Journal of structural biology最新文献_第9页

Biochemical, structural and dynamical characterizations of the lactate dehydrogenase from Selenomonas ruminantium provide information about an intermediate evolutionary step prior to complete allosteric regulation acquisition in the super family of lactate and malate dehydrogenases 反刍硒单胞菌乳酸脱氢酶的生化、结构和动力学特征提供了关于乳酸和苹果酸脱氢酶超家族中完全变构调节获得之前的中间进化步骤的信息。

IF 3 3区生物学

Journal of structural biology Pub Date : 2023-10-24 DOI: 10.1016/j.jsb.2023.108039

Quentin Bertrand , Sandrine Coquille , Antonio Iorio , Fabio Sterpone , Dominique Madern

{"title":"Biochemical, structural and dynamical characterizations of the lactate dehydrogenase from Selenomonas ruminantium provide information about an intermediate evolutionary step prior to complete allosteric regulation acquisition in the super family of lactate and malate dehydrogenases","authors":"Quentin Bertrand , Sandrine Coquille , Antonio Iorio , Fabio Sterpone , Dominique Madern","doi":"10.1016/j.jsb.2023.108039","DOIUrl":"10.1016/j.jsb.2023.108039","url":null,"abstract":"<div>In this work, we investigated the lactate dehydrogenase (LDH) from Selenomonas ruminantium (S. rum), an enzyme that differs at key amino acid positions from canonical allosteric LDHs. The wild type (Wt) of this enzyme recognises pyuvate as all LDHs. However, introducing a single point mutation in the active site loop (I85R) allows S. Rum LDH to recognize the oxaloacetate substrate as a typical malate dehydrogenase (MalDH), whilst maintaining homotropic activation as an LDH. We report the tertiary structure of the Wt and I85RLDH mutant.The Wt S. rum enzyme structure binds NADH and malonate, whilst also resembling the typical compact R-active state of canonical LDHs. The structure of the mutant with I85R was solved in the Apo State (without ligand), and shows no large conformational reorganization such as that observed with canonical allosteric LDHs in Apo state. This is due to a local structural feature typical of S. rum LDH that prevents large-scale conformational reorganization. The S. rum LDH was also studied using Molecular Dynamics simulations, probing specific local deformations of the active site that allow the S. rum LDH to sample the T-inactive state. We propose that, with respect to the LDH/MalDH superfamily, the S. rum enzyme possesses a specificstructural and dynamical way to ensure homotropic activation.</div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2023-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"54229744","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

Crystal structures of Streptomyces tsukubaensis sigma factor SigG1 and anti-sigma RsfG tsukubaensis链霉菌西格玛因子SigG1和抗西格玛RsfG的晶体结构。

IF 3 3区生物学

Journal of structural biology Pub Date : 2023-10-18 DOI: 10.1016/j.jsb.2023.108038

José P. Leite , Frederico Lourenço , Rute Oliveira , Sérgio F. Sousa , Marta V. Mendes , Luís Gales

引用次数: 0

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>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 Porites astreoides (Lamarck, 1816; Hexacorallia: Poritidae) 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.</div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":null,"pages":null},"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>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 in vivo 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.</div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":null,"pages":null},"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>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 Escherichia coli (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 E. coli (EcCra) in complex with HEPES molecule. Based on the EcCra-HEPES complex structure, ligand screening was performed that identified sulisobenzone as an potential inhibitor of EcCra. The electrophoretic mobility shift assay (EMSA) and in vitro transcription assay validated the sulisobenzone binding to EcCra. Moreover, the isothermal titration calorimetry (ITC) experiments demonstrated a 40-fold higher binding affinity of sulisobenzone (KD 360 nM) compared to the HEPES molecule. Finally, the sulisobenzone bound EcCra complex crystal structure was determined to elucidate the binding mechanism of sulisobenzone to the effector binding pocket of EcCra. Together, this study suggests that sulisobenzone may be a promising candidate that can be studied and developed as an effective antivirulence agent against EHEC.</div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":null,"pages":null},"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>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.Availability: The Daisy web service is freely accessible at daisy.bioinformatica.org<svg><path></path></svg>.</div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":null,"pages":null},"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>Two homologous cytochromes c', SBCP and SVCP, from deep-sea Shewanella benthica and Shewanella violacea respectively exhibit only nine surface amino acid substitutions, 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 hydrogen bond 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.</div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":null,"pages":null},"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

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>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.</div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":null,"pages":null},"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