Journal of Structural Biology: X最新文献

Corrigendum to “Minimizing ice contamination during specimen preparation for cryo-soft X-ray tomography and cryo-electron tomography” [J. Struct. Biol.: X 10(2024) 100113] 对 "尽量减少低温软 X 射线断层成像和低温电子断层成像标本制备过程中的冰污染 "的更正[J. Struct.

IF 3.5

Journal of Structural Biology: X Pub Date : 2024-10-30 DOI: 10.1016/j.yjsbx.2024.100115

引用次数: 0

Structural analysis of the stable form of fibroblast growth factor 2 – FGF2-STAB 成纤维细胞生长因子 2（FGF2-STAB）稳定形式的结构分析

IF 3.5

Journal of Structural Biology: X Pub Date : 2024-10-24 DOI: 10.1016/j.yjsbx.2024.100112

{"title":"Structural analysis of the stable form of fibroblast growth factor 2 – FGF2-STAB","authors":"","doi":"10.1016/j.yjsbx.2024.100112","DOIUrl":"10.1016/j.yjsbx.2024.100112","url":null,"abstract":"<div><div>Fibroblast growth factor 2 (FGF2) is a signaling protein that plays a significant role in tissue development and repair. FGF2 binds to fibroblast growth factor receptors (FGFRs) alongside its co-factor heparin, which protects FGF2 from degradation. The binding between FGF2 and FGFRs induces intracellular signaling pathways such as RAS-MAPK, PI3K-AKT, and STAT. FGF2 has strong potential for application in cell culturing, wound healing, and cosmetics but the potential is severely limited by its low protein stability. The thermostable variant FGF2-STAB was constructed by computer-assisted protein engineering to overcome the natural limitation of FGF2. Previously reported characterization of FGF2-STAB revealed an enhanced ability to induce MAP/ERK signaling while having a lower dependence on heparin when compared with FGF2-wt. Here we report the crystal structure of FGF2-STAB solved at 1.3 Å resolution. Protein stabilization is achieved by newly formed hydrophobic interactions, polar contacts, and one additional hydrogen bond. The overall structure of FGF2-STAB is similar to FGF2-wt and does not reveal information on the experimentally observed lower dependence on heparin. A noticeable difference in flexibility in the receptor binding region can explain the differences in signaling between FGF2-STAB and its wild-type counterpart. Our structural analysis provided molecular insights into the stabilization and unique biological properties of FGF2-STAB.</div></div>","PeriodicalId":17238,"journal":{"name":"Journal of Structural Biology: X","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142531009","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Localization of albumin with correlative super resolution light- and electron microscopy in the kidney 利用相关超分辨率光镜和电子显微镜确定肾脏中白蛋白的位置

IF 3.5

Journal of Structural Biology: X Pub Date : 2024-10-21 DOI: 10.1016/j.yjsbx.2024.100114

{"title":"Localization of albumin with correlative super resolution light- and electron microscopy in the kidney","authors":"","doi":"10.1016/j.yjsbx.2024.100114","DOIUrl":"10.1016/j.yjsbx.2024.100114","url":null,"abstract":"<div><div>The functioning of vertebrate life relies on renal filtration of surplus fluid and elimination of low-molecular-weight waste products, while keeping serum proteins in the blood. In disease, however, there is leak of serum proteins and tracing them to identify the leaking position within tissue with a nanometer resolution poses a significant challenge. Correlative microscopy integrates the specificity of fluorescent protein labeling into high-resolution electron micrographs. Using chemical tagging of albumin with synthetic fluorophores we achieve protein-specific labeling that preserve their post-embedding fluorescence after high-pressure freezing and freeze-substitution of murine kidney tissue. Using advanced registration techniques for super-resolution correlative light and electron microscopy, we can localize the labeled albumin with a high precision in the x-y plane of electron micrographs and cartograph its distribution. Thereby we can quantify the albumin concentration and measure a linear reduction gradient across the kidney filtration barrier. Our study shows the feasibility of combining different microscopy contrasts for tracing fluorescently labeled protein markers with super resolution in various tissue samples and opens new perspectives for correlative imaging in volume electron microscopy.</div></div>","PeriodicalId":17238,"journal":{"name":"Journal of Structural Biology: X","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142538214","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Minimizing ice contamination during specimen preparation for cryo-soft X-ray tomography and cryo-electron tomography 尽量减少低温软 X 射线断层扫描和低温电子断层扫描标本制备过程中的冰污染

IF 3.5

Journal of Structural Biology: X Pub Date : 2024-10-18 DOI: 10.1016/j.yjsbx.2024.100113

{"title":"Minimizing ice contamination during specimen preparation for cryo-soft X-ray tomography and cryo-electron tomography","authors":"","doi":"10.1016/j.yjsbx.2024.100113","DOIUrl":"10.1016/j.yjsbx.2024.100113","url":null,"abstract":"<div><div>Cryo-soft X-ray tomography (cryo-SXT) is a newly developed technique for imaging 3D whole cells in nearly native states. Cryo-SXT users require the preparation of numerous cryo-sample grids to use the allocated beamtime to study cellular phenomena under various conditions. Therefore, it is important to promptly prepare cryo-sample grids as efficiently and carefully as possible to minimize ice contamination on the frozen sample grid. In this study, we designed a cryo-multi-grid-box storage system, which includes a shell, funnel holder, and multi-grid-box container. Our system not only increases the number of cryo-sample grids that can be temporarily stored but also reduces the frequency of cryo grid-box container transfers, thus decreasing the probability of forming ice on the grid. We have also applied this system to A549 cryo cell grid preparation. The correlative images from cryo-light microscopy and cryo-SXT showed that limited ice had formed on the grid when preparation was performed using our system. Additionally, 3D images of mitochondria with the lamellar shape of the cristae could be observed in our cryo-SXT results. Our cryo-multi-grid-box storage system can be used for cryo-SXT and cryo-electron tomography (cryo-ET) applications.</div></div>","PeriodicalId":17238,"journal":{"name":"Journal of Structural Biology: X","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142530489","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Assessment of submicron bone tissue composition in plastic-embedded samples using optical photothermal infrared (O-PTIR) spectral imaging and machine learning 利用光学光热红外（O-PTIR）光谱成像和机器学习评估塑料包埋样本中的亚微米骨组织成分

IF 3.5

Journal of Structural Biology: X Pub Date : 2024-10-09 DOI: 10.1016/j.yjsbx.2024.100111

{"title":"Assessment of submicron bone tissue composition in plastic-embedded samples using optical photothermal infrared (O-PTIR) spectral imaging and machine learning","authors":"","doi":"10.1016/j.yjsbx.2024.100111","DOIUrl":"10.1016/j.yjsbx.2024.100111","url":null,"abstract":"<div><div>Understanding the composition of bone tissue at the submicron level is crucial to elucidate factors contributing to bone disease and fragility. Here, we introduce a novel approach utilizing optical photothermal infrared (O-PTIR) spectroscopy and imaging coupled with machine learning analysis to assess bone tissue composition at 500 nm spatial resolution. This approach was used to evaluate thick bone samples embedded in typical poly(methyl methacrylate) (PMMA) blocks, eliminating the need for cumbersome thin sectioning. We demonstrate the utility of O-PTIR imaging to assess the distribution of bone tissue mineral and protein, as well as to explore the structure-composition relationship surrounding microporosity at a spatial resolution unattainable by conventional infrared imaging modalities. Using bone samples from wildtype (WT) mice and from a mouse model of osteogenesis imperfecta (OIM), we further showcase the application of O-PTIR spectroscopy to quantify mineral content, crystallinity, and carbonate content in spatially defined regions across the cortical bone. Notably, we show that machine learning analysis using support vector machine (SVM) was successful in identifying bone phenotypes (typical in WT, fragile in OIM) based on input of spectral data, with over 86 % of samples correctly identified when using the collagen spectral range. Our findings highlight the potential of O-PTIR spectroscopy and imaging as valuable tools for exploring bone submicron composition.</div></div>","PeriodicalId":17238,"journal":{"name":"Journal of Structural Biology: X","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142530909","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Conformational variability in the D2 loop of Plasmodium Apical Membrane antigen 1 疟原虫顶膜抗原 1 D2 环的构象变异性

IF 3.5

Journal of Structural Biology: X Pub Date : 2024-09-10 DOI: 10.1016/j.yjsbx.2024.100110

{"title":"Conformational variability in the D2 loop of Plasmodium Apical Membrane antigen 1","authors":"","doi":"10.1016/j.yjsbx.2024.100110","DOIUrl":"10.1016/j.yjsbx.2024.100110","url":null,"abstract":"<div><p>Apical Membrane Antigen 1 (AMA1) plays a vital role in the invasion of the host erythrocyte by the malaria parasite, <em>Plasmodium</em>. It is thus an important target for vaccine and anti-malaria therapeutic strategies that block the invasion process. AMA1, present on the surface of the parasite, interacts with RON2, a component of the parasite’s rhoptry neck (RON) protein complex, which is transferred to the erythrocyte membrane during invasion. The D2 loop of AMA1 plays an essential role in invasion as it partially covers the RON2-binding site and must therefore be displaced for invasion to proceed. Several structural studies have shown that the D2 loop is very mobile, a property that is probably important for the function of AMA1. Here we present three crystal structures of AMA1 from <em>P. falciparum</em> (strains 3D7 and FVO) and <em>P. vivax</em> (strain Sal1), in which the D2 loop could be largely traced in the electron density maps. The D2 loop of PfAMA1-FVO and PvAMA1 (as a complex with a monoclonal antibody Fab) has a conformation previously noted in the <em>P. knowlesi</em> AMA1 structure. The D2 loop of PfAMA1-3D7, however, reveals a novel conformation. We analyse the conformational variability of the D2 loop in these structures, together with those previously reported. Three different conformations can be distinguished, all of which are highly helical and show some similarity in their secondary structure organisation. We discuss the significance of these observations in the light of the flexible nature of the D2 loop and its role in AMA1 function.</p></div>","PeriodicalId":17238,"journal":{"name":"Journal of Structural Biology: X","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2590152424000151/pdfft?md5=18146cbe19a02e66f922067a1ea42cae&pid=1-s2.0-S2590152424000151-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142243547","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Structure of SARS-CoV-2 MTase nsp14 with the inhibitor STM957 reveals inhibition mechanism that is shared with a poxviral MTase VP39 SARS-CoV-2 MT 酶 nsp14 与抑制剂 STM957 的结构揭示了与痘病毒 MT 酶 VP39 共享的抑制机制

IF 3.5

Journal of Structural Biology: X Pub Date : 2024-07-29 DOI: 10.1016/j.yjsbx.2024.100109

{"title":"Structure of SARS-CoV-2 MTase nsp14 with the inhibitor STM957 reveals inhibition mechanism that is shared with a poxviral MTase VP39","authors":"","doi":"10.1016/j.yjsbx.2024.100109","DOIUrl":"10.1016/j.yjsbx.2024.100109","url":null,"abstract":"<div><p>Nsp14 is an RNA methyltransferase (MTase) encoded by all coronaviruses. In fact, many viral families, including DNA viruses, encode MTases that catalyze the methylation of the RNA precap structure, resulting in fully capped viral RNA. This capping is crucial for efficient viral RNA translation, stability, and immune evasion. Our previous research identified nsp14 inhibitors based on the chemical scaffold of its methyl donor − the S-adenosyl methionine (SAM) − featuring a modified adenine base and a substituted arylsulfonamide. However, the binding mode of these inhibitors was based only on docking experiments. To uncover atomic details of nsp14 inhibition we solved the crystal structure of nsp14 bound to STM957. The structure revealed the atomic details of nsp14 inhibition such that the 7-deaza-adenine moiety of STM957 forms specific interactions with Tyr368, Ala353, and Phe367, while the arylsulfonamide moiety engages with Asn388 and Phe506. The large aromatic substituent at the 7-deaza position displaces a network of water molecules near the adenine base. Surprisingly, this was recently observed in the case of an unrelated monkeypox MTase VP39, where the 7-deaza modified SAH analogs also displaced water molecules from the vicinity of the active site.</p></div>","PeriodicalId":17238,"journal":{"name":"Journal of Structural Biology: X","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S259015242400014X/pdfft?md5=adc7af4fba68360ac9d28aa0d253354d&pid=1-s2.0-S259015242400014X-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141962088","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Do selectivity filter carbonyls in K+ channels flip away from the pore? Two-dimensional infrared spectroscopy study K+ 通道中的选择性过滤羰基是否会从孔中翻转？二维红外光谱研究

IF 3.5

Journal of Structural Biology: X Pub Date : 2024-07-15 DOI: 10.1016/j.yjsbx.2024.100108

{"title":"Do selectivity filter carbonyls in K+ channels flip away from the pore? Two-dimensional infrared spectroscopy study","authors":"","doi":"10.1016/j.yjsbx.2024.100108","DOIUrl":"10.1016/j.yjsbx.2024.100108","url":null,"abstract":"<div><p>Molecular dynamics simulations revealed that the carbonyls of the Val residue in the conserved selectivity filter sequence TVGTG of potassium ion channels can flip away from the pore to form hydrogen bonds with the network of water molecules residing behind the selectivity filter. Such a configuration has been proposed to be relevant for C-type inactivation. Experimentally, X-ray crystallography of the KcsA channel admits the possibility that the Val carbonyls can flip, but it cannot decisively confirm the existence of such a configuration. In this study, we combined molecular dynamics simulations and line shape theory to design two-dimensional infrared spectroscopy experiments that can corroborate the existence of the selectivity filter configuration with flipped Val carbonyls. This ability to distinguish between flipped and unflipped carbonyls is based on the varying strength of the electric field inside and outside the pore, which is directly linked to carbonyl stretching frequencies that can be resolved using infrared spectroscopy.</p></div>","PeriodicalId":17238,"journal":{"name":"Journal of Structural Biology: X","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2590152424000138/pdfft?md5=13bf2c257aaf33fbd68799a7ce5f4412&pid=1-s2.0-S2590152424000138-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141689647","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

MicroED structure of the C11 cysteine protease clostripain C11 半胱氨酸蛋白酶 Clostripain 的显微电子数据结构

IF 3.5

Journal of Structural Biology: X Pub Date : 2024-07-06 DOI: 10.1016/j.yjsbx.2024.100107

Yasmeen N. Ruma , Guanhong Bu , Johan Hattne , Tamir Gonen

{"title":"MicroED structure of the C11 cysteine protease clostripain","authors":"Yasmeen N. Ruma , Guanhong Bu , Johan Hattne , Tamir Gonen","doi":"10.1016/j.yjsbx.2024.100107","DOIUrl":"https://doi.org/10.1016/j.yjsbx.2024.100107","url":null,"abstract":"<div><p>Clostripain secreted from <em>Clostridium histolyticum</em> is the founding member of the C11 family of Clan CD cysteine peptidases, which is an important group of peptidases secreted by numerous bacteria. Clostripain is an arginine-specific endopeptidase. Because of its efficacy as a cysteine peptidase, it is widely used in laboratory settings. Despite its importance the structure of clostripain remains unsolved. Here we describe the first structure of an active form of <em>C. histolyticum</em> clostripain determined at 2.5 Å resolution using microcrystal electron diffraction (MicroED). The structure was determined from a single nanocrystal after focused ion beam milling. The structure of clostripain shows a typical Clan CD α/β/α sandwich architecture and the Cys231/His176 catalytic dyad in the active site. It has a large electronegative substrate binding pocket showing its ability to accommodate large and diverse substrates. A loop in the heavy chain formed between residues 452 and 457 is potentially important for substrate binding. In conclusion, this result demonstrates the importance of MicroED to determine the unknown structure of macromolecules such as clostripain, which can be further used as a platform to study substrate binding and design of potential inhibitors against this class of peptidases.</p></div>","PeriodicalId":17238,"journal":{"name":"Journal of Structural Biology: X","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-07-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2590152424000126/pdfft?md5=42cb6b31866b2698d485367c031389f5&pid=1-s2.0-S2590152424000126-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141594445","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Nucleic acid-binding KH domain proteins influence a spectrum of biological pathways including as part of membrane-localized complexes 核酸结合 KH 结构域蛋白影响一系列生物通路，包括作为膜定位复合物的一部分发挥作用

IF 3.5

Journal of Structural Biology: X Pub Date : 2024-06-27 DOI: 10.1016/j.yjsbx.2024.100106

Md Kamrul Hasan , L. Jeannine Brady

{"title":"Nucleic acid-binding KH domain proteins influence a spectrum of biological pathways including as part of membrane-localized complexes","authors":"Md Kamrul Hasan , L. Jeannine Brady","doi":"10.1016/j.yjsbx.2024.100106","DOIUrl":"https://doi.org/10.1016/j.yjsbx.2024.100106","url":null,"abstract":"<div><p>K-Homology domain (KH domain) proteins bind single-stranded nucleic acids, influence protein–protein interactions of proteins that harbor them, and are found in all kingdoms of life. In concert with other functional protein domains KH domains contribute to a variety of critical biological activities, often within higher order machineries including membrane-localized protein complexes. Eukaryotic KH domain proteins are linked to developmental processes, morphogenesis, and growth regulation, and their aberrant expression is often associated with cancer. Prokaryotic KH domain proteins are involved in integral cellular activities including cell division and protein translocation. Eukaryotic and prokaryotic KH domains share structural features, but are differentiated based on their structural organizations. In this review, we explore the structure/function relationships of known examples of KH domain proteins, and highlight cases in which they function within or at membrane surfaces. We also summarize examples of KH domain proteins that influence bacterial virulence and pathogenesis. We conclude the article by discussing prospective research avenues that could be pursued to better investigate this largely understudied protein category.</p></div>","PeriodicalId":17238,"journal":{"name":"Journal of Structural Biology: X","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2590152424000114/pdfft?md5=0e422cb348e848d0c60e6c2df8352de4&pid=1-s2.0-S2590152424000114-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141486539","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0