Journal of structural biology最新文献_第6页

Phylogenetic analysis and homology modelling of a new Cry8A crystal protein expressed in a sporulating soil bacterium 一种新的Cry8A晶体蛋白在产孢土壤细菌中表达的系统发育分析和同源性建模。

IF 3 3区生物学

Journal of structural biology Pub Date : 2025-01-05 DOI: 10.1016/j.jsb.2025.108167

José D. Antonino , Shalini Chaudhary , Mark Lubberts , Brendan J. McConkey , Camilla A.S. Valença , Marcus V. de Aragão Batista , Patricia Severino , Marcelo da Costa Mendonça , Eliana B. Souto , Silvio S. Dolabella , Sona Jain

{"title":"Phylogenetic analysis and homology modelling of a new Cry8A crystal protein expressed in a sporulating soil bacterium","authors":"José D. Antonino , Shalini Chaudhary , Mark Lubberts , Brendan J. McConkey , Camilla A.S. Valença , Marcus V. de Aragão Batista , Patricia Severino , Marcelo da Costa Mendonça , Eliana B. Souto , Silvio S. Dolabella , Sona Jain","doi":"10.1016/j.jsb.2025.108167","DOIUrl":"10.1016/j.jsb.2025.108167","url":null,"abstract":"<div><div>Cry proteins, commonly found in Gram-positive soil bacteria, are used worldwide as aerial sprays or in transgenic plants for controlling crop pest populations and insect vectors<em>.</em> Via PCR analysis, a spore producing soil isolate (BV5) was speculated to encode a Cry gene. Partial nucleotide sequence of the amplified PCR fragment showed homology with the Cry8 genes present in GenBank. A full-length Cry gene was cloned, and the predicted protein sequence grouped the newly isolated Cry protein with other Cry8A present in GenBank with a high possibility of it being a new Cry8. SDS-PAGE and MALDI-TOF mass spectrometry confirmed the expression of a single 135 KDa protein matching uniquely to the putative protein sequence of the BV5 Cry gene. However, bioassay against the coleopteran <em>Anthonomus grandis</em> (Coleopterans are a known Cry8A target), showed no activity. Phylogenetic analysis and homology modelling was performed to characterize the protein structure and function. These analyses suggest a series of mutations in one of the variable loops on the surface of the protein.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"217 1","pages":"Article 108167"},"PeriodicalIF":3.0,"publicationDate":"2025-01-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142971462","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

Modelling components of nacre structure in silico: Interactions of a nacre peptide with chitin and an aragonite surface 用硅模拟珍珠层结构的组成部分：珍珠层肽与几丁质和文石表面的相互作用。

IF 3 3区生物学

Journal of structural biology Pub Date : 2024-12-26 DOI: 10.1016/j.jsb.2024.108165

Elena Macias-Sánchez , Yumeida Meruvia-Rojas , Julyan H.E. Cartwright , Antonio G. Checa , C.Ignacio Sainz-Díaz

{"title":"Modelling components of nacre structure in silico: Interactions of a nacre peptide with chitin and an aragonite surface","authors":"Elena Macias-Sánchez , Yumeida Meruvia-Rojas , Julyan H.E. Cartwright , Antonio G. Checa , C.Ignacio Sainz-Díaz","doi":"10.1016/j.jsb.2024.108165","DOIUrl":"10.1016/j.jsb.2024.108165","url":null,"abstract":"<div><div>The nacre formation process is a fascinating phenomenon involving mineral phase transformations, self-assembly processes, and protein–mineral interactions, resulting in a hierarchical structure that exhibits outstanding mechanical properties. However, this process is only partially known, and many aspects of nacre structure are not well understood, especially at the molecular scale. To understand the interplay between components—aragonite, protein and chitin—of the structure of nacre observed experimentally, we investigate the interactions of a peptide that is part of the protein lustrin A, identified in the nacreous layer of the shell of the abalone <em>Haliotis rufescens</em>, with the (001) crystal surface of aragonite and the chitin molecule. We report the results of atomistic molecular-modelling calculations and molecular-dynamics simulations of the peptide interacting with both the aragonite surface and the chitin polymer. The peptide shows an energetically favourable binding to the aragonite surface. The interaction of the carboxylic groups of the glutamic unit with the crystalline surface is essential to reproduce the characteristic elastomeric properties of this peptide in nacre.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"217 1","pages":"Article 108165"},"PeriodicalIF":3.0,"publicationDate":"2024-12-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142895584","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

Structural insights into the engagement of lysophosphatidic acid receptor 1 with different G proteins 溶血磷脂酸受体1与不同G蛋白结合的结构见解。

IF 3 3区生物学

Journal of structural biology Pub Date : 2024-12-24 DOI: 10.1016/j.jsb.2024.108164

Shota Suzuki , Kotaro Tanaka , Akiko Kamegawa , Kouki Nishikawa , Hiroshi Suzuki , Atsunori Oshima , Yoshinori Fujiyoshi

{"title":"Structural insights into the engagement of lysophosphatidic acid receptor 1 with different G proteins","authors":"Shota Suzuki , Kotaro Tanaka , Akiko Kamegawa , Kouki Nishikawa , Hiroshi Suzuki , Atsunori Oshima , Yoshinori Fujiyoshi","doi":"10.1016/j.jsb.2024.108164","DOIUrl":"10.1016/j.jsb.2024.108164","url":null,"abstract":"<div><div>Lysophosphatidic acid (LPA) and sphingosine-1-phosphate (S1P) are bioactive lysophospholipids derived from cell membranes that activate the endothelial differentiation gene family of G protein-coupled receptors. Activation of these receptors triggers multiple downstream signaling cascades through G proteins such as Gi/o, Gq/11, and G12/13. Therefore, LPA and S1P mediate several physiological processes, including cytoskeletal dynamics, neurite retraction, cell migration, cell proliferation, and intracellular ion fluxes. The basis for the G-protein coupling selectivity of EDG receptors, however, remains unknown. Here, we present cryo-electron microscopy structures of LPA-activated LPA1 in complexes with G<sub>i</sub>, G<sub>q</sub>, and G<sub>13</sub> heterotrimers<sub>.</sub> Comparison of the three LPA1-G protein structures shows clearly different conformations of intracellular loop 2 (ICL2) and ICL3 that are likely induced by the different Gα protein interfaces. Interestingly, this G-protein interface interaction is a common feature of LPA and S1P receptors. Our findings provide clues to understanding the promiscuity of G-protein coupling in the endothelial differentiation gene family.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"217 1","pages":"Article 108164"},"PeriodicalIF":3.0,"publicationDate":"2024-12-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142895602","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

CryoSamba: Self-supervised deep volumetric denoising for cryo-electron tomography data CryoSamba：用于低温电子断层成像数据的自监督深度体积去噪。

IF 3 3区生物学

Journal of structural biology Pub Date : 2024-12-20 DOI: 10.1016/j.jsb.2024.108163

Jose Inacio Costa-Filho , Liam Theveny , Marilina de Sautu , Tom Kirchhausen

{"title":"CryoSamba: Self-supervised deep volumetric denoising for cryo-electron tomography data","authors":"Jose Inacio Costa-Filho , Liam Theveny , Marilina de Sautu , Tom Kirchhausen","doi":"10.1016/j.jsb.2024.108163","DOIUrl":"10.1016/j.jsb.2024.108163","url":null,"abstract":"<div><div>Cryogenic electron tomography (cryo-ET) has rapidly advanced as a high-resolution imaging tool for visualizing subcellular structures in 3D with molecular detail. Direct image inspection remains challenging due to inherent low signal-to-noise ratios (SNR). We introduce CryoSamba, a self-supervised deep learning-based model designed for denoising cryo-ET images. CryoSamba enhances single consecutive 2D planes in tomograms by averaging motion-compensated nearby planes through deep learning interpolation, effectively mimicking increased exposure. This approach amplifies coherent signals and reduces high-frequency noise, substantially improving tomogram contrast and SNR. CryoSamba operates on 3D volumes without needing pre-recorded images, synthetic data, labels or annotations, noise models, or paired volumes. CryoSamba suppresses high-frequency information less aggressively than do existing cryo-ET denoising methods, while retaining real information, as shown both by visual inspection and by Fourier Shell Correlation (FSC) analysis of icosahedrally symmetric virus particles. Thus, CryoSamba enhances the analytical pipeline for direct 3D tomogram visual interpretation.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"217 1","pages":"Article 108163"},"PeriodicalIF":3.0,"publicationDate":"2024-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142877148","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

Automatic detection of alignment errors in cryo-electron tomography 低温电子断层扫描中对准误差的自动检测。

IF 3 3区生物学

Journal of structural biology Pub Date : 2024-12-16 DOI: 10.1016/j.jsb.2024.108153

F.P. de Isidro-Gómez , J.L. Vilas , J.M. Carazo , C.O.S. Sorzano

{"title":"Automatic detection of alignment errors in cryo-electron tomography","authors":"F.P. de Isidro-Gómez , J.L. Vilas , J.M. Carazo , C.O.S. Sorzano","doi":"10.1016/j.jsb.2024.108153","DOIUrl":"10.1016/j.jsb.2024.108153","url":null,"abstract":"<div><div>Cryo-electron tomography is an imaging technique that allows the study of the three-dimensional structure of a wide range of biological samples, from entire cellular environments to purified specimens. This technique collects a series of images from different views of the specimen by tilting the sample stage in the microscope. Subsequently, this information is combined into a three-dimensional reconstruction. To obtain reliable representations of the specimen of study, it is mandatory to define the acquisition geometry accurately. This is achieved by aligning all tilt images to a standard reference scheme. Errors in this step introduce artifacts into the final reconstructed tomograms, leading to loss of resolution and making them unsuitable for detailed sample analysis. This publication presents algorithms for automatically assessing the alignment quality of the tilt series and their classification based on the residual errors provided by the alignment algorithms. If no alignment information is available, a set of algorithms for calculating the residual vectors focused on fiducial markers is also presented. This software is accessible as part of the Xmipp software package and the Scipion framework.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"217 1","pages":"Article 108153"},"PeriodicalIF":3.0,"publicationDate":"2024-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142854631","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

Characterization of SARS-CoV-2 nucleocapsid protein oligomers SARS-CoV-2 核苷酸蛋白寡聚体的特征。

IF 3 3区生物学

Journal of structural biology Pub Date : 2024-12-13 DOI: 10.1016/j.jsb.2024.108162

Domenica Farci , André T. Graça , Michael Hall , Patrycja Haniewicz , Sami Kereïche , Peter Faull , Joanna Kirkpatrick , Enzo Tramontano , Wolfgang P. Schröder , Dario Piano

{"title":"Characterization of SARS-CoV-2 nucleocapsid protein oligomers","authors":"Domenica Farci , André T. Graça , Michael Hall , Patrycja Haniewicz , Sami Kereïche , Peter Faull , Joanna Kirkpatrick , Enzo Tramontano , Wolfgang P. Schröder , Dario Piano","doi":"10.1016/j.jsb.2024.108162","DOIUrl":"10.1016/j.jsb.2024.108162","url":null,"abstract":"<div><div>Oligomers of the SARS-CoV-2 nucleocapsid (N) protein are characterized by pronounced instability resulting in fast degradation. This property likely relates to two contrasting behaviors of the N protein: genome stabilization through a compact nucleocapsid during cell evasion and genome release by nucleocapsid disassembling during infection. <em>In vivo</em>, the N protein forms rounded complexes of high molecular mass from its interaction with the viral genome. To study the N protein and understand its instability, we analyzed degradation profiles under different conditions by size-exclusion chromatography and characterized samples by mass spectrometry and cryo-electron microscopy. We identified self-cleavage properties of the N protein based on specific Proprotein convertases activities, with Cl<sup>-</sup> playing a key role in modulating stability and degradation. These findings allowed isolation of a stable oligomeric complex of N, for which we report the 3D structure at ∼6.8 Å resolution. Findings are discussed considering available knowledge about the coronaviruses’ infection cycle.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"217 1","pages":"Article 108162"},"PeriodicalIF":3.0,"publicationDate":"2024-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142829055","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

JBP1 and JBP3 have conserved structures but different affinity to base-J JBP1 和 JBP3 的结构一致，但与碱基-J 的亲和力不同。

IF 3 3区生物学

Journal of structural biology Pub Date : 2024-12-12 DOI: 10.1016/j.jsb.2024.108161

Ida de Vries , Athanassios Adamopoulos , Justina Kazokaitė-Adomaitienė, Tatjana Heidebrecht, Alex Fish, Patrick H.N. Celie, Robbie P. Joosten, Anastassis Perrakis

{"title":"JBP1 and JBP3 have conserved structures but different affinity to base-J","authors":"Ida de Vries , Athanassios Adamopoulos , Justina Kazokaitė-Adomaitienė, Tatjana Heidebrecht, Alex Fish, Patrick H.N. Celie, Robbie P. Joosten, Anastassis Perrakis","doi":"10.1016/j.jsb.2024.108161","DOIUrl":"10.1016/j.jsb.2024.108161","url":null,"abstract":"<div><div>Base-J (β-D-glucopyranosyloxymethyluracil) is an unusual kinetoplastid-specific DNA modification, recognized by base-J containing DNA (J-DNA) binding proteins JBP1 and JBP3. Recognition of J-DNA by both JBP1 and JBP3 takes place by a conserved J-DNA binding domain (JDBD). Here we show that JDBD-JBP3 has about 1,000-fold weaker affinity to base-J than JDBD-JBP1 and discriminates between J-DNA and unmodified DNA with a factor ∼5, whereas JDBD-JBP1 discriminates with a factor ∼10,000. Comparison of the crystal structures of JDBD-JBP3 we present here, with that of the previously characterized JDBD-JBP1, shows a flexible α5-helix that lacks a positively charged patch in JBP3. Mutations removing this positive charge in JDBD-JBP1, resulted in decreased binding affinity relative to wild-type JDBD-JBP1, indicating this patch is involved in DNA binding. We suggest that the α5-helix might rearrange upon JBP1 binding to J-DNA stabilizing the complex. This work contributes to our understanding of how JBPs bind to this unique DNA modification, which may contribute to identifying potential drug targets to end the base-J dependent parasite life cycle.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"217 1","pages":"Article 108161"},"PeriodicalIF":3.0,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142823909","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

Kinetic and structural studies of gamma-carbonic anhydrase from the oral pathogen Porphyromonas gingivalis 口腔病原菌牙龈卟啉单胞菌γ -碳酸酐酶的动力学和结构研究。

IF 3 3区生物学

Journal of structural biology Pub Date : 2024-12-06 DOI: 10.1016/j.jsb.2024.108154

Marta Ferraroni , Andrea Angeli , Viviana De Luca , Clemente Capasso , Claudiu T. Supuran

{"title":"Kinetic and structural studies of gamma-carbonic anhydrase from the oral pathogen Porphyromonas gingivalis","authors":"Marta Ferraroni , Andrea Angeli , Viviana De Luca , Clemente Capasso , Claudiu T. Supuran","doi":"10.1016/j.jsb.2024.108154","DOIUrl":"10.1016/j.jsb.2024.108154","url":null,"abstract":"<div><div><em>Porphyromonas gingivalis</em>, a key pathogen in periodontal, plays a critical role in systemic pathologiesdiseases by evading host defence mechanisms and invading periodontal tissues. Targeting its virulence mechanisms and overcoming drug resistance are essential steps toward effective therapeutic development. In this study, we focused on the Carbonic Anhydrase (CA, EC: 4.2.1.1) encoded by <em>P. gingivalis</em> as a potential drug target.</div><div>We determined the crystal structure of PgiCA γ at a resolution of 2.4 Å and conducted kinetic characterization. The structure revealed that active PgiCA γ forms a trimer, with each monomer comprising a left-handed β-helix capped by a C-terminal α-helix and coordinated to a catalytic zinc ion through three histidine residues. Interestingly, one monomer displayed an atypical α-helix conformation, likely due to close interactions with neighbouring trimers within the crystal lattice (a probable crystallographic artefact).</div><div>These findings provide new insights into the structural and functional properties of PgiCA γ, emphasizing its potential as a target for the development of novel anti-virulence therapies against <em>P. gingivalis.</em></div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"217 1","pages":"Article 108154"},"PeriodicalIF":3.0,"publicationDate":"2024-12-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142794925","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

Investigating the role of elastin and extracellular matrix damage in cardiovascular calcification 研究弹性蛋白和细胞外基质损伤在心血管钙化中的作用。

IF 3 3区生物学

Journal of structural biology Pub Date : 2024-12-04 DOI: 10.1016/j.jsb.2024.108140

Elham Radvar , Khushbu Mehta , Alexander D’Ambrosio , Giulia Mastroianni , Maisoon Al-Jawad , Molly M. Stevens , Alvaro Mata , Sherif Elsharkawy

引用次数: 0

Cryo-EM phase-plate images reveal unexpected levels of apparent specimen damage 低温电子显微镜相板图像显示出意想不到的试样明显损伤程度。

IF 3 3区生物学

Journal of structural biology Pub Date : 2024-12-01 DOI: 10.1016/j.jsb.2024.108150

Jonathan Remis , Petar N. Petrov , Jessie T. Zhang , Jeremy J. Axelrod , Hang Cheng , Shahar Sandhaus , Holger Mueller , Robert M. Glaeser

{"title":"Cryo-EM phase-plate images reveal unexpected levels of apparent specimen damage","authors":"Jonathan Remis , Petar N. Petrov , Jessie T. Zhang , Jeremy J. Axelrod , Hang Cheng , Shahar Sandhaus , Holger Mueller , Robert M. Glaeser","doi":"10.1016/j.jsb.2024.108150","DOIUrl":"10.1016/j.jsb.2024.108150","url":null,"abstract":"<div><div>Apoferritin (apoF) is commonly used as a test specimen in single-particle electron cryo-microscopy (cryo-EM), since it consistently produces density maps that go to 3 Å resolution or higher. When we imaged apoF with a laser phase plate (LPP), however, we observed more severe particle-to-particle variation in the images than we had previously thought to exist. Similarly, we found that images of ribulose bisphosphate carboxylase/oxygenase (rubisco) also exhibited a much greater amount of heterogeneity than expected. By comparison to simulations of images, we verified that the heterogeneity is not explained by the known features of the LPP, shot noise, or differences in particle orientation. We also demonstrate that our specimens are comparable to those previously used in the literature, based on using the final-reconstruction resolution as the metric for evaluation. All of this leads us to the hypothesis that the heterogeneity is due to damage that has occurred either during purification of the specimen or during preparation of the grids. It is not, however, our goal to explain the causes of heterogeneity; rather, we report that using the LPP has made the apparent damage too obvious to be ignored. In hindsight, similar heterogeneity can be seen in images of apoF and the 20S proteasome which others had recorded with a Volta phase plate. We therefore conclude that the increased contrast of phase-plate images (at low spatial frequencies) should also make it possible to visualize, on a single-particle basis, various forms of biologically functional heterogeneity in structure that had previously gone unnoticed.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"216 4","pages":"Article 108150"},"PeriodicalIF":3.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142622824","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