Journal of structural biology最新文献_第2页

An inducible model for medial calcification based on matrix Gla protein deficiency 基于基质 Gla 蛋白缺乏症的内侧钙化诱导模型。

IF 3 3区生物学

Journal of structural biology Pub Date : 2024-10-24 DOI: 10.1016/j.jsb.2024.108144

Kyoungmi Bak , Abhinav Parashar , Raphaela Allgayer , Juliana Marulanda , Ophélie Gourgas , Marta Cerruti , Monzur Murshed

{"title":"An inducible model for medial calcification based on matrix Gla protein deficiency","authors":"Kyoungmi Bak , Abhinav Parashar , Raphaela Allgayer , Juliana Marulanda , Ophélie Gourgas , Marta Cerruti , Monzur Murshed","doi":"10.1016/j.jsb.2024.108144","DOIUrl":"10.1016/j.jsb.2024.108144","url":null,"abstract":"<div><div>Calcific deposits in the arterial media have been associated with a number of metabolic and genetic disorders including diabetes, chronic kidney disease and generalized arterial calcification of infancy. The loss of matrix Gla protein (MGP) leads to medial elastic lamina calcification (elastocalcinosis) in both humans and animal models. While MGP-deficient (<em>Mgp<sup>-/-</sup></em>) mice have been used as a reliable model to study medial elastocalcinosis, these mice are difficult to maintain because of their fragility. Also, these mice are unsuitable for long-term calcification studies in relation to age and sex as most often they die prematurely. In order to circumvent these problems we generated <em>Mgp<sup>-/-</sup>;ApoE-FGF23</em> mice, which in addition to the ablation of <em>Mgp</em> alleles, carries a transgene expressing the phosphaturic hormone FGF23. Increased FGF23 levels in the circulation and ensuing hypophosphatemia in these mice lead to a complete prevention of medial calcification until late adulthood. Interestingly, upon feeding a high phosphorus diet for 10 days, we were able to induce medial calcification in 3-week-old <em>Mgp<sup>-/-</sup>;ApoE-FGF23</em> mice. Our mineral analyses showed that the Ca/P% in the calcific deposits in these mice were comparable to that of 5-week-old <em>Mgp<sup>-/-</sup></em> mice although the level of crystallinity differed. The aorta explants from <em>Mgp<sup>-/-</sup>;ApoE-FGF23</em> mice resulted in elastocalcinosis in the presence of 2 mM phosphate in the culture medium which was completely prevented by pyrophosphate analogue alendronate. <em>Mgp<sup>-/-</sup>;ApoE-FGF23</em> mice will be suitable for future in vivo or ex vivo studies examining the effects of age, sex and mineralization inhibitors on medial elastocalcinosis.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"216 4","pages":"Article 108144"},"PeriodicalIF":3.0,"publicationDate":"2024-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142502744","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

NMR residual dipolar couplings investigation in the topology of house dust mite Group V allergens 屋尘螨 V 组过敏原拓扑结构中的核磁共振残余偶极耦合研究。

IF 3 3区生物学

Journal of structural biology Pub Date : 2024-10-22 DOI: 10.1016/j.jsb.2024.108138

Mandar T. Naik , Nandita Naik , Camy C.-H. Kung , Tai-Huang Huang

引用次数: 0

Correlative Raman spectroscopy and electron microscopy identifies glycogen rich deposits correlated with local structural defects in long bones of type IV osteogenesis imperfecta patients 拉曼光谱和电子显微镜的相关研究发现，富含糖原的沉积物与 IV 型成骨不全症患者长骨的局部结构缺陷有关。

IF 3 3区生物学

Journal of structural biology Pub Date : 2024-10-22 DOI: 10.1016/j.jsb.2024.108142

R.H.M. Van der Meijden , M.H. Scholten , W.H. Nijhuis , R.J.B. Sakkers , N. Sommerdijk , A. Akiva

{"title":"Correlative Raman spectroscopy and electron microscopy identifies glycogen rich deposits correlated with local structural defects in long bones of type IV osteogenesis imperfecta patients","authors":"R.H.M. Van der Meijden , M.H. Scholten , W.H. Nijhuis , R.J.B. Sakkers , N. Sommerdijk , A. Akiva","doi":"10.1016/j.jsb.2024.108142","DOIUrl":"10.1016/j.jsb.2024.108142","url":null,"abstract":"<div><div>Osteogenesis imperfecta (OI) is a genetic bone disease occurring in approximately 1 in 10,000 births, usually as a result of genetic mutation. OI patients suffer from increased fracture risk and – depending on the severity of the disease – deformation of the limbs, which can even lead to perinatal death.</div><div>Despite extensive studies, the way in which the genetic mutation is translated into structural and compositional anomalies of the tissue is still an open question. Different observations have been reported, ranging from no structural (or chemical) differences to completely chaotic bone structure and composition.</div><div>Here, we investigated bone samples from two adolescent OI-IV patients, focusing on the bone structure and chemistry in naturally occurring fractures. The exposed fracture plane allows the investigation of the structure and composition of the weakest bone plane. We do so by combining scanning electron microscopy (SEM) imaging with chemical information from Raman microscopy.</div><div>The exposed fracture planes show different regions within the same tissue, displaying normal osteonal structures next to disorganized osteons and totally disordered structures, while the collagen mineralization in all cases is similar to that of a healthy bone.</div><div>In addition, we also detected significant amounts of depositions of glycogen-rich, organic, globules of 250–1000 nm in size. These depositions point to a role of cellular disfunction in the disorganization of the collagen in qualitative OI.</div><div>Overall, our results unite multiple, sometimes contradicting views from the literature on qualitative OI.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"216 4","pages":"Article 108142"},"PeriodicalIF":3.0,"publicationDate":"2024-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142502746","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

Bone strength and residual compressive stress in apatite crystals 骨强度和磷灰石晶体中的残余压应力

IF 3 3区生物学

Journal of structural biology Pub Date : 2024-10-22 DOI: 10.1016/j.jsb.2024.108141

Victoria Schemenz , Ernesto Scoppola , Paul Zaslansky , Peter Fratzl

引用次数: 0

Deletion within ameloblastin multitargeting domain reduces its interaction with artificial cell membrane 缺失母细胞蛋白多靶向结构域会降低其与人工细胞膜的相互作用。

IF 3 3区生物学

Journal of structural biology Pub Date : 2024-10-22 DOI: 10.1016/j.jsb.2024.108143

Natalie C. Kegulian, Janet Moradian-Oldak

{"title":"Deletion within ameloblastin multitargeting domain reduces its interaction with artificial cell membrane","authors":"Natalie C. Kegulian, Janet Moradian-Oldak","doi":"10.1016/j.jsb.2024.108143","DOIUrl":"10.1016/j.jsb.2024.108143","url":null,"abstract":"<div><div>In human, mutations in the gene encoding the enamel matrix protein ameloblastin (Ambn) have been identified in cases of <em>amelogenesis imperfecta</em>. In mouse models, perturbations in the <em>Ambn</em> gene have caused loss of enamel and dramatic disruptions in enamel-making ameloblast cell function. Critical roles for Ambn in ameloblast cell signaling and polarization as well as adhesion to the nascent enamel matrix have been supported. Recently, we have identified a multitargeting domain (MTD) in Ambn that interacts with cell membrane, with the majority enamel matrix protein amelogenin, and with itself. This domain includes an amphipathic helix (AH) motif that directly interacts with cell membrane. In this study, we analyzed the sequence of the MTD for evolutionary conservation and found high conservation among mammals within the MTD and particularly within the AH motif. We computationally predicted that the AH motif lost its hydrophobic moment upon deleting hydrophobic but not hydrophilic residues from the motif. Furthermore, we rationally designed peptides that encompassed the Ambn MTD and contained deletions of largely hydrophobic or hydrophilic stretches of residues. To assess their AH-forming and membrane-binding abilities, we combined those peptides with synthetic phospholipid membrane vesicles and performed circular dichroism, membrane leakage, and vesicle clearance measurements. Circular dichroism showed retention of α-helix formation in all peptides except the one with the largest deletion of eleven amino acids including seven that were hydrophobic. This same peptide variant failed to cause leakage or clearance of synthetic membranes, while smaller deletions yielded intermediate membrane interaction as measured by leakage and clearance assays. Our data revealed that deletion of key hydrophobic residues from the AH leads to the most dramatic loss of Ambn–membrane interaction. Pinpointing roles of residues within the MTD has important implications for the multifunctionality of Ambn.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"216 4","pages":"Article 108143"},"PeriodicalIF":3.0,"publicationDate":"2024-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142502747","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

On the role of the glycosylation of type I collagen in bone 关于 I 型胶原蛋白糖基化在骨骼中的作用。

IF 3 3区生物学

Journal of structural biology Pub Date : 2024-10-22 DOI: 10.1016/j.jsb.2024.108145

Luco Rutten , Elena Macías-Sánchez , Nico Sommerdijk

{"title":"On the role of the glycosylation of type I collagen in bone","authors":"Luco Rutten , Elena Macías-Sánchez , Nico Sommerdijk","doi":"10.1016/j.jsb.2024.108145","DOIUrl":"10.1016/j.jsb.2024.108145","url":null,"abstract":"<div><div>Glycan-protein interactions play a crucial role in biology, providing additional functions capable of inducing biochemical and cellular responses. In the extracellular matrix of bone, this type of interactions is ubiquitous. During the synthesis of the collagen molecule, glycans are post-translationally added to specific lysine residues through an enzymatically catalysed hydroxylation and subsequent glycosylation. During and after fibril assembly, proteoglycans are essential for maintaining tissue structure, porosity, and integrity. Glycosaminoglycans (GAGs), the carbohydrate chains attached to interstitial proteoglycans, are known to be involved in mineralization. They can attract and retain water, which is critical for the mechanical properties of bone. In addition, like other long-lived proteins, collagen is susceptible to glycation. Prolonged exposure of the amine group to glucose eventually leads to the formation of advanced glycation end-products (AGEs). Changes in the degree of glycosylation and glycation have been identified in bone pathologies such as osteogenesis imperfecta and diabetes and appear to be associated with a reduction in bone quality. However, how these changes affect mineralization is not well understood.</div><div>Based on the literature review, we hypothesize that the covalently attached carbohydrates may have a water-attracting function similar to that of GAGs, but at different lengths and timescales in the bone formation process. Glycosylation potentially increases the hydration around the collagen triple helix, leading to increased mineralization (hypermineralization) after water has been replaced by mineral. Meanwhile, glycation leads to the formation of crosslinking AGEs, which are associated with a decrease in hydration levels, reducing the mechanical properties of bone.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"216 4","pages":"Article 108145"},"PeriodicalIF":3.0,"publicationDate":"2024-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142502750","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

Introduction to the special issue on the 14th International conference on the chemistry and biology of mineralized tissues 第 14 届矿化组织化学与生物学国际会议特刊导言。

IF 3 3区生物学

Journal of structural biology Pub Date : 2024-10-22 DOI: 10.1016/j.jsb.2024.108146

Nico Sommerdijk, Bernhard Ganss, Mina Mina

引用次数: 0

Ice thickness control and measurement in the VitroJet for time-efficient single particle structure determination 在 VitroJet 中进行冰厚度控制和测量，以实现高效的单颗粒结构测定。

IF 3 3区生物学

Journal of structural biology Pub Date : 2024-10-20 DOI: 10.1016/j.jsb.2024.108139

Rene J.M. Henderikx , Maaike J.G. Schotman , Saba Shahzad , Simon A. Fromm , Daniel Mann , Julian Hennies , Thomas V. Heidler , Dariush Ashtiani , Wim J.H. Hagen , Roger J.M. Jeurissen , Simone Mattei , Peter J. Peters , Carsten Sachse , Bart W.A.M.M. Beulen

{"title":"Ice thickness control and measurement in the VitroJet for time-efficient single particle structure determination","authors":"Rene J.M. Henderikx , Maaike J.G. Schotman , Saba Shahzad , Simon A. Fromm , Daniel Mann , Julian Hennies , Thomas V. Heidler , Dariush Ashtiani , Wim J.H. Hagen , Roger J.M. Jeurissen , Simone Mattei , Peter J. Peters , Carsten Sachse , Bart W.A.M.M. Beulen","doi":"10.1016/j.jsb.2024.108139","DOIUrl":"10.1016/j.jsb.2024.108139","url":null,"abstract":"<div><div>Embedding biomolecules in vitreous ice of optimal thickness is critical for structure determination by cryo-electron microscopy. Ice thickness assessment and selection of suitable holes for data collection are currently part of time-consuming preparatory routines performed on expensive electron microscopes. To address this challenge, a routine has been developed to measure ice thickness during sample preparation using an optical camera integrated in the VitroJet. This method allows to estimate the ice thickness with an error below ±20 nm for ice layers in the range of 0–70 nm. Additionally, we characterized the influence of pin printing parameters and found that the median ice thickness can be reproduced with a standard deviation below ±11 nm for thicknesses up to 75 nm. Therefore, the ice thickness of buffer-suspended holes on an EM grid can be tuned and measured within the working range relevant for single particle cryo-EM. Single particle structures of apoferritin were determined at two distinct thicknesses of 30 nm and 70 nm. These reconstructions demonstrate the importance of ice thickness for time-efficient cryo-EM structure determination.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"216 4","pages":"Article 108139"},"PeriodicalIF":3.0,"publicationDate":"2024-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142468487","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

Common structural features in some of the sequentially distant neurotransmitter transporters N-termini 一些相距较远的神经递质转运体 N 端的共同结构特征。

IF 3 3区生物学

Journal of structural biology Pub Date : 2024-10-18 DOI: 10.1016/j.jsb.2024.108137

Martina Baliova, Frantisek Jursky

{"title":"Common structural features in some of the sequentially distant neurotransmitter transporters N-termini","authors":"Martina Baliova, Frantisek Jursky","doi":"10.1016/j.jsb.2024.108137","DOIUrl":"10.1016/j.jsb.2024.108137","url":null,"abstract":"<div><div>The N-terminal regions of SLC6 transporters are sequentially unrelated, and the majority of such transporters contain only relatively short peptide N-terminal extensions. Currently, it is not clear if a diversity of N-terminal sequences represents diverse functions among the transporters or if there are common functions hidden behind similar, as yet unidentified, structures. Using alignment of amino acid sequences with the hydropathy plot, disorder prediction, and calpain recognition sites, we show that common structural features among the N-termini of some transporters might exist.We previously showed that polymeric neurotransmitter transporter N-termini exhibit very similar profiles of dynamic, time-dependent 465-595-350-750 nm absorbance metachromasia in the Bradford assay. Here we report that under certain mild denaturing conditions, filamentous aggregation of glutathione S-transferase (GST) protein results in similar near-infrared metachromasia. This effect was eliminated by further GST protein denaturation and solubilization. The results suggest that aggregation of partially denatured GST stabilizes Coomassie dye docking sites, producing a near-infrared absorbance shift similar to that observed in the polymeric unstructured N-termini of transporters.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"216 4","pages":"Article 108137"},"PeriodicalIF":3.0,"publicationDate":"2024-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142468486","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

3D distribution of biomineral and chitin matrix in the stomatopod dactyl club by high energy XRD-CT 通过高能 XRD-CT 观察口足类双足俱乐部中生物矿物质和甲壳素基质的三维分布。

IF 3 3区生物学

Journal of structural biology Pub Date : 2024-10-09 DOI: 10.1016/j.jsb.2024.108136

Thorbjørn Erik Køppen Christensen , Maja Østergaard , Olof Gutowski , Ann-Christin Dippel , Henrik Birkedal

{"title":"3D distribution of biomineral and chitin matrix in the stomatopod dactyl club by high energy XRD-CT","authors":"Thorbjørn Erik Køppen Christensen , Maja Østergaard , Olof Gutowski , Ann-Christin Dippel , Henrik Birkedal","doi":"10.1016/j.jsb.2024.108136","DOIUrl":"10.1016/j.jsb.2024.108136","url":null,"abstract":"<div><div>Stomatopods are ferocious hunters that use weaponized appendages to strike down their pray. The clubs of species such as <em>Odontodactylus scyllarus</em> undergo tremendous forces, and in consequence they have intricate structures, consisting of hydroxyapatite, chitin, amorphous calcium phosphate and carbonate, and occasionally calcite. These materials are distributed differently across the four major zones of the dactyl club: the impact, periodic lateral and medial, and striated regions. While stomatopod clubs and their structure have been studied for a long time, studies have thus far been constrained to 2D mapping experiments with moderate resolution due to difficulties in preparing whole club thin sections, and absorption tomography that gives information on densities but not molecular length scales. To address this problem, and shed light on the structure of entire clubs, we herein used X-ray powder diffraction computed tomography (XRD-CT) using high energy X-rays at the P07 beamline of PETRA-III to allow penetrating the large samples whilst still obtaining high resolution information. This allowed mapping the 3D distribution of diffraction phases including the biomineral apatite and the semi-crystal chitin matrix. This showed that hydroxyapatite forms an envelope around the club, and that chitin forms 2D sheets in the periodic region of the club.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"216 4","pages":"Article 108136"},"PeriodicalIF":3.0,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142391446","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