprocal space map to investigate the detailed non-uniform scattering intensity distribution in all directions. The initial SASTT data provide insights into dentine structural alterations caused by caries and artificial demineralisation, facilitating further exploration of structure–mechanical property relationships, which may lead to improve the development of novel biomimetic materials for dental applications.
{"title":"Nanostructural evolution during carious and demineralisation process of human dentine using small angle X-ray scattering tensor tomography","authors":"Tayyaba Rabnawaz , Nathanael Leung , Leonard C. Nielsen , Robert A. Harper , Richard M. Shelton , Gabriel Landini , Tim Snow , Andy Smith , Nick Terrill , Marianne Liebi , Tan Sui","doi":"10.1016/j.jsb.2025.108284","DOIUrl":"10.1016/j.jsb.2025.108284","url":null,"abstract":"<div><div>Dental caries, one of the most prevalent non-communicable diseases worldwide, is characterised by the progressive deterioration of the structure and mechanical properties of dental hard tissues. In human teeth, dentine is the most abundant mineralised tissue, forming the primary support material. To assess changes in the mechanical properties of dentine caused by dental caries and acid erosion, it is crucial to understand the relationship between organic and inorganic dentine components and their organisation into a 3D anisotropic structure at the nanoscale. Over the past 20 years, alterations in dentine structure caused by caries and artificial demineralisation have been reported using conventional microscopy techniques. However, due to the limited spatial resolution of these techniques, the 3D structural organisation including orientation and degree of alignment of mineralised collagen fibrils at the nanoscale, has not been fully explored. This study investigated alterations in the 3D structure of normal, carious and artificially demineralised dentine using SAXS tensor tomography (SASTT). This technique enabled the observation of differences in the local orientation of organic and inorganic components, as well as variations in local scattering intensity, resulting from natural caries and artificial demineralisation. In comparison to normal dentine, caries caused minor orientational differences of both components but had a major impact on the local X-ray scattering intensity. After artificial demineralisation of the dentine, most of the mineral was lost in the outer layers, resulting in a greater reduction in scattering intensity than that caused by caries.</div></div><div><h3>Significance</h3><div>The remarkable mechanical properties of human dentine arise from its complex hierarchical 3D structure. In this article, we have investigated the 3D structural alterations in dentine, caused by caries and artificial demineralisation. For this detailed investigation, SAXS tensor tomography (SASTT) has been implemented on the I22 beamline at Diamond Light Source, UK. SASTT is a technique that can probe the nanostructure of dentine, yielding orientation and degree of alignment of the mineralised collagen fibrils, while also providing a 3D reciprocal space map to investigate the detailed non-uniform scattering intensity distribution in all directions. The initial SASTT data provide insights into dentine structural alterations caused by caries and artificial demineralisation, facilitating further exploration of structure–mechanical property relationships, which may lead to improve the development of novel biomimetic materials for dental applications.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"218 1","pages":"Article 108284"},"PeriodicalIF":2.7,"publicationDate":"2026-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145880745","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 : 2025-12-28DOI: 10.1016/j.jsb.2025.108283
Madhurima Khamaru, Debarshi Bose, Anwesha Deb, Devrani Mitra
The blue light photoreceptor cum transcription factors, aureochromes (Aureos), are present exclusively in photosynthetic stramenopiles. Co-existence of Light-Oxygen-Voltage (LOV) and basic leucine zipper (bZIP) is unique to Aureos – therefore ideal to study light-dependent DNA binding/transcriptional regulation. Further, Aureos’ inverse effector-sensor topology, resembling several sensory eukaryotic transcription factors, makes them prototypical optogenetic scaffolds. In absence of 3D data, this study aims for a thorough investigation of the bZIP domains from Aureos and others, and their interaction with substrate DNA using tools from sequence/structural bioinformatics, network theory, molecular dynamics simulation and in vitro experiments. An in-depth comparison of 173 Aureo/plant/opisthokont bZIPs reveals Aureos’ uniqueness and evolutionary significance in DNA binding specificity as well as dimer stability. An all-atom network analysis on representative bZIP-DNA co-crystal structures, especially the measurement of eigenvector centrality, further adds importance to hydrophobic interactions in the zipper region to stabilize bZIP dimer and facilitate DNA binding in Aureos and other bZIPs. The most notable finding is the unique presence of histidine at the basic region of Aureos unlike other bZIPs. Histidine not just promotes blue light independent substrate DNA-binding affinity but also serves as a potential switch point in Aureo/bZIP evolution.
{"title":"Decoding sequence-structure-function-evolution of basic leucine zippers of aureochromes from heterokont algae","authors":"Madhurima Khamaru, Debarshi Bose, Anwesha Deb, Devrani Mitra","doi":"10.1016/j.jsb.2025.108283","DOIUrl":"10.1016/j.jsb.2025.108283","url":null,"abstract":"<div><div>The blue light photoreceptor cum transcription factors, aureochromes (Aureos), are present exclusively in photosynthetic stramenopiles. Co-existence of Light-Oxygen-Voltage (LOV) and basic leucine zipper (bZIP) is unique to Aureos – therefore ideal to study light-dependent DNA binding/transcriptional regulation. Further, Aureos’ inverse effector-sensor topology, resembling several sensory eukaryotic transcription factors, makes them prototypical optogenetic scaffolds. In absence of 3D data, this study aims for a thorough investigation of the bZIP domains from Aureos and others, and their interaction with substrate DNA using tools from sequence/structural bioinformatics, network theory, molecular dynamics simulation and <em>in vitro</em> experiments. An in-depth comparison of 173 Aureo/plant/opisthokont bZIPs reveals Aureos’ uniqueness and evolutionary significance in DNA binding specificity as well as dimer stability. An all-atom network analysis on representative bZIP-DNA co-crystal structures, especially the measurement of eigenvector centrality, further adds importance to hydrophobic interactions in the zipper region to stabilize bZIP dimer and facilitate DNA binding in Aureos and other bZIPs. The most notable finding is the unique presence of histidine at the basic region of Aureos unlike other bZIPs. Histidine not just promotes blue light independent substrate DNA-binding affinity but also serves as a potential switch point in Aureo/bZIP evolution.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"218 1","pages":"Article 108283"},"PeriodicalIF":2.7,"publicationDate":"2025-12-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145862904","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 : 2025-12-26DOI: 10.1016/j.jsb.2025.108282
Magdalena Bejger , Piotr H. Małecki , Katarzyna Biniek-Antosiak, Wojciech Rypniewski
Studies of protein structure and stability have traditionally focused on individual domains, treating them as autonomous units, even though most proteins consist of multiple domains. This raises the question to what extent can multidomain proteins be considered as sums of their individual domains, and how neighboring domains influence one another. Chitinase Chi60 from the psychrophilic bacterium Moritella marina consists of four domains linked in sequence: a catalytic domain, two consecutive Ig-like domains, and a chitin-binding module. The modular architecture of this enzyme provides an opportunity to examine the structure and stability of a protein from which domains are systematically excised. A series of deletion mutants of the chitinase was designed and constructed, and their structures and thermal melting profiles were analyzed. The different domains exhibit distinct melting temperatures. The catalytic domain shows a complex melting profile. Each domain can fold and maintain its structural integrity when isolated, including the two tandem Ig-like domains that share sequence similarity. Although the interfaces between domains in this modular protein are small, it is still possible to detect the influence neighboring domains exert on one another. Some artificial combinations of domains are unstable and prone to degradation. This long, flexible molecule may be stabilized through dimerization when not engaged with the chitin substrate, with two of its domains participating in the interaction.
{"title":"Probing the structure and thermodynamics of a multidomain psychrophilic chitinase from Moritella marina","authors":"Magdalena Bejger , Piotr H. Małecki , Katarzyna Biniek-Antosiak, Wojciech Rypniewski","doi":"10.1016/j.jsb.2025.108282","DOIUrl":"10.1016/j.jsb.2025.108282","url":null,"abstract":"<div><div>Studies of protein structure and stability have traditionally focused on individual domains, treating them as autonomous units, even though most proteins consist of multiple domains. This raises the question to what extent can multidomain proteins be considered as sums of their individual domains, and how neighboring domains influence one another. Chitinase Chi60 from the psychrophilic bacterium <em>Moritella marina</em> consists of four domains linked in sequence: a catalytic domain, two consecutive Ig-like domains, and a chitin-binding module. The modular architecture of this enzyme provides an opportunity to examine the structure and stability of a protein from which domains are systematically excised. A series of deletion mutants of the chitinase was designed and constructed, and their structures and thermal melting profiles were analyzed. The different domains exhibit distinct melting temperatures. The catalytic domain shows a complex melting profile. Each domain can fold and maintain its structural integrity when isolated, including the two tandem Ig-like domains that share sequence similarity. Although the interfaces between domains in this modular protein are small, it is still possible to detect the influence neighboring domains exert on one another. Some artificial combinations of domains are unstable and prone to degradation. This long, flexible molecule may be stabilized through dimerization when not engaged with the chitin substrate, with two of its domains participating in the interaction.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"218 1","pages":"Article 108282"},"PeriodicalIF":2.7,"publicationDate":"2025-12-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145850248","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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