Journal of structural biology最新文献_第10页

Morphological and genetic mechanisms underlying the plasticity of the coral Porites astreoides across depths in Bermuda 百慕大群岛不同深度的珊瑚虫的可塑性的形态学和遗传学机制。

IF 3 3区生物学

Journal of structural biology Pub Date : 2023-10-11 DOI: 10.1016/j.jsb.2023.108036

Federica Scucchia , Kevin Wong , Paul Zaslansky , Hollie M. Putnam , Gretchen Goodbody-Gringley , Tali Mass

{"title":"Morphological and genetic mechanisms underlying the plasticity of the coral Porites astreoides across depths in Bermuda","authors":"Federica Scucchia , Kevin Wong , Paul Zaslansky , Hollie M. Putnam , Gretchen Goodbody-Gringley , Tali Mass","doi":"10.1016/j.jsb.2023.108036","DOIUrl":"10.1016/j.jsb.2023.108036","url":null,"abstract":"<div><p>The widespread decline of shallow-water coral reefs has fueled interest in assessing whether mesophotic reefs can act as refugia replenishing deteriorated shallower reefs through larval exchange. Here we explore the morphological and molecular basis facilitating survival of planulae and adults of the coral <em>Porites astreoides</em> (<em>Lamarck, 1816; Hexacorallia: Poritidae</em>) along the vertical depth gradient in Bermuda. We found differences in micro-skeletal features such as bigger calyxes and coarser surface of the skeletal spines in shallow corals. Yet, tomographic reconstructions reveal an analogous mineral distribution between shallow and mesophotic adults, pointing to similar skeleton growth dynamics. Our study reveals patterns of host genetic connectivity and minimal symbiont depth-zonation across a broader depth range than previously known for this species in Bermuda. Transcriptional variations across life stages showed different regulation of metabolism and stress response functions, unraveling molecular responses to environmental conditions at different depths. Overall, these findings increase our understanding of coral acclimatory capability across broad vertical gradients, ultimately allowing better evaluation of the refugia potential of mesophotic reefs.</p></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"215 4","pages":"Article 108036"},"PeriodicalIF":3.0,"publicationDate":"2023-10-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41203959","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

Announcement: Journal of Structural Biology – Paper of the Year 2022 公告：结构生物学杂志-2022年度论文。

IF 3 3区生物学

Journal of structural biology Pub Date : 2023-10-11 DOI: 10.1016/j.jsb.2023.108037

Martin Pilhofer

引用次数: 0

Beyond the surface: Investigation of tumorsphere morphology using volume electron microscopy 超越表面：使用体积电子显微镜研究肿瘤球体形态。

IF 3 3区生物学

Journal of structural biology Pub Date : 2023-10-05 DOI: 10.1016/j.jsb.2023.108035

Nickhil Jadav , Sailakshmi Velamoor , Daniel Huang , Léna Cassin , Niki Hazelton , Alice-Roza Eruera , Laura N. Burga , Mihnea Bostina

{"title":"Beyond the surface: Investigation of tumorsphere morphology using volume electron microscopy","authors":"Nickhil Jadav , Sailakshmi Velamoor , Daniel Huang , Léna Cassin , Niki Hazelton , Alice-Roza Eruera , Laura N. Burga , Mihnea Bostina","doi":"10.1016/j.jsb.2023.108035","DOIUrl":"10.1016/j.jsb.2023.108035","url":null,"abstract":"<div><p>The advent of volume electron microscopy (vEM) has provided unprecedented insights into cellular and subcellular organization, revolutionizing our understanding of cancer biology. This study presents a previously unexplored comparative analysis of the ultrastructural disparities between cancer cells cultured as monolayers and tumorspheres. By integrating a robust workflow that incorporates high-pressure freezing followed by freeze substitution (HPF/FS), serial block face scanning electron microscopy (SBF-SEM), manual and deep learning-based segmentation, and statistical analysis, we have successfully generated three-dimensional (3D) reconstructions of monolayer and tumorsphere cells, including their subcellular organelles. Our findings reveal a significant degree of variation in cellular morphology in tumorspheres. We observed the increased prevalence of nuclear envelope invaginations in tumorsphere cells compared to monolayers. Furthermore, we detected a diverse range of mitochondrial morphologies exclusively in tumorsphere cells, as well as intricate cellular interconnectivity within the tumorsphere architecture. These remarkable ultrastructural differences emphasize the use of tumorspheres as a superior model for cancer research due to their relevance to <em>in vivo</em> conditions. Our results strongly advocate for the utilization of tumorsphere cells in cancer research studies, enhancing the precision and relevance of experimental outcomes, and ultimately accelerating therapeutic advancements.</p></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"215 4","pages":"Article 108035"},"PeriodicalIF":3.0,"publicationDate":"2023-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41130920","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

Sulisobenzone is a potent inhibitor of the global transcription factor Cra 硫异苯酮是一种有效的全球转录因子Cra抑制剂。

IF 3 3区生物学

Journal of structural biology Pub Date : 2023-10-05 DOI: 10.1016/j.jsb.2023.108034

Neetu Neetu , Jai Krishna Mahto , Monica Sharma , Madhusudhanarao Katiki , Preeti Dhaka , Partha Roy , Shailly Tomar , Anoop Narayan , Dinesh Yernool , Pravindra Kumar

{"title":"Sulisobenzone is a potent inhibitor of the global transcription factor Cra","authors":"Neetu Neetu , Jai Krishna Mahto , Monica Sharma , Madhusudhanarao Katiki , Preeti Dhaka , Partha Roy , Shailly Tomar , Anoop Narayan , Dinesh Yernool , Pravindra Kumar","doi":"10.1016/j.jsb.2023.108034","DOIUrl":"10.1016/j.jsb.2023.108034","url":null,"abstract":"<div><p>Transcription is carried out by the RNA polymerase and is regulated through a series of interactions with transcription factors. Catabolite activator repressor (Cra), a LacI family transcription factor regulates the virulence gene expression in Enterohaemorrhagic <em>Escherichia coli</em> (EHEC) and thus is a promising drug target for the discovery of antivirulence molecules. Here, we report the crystal structure of the effector molecule binding domain of Cra from <em>E. coli</em> (<em>Ec</em>Cra) in complex with HEPES molecule. Based on the <em>Ec</em>Cra-HEPES complex structure, ligand screening was performed that identified sulisobenzone as an potential inhibitor of <em>Ec</em>Cra. The electrophoretic mobility shift assay (EMSA) and <em>in vitro</em> transcription assay validated the sulisobenzone binding to <em>Ec</em>Cra. Moreover, the isothermal titration calorimetry (ITC) experiments demonstrated a 40-fold higher binding affinity of sulisobenzone (<em>K</em><sub>D</sub> 360 nM) compared to the HEPES molecule. Finally, the sulisobenzone bound <em>Ec</em>Cra complex crystal structure was determined to elucidate the binding mechanism of sulisobenzone to the effector binding pocket of <em>Ec</em>Cra. Together, this study suggests that sulisobenzone may be a promising candidate that can be studied and developed as an effective antivirulence agent against EHEC.</p></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"215 4","pages":"Article 108034"},"PeriodicalIF":3.0,"publicationDate":"2023-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41136674","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

Daisy: An integrated repeat protein curation service 黛西：一个完整的重复蛋白质管理服务。

IF 3 3区生物学

Journal of structural biology Pub Date : 2023-10-03 DOI: 10.1016/j.jsb.2023.108033

Manuel Bezerra-Brandao, Ronaldo Romario Tunque Cahui, Layla Hirsh

{"title":"Daisy: An integrated repeat protein curation service","authors":"Manuel Bezerra-Brandao, Ronaldo Romario Tunque Cahui, Layla Hirsh","doi":"10.1016/j.jsb.2023.108033","DOIUrl":"10.1016/j.jsb.2023.108033","url":null,"abstract":"<div><p>Tandem repeats in proteins identification, classification and curation is a complex process that requires manual processing from experts, processing power and time. There are recent and relevant advances applying machine learning for protein structure prediction and repeat classification that are useful for this process. However, no service contemplates required databases and software to supplement researching on repeat proteins. In this publication we present Daisy, an integrated repeat protein curation web service. This service can process Protein Data Bank (PDB) and the AlphaFold Database entries for tandem repeats identification. In addition, it uses an algorithm to search a sequence against a library of Pfam hidden Markov model (HMM). Repeat classifications are associated with the identified families through RepeatsDB. This prediction is considered for enhancing the ReUPred algorithm execution and hastening the repeat units identification process. The service can also operate every associated PDB and AlphaFold structure with a UniProt proteome registry.</p><p><strong>Availability:</strong> The Daisy web service is freely accessible at <span>daisy.bioinformatica.org</span><svg><path></path></svg>.</p></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"215 4","pages":"Article 108033"},"PeriodicalIF":3.0,"publicationDate":"2023-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41148353","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

Contribution of a surface salt bridge to the protein stability of deep-sea Shewanella benthica cytochrome c' 表面盐桥对深海本氏谢瓦尼拉细胞色素c'蛋白质稳定性的贡献。

IF 3 3区生物学

Journal of structural biology Pub Date : 2023-09-25 DOI: 10.1016/j.jsb.2023.108031

Sotaro Fujii , Riku Sakaguchi , Hiroya Oki , Kazuki Kawahara , Tadayasu Ohkubo , So Fujiyoshi , Yoshihiro Sambongi

{"title":"Contribution of a surface salt bridge to the protein stability of deep-sea Shewanella benthica cytochrome c'","authors":"Sotaro Fujii , Riku Sakaguchi , Hiroya Oki , Kazuki Kawahara , Tadayasu Ohkubo , So Fujiyoshi , Yoshihiro Sambongi","doi":"10.1016/j.jsb.2023.108031","DOIUrl":"10.1016/j.jsb.2023.108031","url":null,"abstract":"<div><p><span>Two homologous cytochromes </span><em>c</em>', SBCP and SVCP, from deep-sea <span><em>Shewanella</em><em> benthica</em></span> and <em>Shewanella violacea</em><span><span> respectively exhibit only nine surface amino acid substitutions<span>, along with one at the N-terminus. Despite the small sequence difference, SBCP is thermally more stable than SVCP. Here, we examined the thermal stability of SBCP variants, each containing one of the nine substituted residues in SVCP, and found that the SBCP K87V variant was the most destabilized. We then determined the X-ray crystal structure of the SBCP K87V variant at a resolution of 2.1 Å. The variant retains a four-helix bundle structure similar to the wild-type, but notable differences are observed in the hydration structure around the mutation site. Instead of forming of the intrahelical salt bridge between Lys-87 and Asp-91 in the wild-type, a clathrate-like hydration around Val-87 through a </span></span>hydrogen bond<span> network with the nearby amino acid residues is observed. This network potentially enhances the ordering of surrounding water molecules, leading to an entropic destabilization of the protein. These results suggest that the unfavorable hydrophobic hydration environment around Val-87 and the inability to form the Asp-91-mediated salt bridge contribute to the observed difference in stability between SBCP and SVCP. These findings will be useful in future protein engineering for controlling protein stability through the manipulation of surface intrahelical salt bridges.</span></span></p></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"215 4","pages":"Article 108031"},"PeriodicalIF":3.0,"publicationDate":"2023-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41125553","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

Local defocus estimation in single particle analysis in cryo-electron microscopy 冷冻电子显微镜中单粒子分析中的局部散焦估计。

IF 3 3区生物学

Journal of structural biology Pub Date : 2023-09-25 DOI: 10.1016/j.jsb.2023.108030

E. Fernandez-Gimenez , J.M. Carazo , C.O.S. Sorzano

{"title":"Local defocus estimation in single particle analysis in cryo-electron microscopy","authors":"E. Fernandez-Gimenez , J.M. Carazo , C.O.S. Sorzano","doi":"10.1016/j.jsb.2023.108030","DOIUrl":"10.1016/j.jsb.2023.108030","url":null,"abstract":"<div><p>Single Particle analysis (SPA) aims to determine the three-dimensional structure of proteins and macromolecular complexes. The current state of the art has allowed us to achieve near-atomic and even atomic resolutions. To obtain high-resolution structures, a set of well-defined image processing steps is required. A critical one is the estimation of the Contrast Transfer Function (CTF), which considers the sample defocus and aberrations of the microscope. Defocus is usually globally estimated; in this case, it is the same for all the particles in each micrograph. But proteins are ice-embedded at different heights, suggesting that defocus should be measured in a local (per particle) manner. There are four state-of-the-art programs to estimate local defocus (Gctf, Relion, CryoSPARC, and Xmipp). In this work, we have compared the results of these software packages to check whether the resolution improves. We have used the Scipion framework and developed a specific program to analyze local defocus. The results produced by different programs do not show a clear consensus using the current test datasets in this study.</p></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"215 4","pages":"Article 108030"},"PeriodicalIF":3.0,"publicationDate":"2023-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41103767","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

Insight into structural biophysics from solution X-ray scattering 从溶液X射线散射透视结构生物物理学。

IF 3 3区生物学

Journal of structural biology Pub Date : 2023-09-22 DOI: 10.1016/j.jsb.2023.108029

Uri Raviv , Roi Asor , Asaf Shemesh , Avi Ginsburg , Tal Ben-Nun , Yaelle Schilt , Yehonatan Levartovsky , Israel Ringel

{"title":"Insight into structural biophysics from solution X-ray scattering","authors":"Uri Raviv , Roi Asor , Asaf Shemesh , Avi Ginsburg , Tal Ben-Nun , Yaelle Schilt , Yehonatan Levartovsky , Israel Ringel","doi":"10.1016/j.jsb.2023.108029","DOIUrl":"10.1016/j.jsb.2023.108029","url":null,"abstract":"<div><p>The current challenges of structural biophysics include determining the structure of large self-assembled complexes, resolving the structure of ensembles of complex structures and their mass fraction, and unraveling the dynamic pathways and mechanisms leading to the formation of complex structures from their subunits. Modern synchrotron solution X-ray scattering data enable simultaneous high-spatial and high-temporal structural data required to address the current challenges of structural biophysics. These data are complementary to crystallography, NMR, and cryo-TEM data. However, the analysis of solution scattering data is challenging; hence many different analysis tools, listed in the SAS Portal (http://smallangle.org/), were developed. In this review, we start by briefly summarizing classical X-ray scattering analyses providing insight into fundamental structural and interaction parameters. We then describe recent developments, integrating simulations, theory, and advanced X-ray scattering modeling, providing unique insights into the structure, energetics, and dynamics of self-assembled complexes. The structural information is essential for understanding the underlying physical chemistry principles leading to self-assembled supramolecular architectures and computational structural refinement.</p></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"215 4","pages":"Article 108029"},"PeriodicalIF":3.0,"publicationDate":"2023-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41141716","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: 1

Domain crossover in the reductase subunit of NADPH-dependent assimilatory sulfite reductase NADPH依赖性同化亚硫酸还原酶还原酶亚基中的结构域交叉。

IF 3 3区生物学

Journal of structural biology Pub Date : 2023-09-12 DOI: 10.1016/j.jsb.2023.108028

Nidhi Walia , Daniel T. Murray , Yashika Garg , Huan He , Kevin L. Weiss , Gergely Nagy , M. Elizabeth Stroupe

{"title":"Domain crossover in the reductase subunit of NADPH-dependent assimilatory sulfite reductase","authors":"Nidhi Walia , Daniel T. Murray , Yashika Garg , Huan He , Kevin L. Weiss , Gergely Nagy , M. Elizabeth Stroupe","doi":"10.1016/j.jsb.2023.108028","DOIUrl":"10.1016/j.jsb.2023.108028","url":null,"abstract":"<div><p>NADPH-dependent assimilatory sulfite reductase (SiR) from <em>Escherichia coli</em> performs a six-electron reduction of sulfite to the bioavailable sulfide. SiR is composed of a flavoprotein (SiRFP) reductase subunit and a hemoprotein (SiRHP) oxidase subunit. There is no known high-resolution structure of SiR or SiRFP, thus we do not yet fully understand how the subunits interact to perform their chemistry. Here, we used small-angle neutron scattering to understand the impact of conformationally restricting the highly mobile SiRFP octamer into an electron accepting (closed) or electron donating (open) conformation, showing that SiR remains active, flexible, and asymmetric even with these conformational restrictions. From these scattering data, we model the first solution structure of SiRFP. Further, computational modeling of the N-terminal 52 amino acids that are responsible for SiRFP oligomerization suggests an eight-helical bundle tethers together the SiRFP subunits to form the SiR core. Finally, mass spectrometry analysis of the closed SiRFP variant show that SiRFP is capable of inter-molecular domain crossover, in which the electron donating domain from one polypeptide is able to interact directly with the electron accepting domain of another polypeptide. This structural characterization suggests that SiR performs its high-volume electron transfer through both inter- and intramolecular pathways between SiRFP domains and, thus, <em>cis</em> or <em>trans</em> transfer from reductase to oxidase subunits. Such highly redundant potential for electron transfer makes this system a potential target for designing synthetic enzymes.</p></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"215 4","pages":"Article 108028"},"PeriodicalIF":3.0,"publicationDate":"2023-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10232829","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

A new algorithm for particle weighted subtraction to decrease signals from unwanted components in single particle analysis 一种新的粒子加权减法算法，用于减少单粒子分析中不需要的分量的信号。

IF 3 3区生物学

Journal of structural biology Pub Date : 2023-09-11 DOI: 10.1016/j.jsb.2023.108024

E. Fernández-Giménez , M.M. Martínez , R. Marabini , D. Strelak , R. Sánchez-García , J.M. Carazo , C.O.S. Sorzano

{"title":"A new algorithm for particle weighted subtraction to decrease signals from unwanted components in single particle analysis","authors":"E. Fernández-Giménez , M.M. Martínez , R. Marabini , D. Strelak , R. Sánchez-García , J.M. Carazo , C.O.S. Sorzano","doi":"10.1016/j.jsb.2023.108024","DOIUrl":"10.1016/j.jsb.2023.108024","url":null,"abstract":"<div><p>Single particle analysis (SPA) in cryo-electron microscopy (cryo-EM) is highly used to obtain the near-atomic structure of biological macromolecules. The current methods allow users to produce high-resolution maps from many samples. However, there are still challenging cases that require extra processing to obtain high resolution. This is the case when the macromolecule of the sample is composed of different components and we want to focus just on one of them. For example, if the macromolecule is composed of several flexible subunits and we are interested in a specific one, if it is embedded in a viral capsid environment, or if it has additional components to stabilize it, such as nanodiscs. The signal from these components, which in principle we are not interested in, can be removed from the particles using a projection subtraction method. Currently, there are two projection subtraction methods used in practice and both have some limitations. In fact, after evaluating their results, we consider that the problem is still open to new solutions, as they do not fully remove the signal of the components that are not of interest. Our aim is to develop a new and more precise projection subtraction method, improving the performance of state-of-the-art methods. We tested our algorithm with data from public databases and an in–house data set. In this work, we show that the performance of our algorithm improves the results obtained by others, including the localization of small ligands, such as drugs, whose binding location is unknown <em>a priori</em>.</p></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"215 4","pages":"Article 108024"},"PeriodicalIF":3.0,"publicationDate":"2023-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10285701","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