Journal of structural biology最新文献

Automatic detection of alignment errors in cryo-electron tomography.

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":"https://doi.org/10.1016/j.jsb.2024.108153","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":" ","pages":"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":"","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":"<p><p>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. In vivo, 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.</p>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":" ","pages":"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":"<p><p>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.</p>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":" ","pages":"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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Ensemble-function relationships: From qualitative to quantitative relationships between protein structure and function. 集合-功能关系：蛋白质结构与功能之间从定性到定量的关系。

IF 3 3区生物学

Journal of structural biology Pub Date : 2024-12-09 DOI: 10.1016/j.jsb.2024.108152

Filip Yabukarski

{"title":"Ensemble-function relationships: From qualitative to quantitative relationships between protein structure and function.","authors":"Filip Yabukarski","doi":"10.1016/j.jsb.2024.108152","DOIUrl":"10.1016/j.jsb.2024.108152","url":null,"abstract":"<p><p>Structure-function relationships are deeply rooted in modern biochemistry and structural biology and have provided the basis for our understanding of how protein structure defines function. While structure-function relationships continue to provide invaluable qualitative information, they cannot, in principle, provide the quantitative information ultimately needed to fully understand how proteins function and to make quantitative predictions about changes in activity from changes in sequence and structure. These limitations appear to arise from fundamental principles of physics, which dictate that proteins exist as interchanging ensembles of conformations, rather than as static structures that underly conventional structure-function relationships. This perspective discusses the concept of ensemble-function relationships as quantitative relationships that build on and extend traditional structure-function relationships. The concepts of free energy landscapes and conformational ensembles and their application to proteins are reviewed. The perspective summarizes a range of approaches that can provide conformational ensemble information and focuses on X-ray crystallography methods for obtaining experimental protein conformational ensembles. Focusing on enzymes as archetypes of protein function, recent literature examples are reviewed that used ensemble-function relationships to understand how protein residues contribute to function and how changes in protein sequence and structure impact activity, leading to new models and providing previously inaccessible mechanistic insights. Potential applications of conformational ensembles and ensemble-function relationships to protein design are examined. The perspective concludes with current limitations of the ensemble-function relationships and potential paths forward toward the next generation of quantitative ensemble-function models.</p>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":" ","pages":"108152"},"PeriodicalIF":3.0,"publicationDate":"2024-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142693247","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

Kinetic and structural studies of gamma-carbonic anhydrase from the oral pathogen Porphyromonas gingivalis.

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":"<p><p>Porphyromonas gingivalis, 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 P. gingivalis as a potential drug target. 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). 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 P. gingivalis.</p>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":" ","pages":"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.

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

Structural basis for the effects of Ser387 phosphorylation of MgcRacGAP on its GTPase-activating activities for CDC42 and RHOA MgcRacGAP 的 Ser387 磷酸化对其 CDC42 和 RHOA 的 GTPase 激活活性的影响的结构基础。

IF 3 3区生物学

Journal of structural biology Pub Date : 2024-11-09 DOI: 10.1016/j.jsb.2024.108151

Kazutaka Murayama , Miyuki Kato-Murayama , Toshiaki Hosaka , Toshio Kitamura , Shigeyuki Yokoyama , Mikako Shirouzu

{"title":"Structural basis for the effects of Ser387 phosphorylation of MgcRacGAP on its GTPase-activating activities for CDC42 and RHOA","authors":"Kazutaka Murayama , Miyuki Kato-Murayama , Toshiaki Hosaka , Toshio Kitamura , Shigeyuki Yokoyama , Mikako Shirouzu","doi":"10.1016/j.jsb.2024.108151","DOIUrl":"10.1016/j.jsb.2024.108151","url":null,"abstract":"<div><div>MgcRacGAP is a GTPase-activating protein (GAP) for the Rho family GTPases. During cytokinesis, MgcRacGAP localizes to the midbody, where it activates the GTPase activity of Rho family GTPases to facilitate cytokinesis. In the midbody, Aurora B phosphorylates Ser387 within the GAP domain of human MgcRacGAP, a modification that is suggested to influence GTPase preference. However, there are conflicting reports, with some studies indicating that Ser387 phosphorylation does not alter the GTPase preference of MgcRacGAP. This controversy highlights the need for a deeper understanding of the molecular interactions involved, which can be clarified through structural analyses. In the present study, we determined the crystal structures of the wild-type MgcRacGAP GAP domain complexed with CDC42•GDP•AlF<sub>4</sub><sup>−</sup> and the S378D phosphomimetic mutant GAP domain fused with RHOA•GDP•AlF<sub>4</sub><sup>−</sup>. Additionally, crystal structures of the GAP domains were determined for the S387D and S387A mutants. Our analysis revealed that neither GTPase binding nor S387D mutation affected the overall structure of the GAP domain. However, comparison of the CDC42•MgcRacGAP (wild-type) complex with the RHOA-MgcRacGAP(S378D) fusion protein structure indicated that the S387D mutation caused positional shifts in both CDC42 and RHOA relative to MgcRacGAP. These shifts reduced interactions with CDC42 more severely than those with RHOA. In fact, the S387D mutation decreased the GTPase-activating activity of MgcRacGAP toward CDC42, while its impact on RHOA was only moderate. This difference in the rate of activity reduction may play an important role in GTPase preference.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"216 4","pages":"Article 108151"},"PeriodicalIF":3.0,"publicationDate":"2024-11-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142622763","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

Computational study of the HLTF ATPase remodeling domain suggests its activity on dsDNA and implications in damage tolerance 对 HLTF ATPase 重塑结构域的计算研究表明了它在 dsDNA 上的活性以及对损伤耐受性的影响。

IF 3 3区生物学

Journal of structural biology Pub Date : 2024-11-02 DOI: 10.1016/j.jsb.2024.108149

Martin Ljubic , Claudia D’Ercole , Yossma Waheed , Ario de Marco , Jure Borišek , Matteo De March

{"title":"Computational study of the HLTF ATPase remodeling domain suggests its activity on dsDNA and implications in damage tolerance","authors":"Martin Ljubic , Claudia D’Ercole , Yossma Waheed , Ario de Marco , Jure Borišek , Matteo De March","doi":"10.1016/j.jsb.2024.108149","DOIUrl":"10.1016/j.jsb.2024.108149","url":null,"abstract":"<div><div>The Helicase-Like Transcription Factor (HLTF) is member of the SWI/SNF-family of ATP dependent chromatin remodellers known primarily for maintaining genome stability. Biochemical and cellular assays support its multiple roles in DNA Damage Tolerance. However, the lack of sufficient structural data limits the comprehension of the molecular basis of its modes of action.</div><div>In this work we have modelled and characterized the HLTF ATPase remodeling domain by using bioinformatic tools and all-atoms molecular dynamics simulations.</div><div><em>In-silico</em> results suggested that its binding to dsDNA is mainly mediated by the positively charged residues Arg563 and Lys913, found conserved in HLTF homologs, and Arg620 and Lys999, found only in HLTF. Interestingly, these residues are mutated in cancer cells. During translocation on dsDNA, HLTF remains persistently bound through the N-terminal ATPase subunit. However, DNA advancement occurs only in the presence of the synergic-anticorrelated action of both motor lobes. In contrast, the C-terminal facilitates substrate remodeling through DNA deformation and generation of bulges according to a wave-model. Finally, the large conformational change suggested between the two motor-remodeling subunits might be activated upon the release of PARP1 on stalled fork and be responsible for the intervention of HLTF-HIRAN in the formation of D-loop and 4-way junction DNA structures.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"216 4","pages":"Article 108149"},"PeriodicalIF":3.0,"publicationDate":"2024-11-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142568819","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

Vesicle Picker: A tool for efficient identification of membrane protein complexes in vesicles 囊泡拾取器：有效识别囊泡中膜蛋白复合物的工具。

IF 3 3区生物学

Journal of structural biology Pub Date : 2024-10-30 DOI: 10.1016/j.jsb.2024.108148

Ryan Karimi , Claire E. Coupland , John L. Rubinstein

{"title":"Vesicle Picker: A tool for efficient identification of membrane protein complexes in vesicles","authors":"Ryan Karimi , Claire E. Coupland , John L. Rubinstein","doi":"10.1016/j.jsb.2024.108148","DOIUrl":"10.1016/j.jsb.2024.108148","url":null,"abstract":"<div><div>Electron cryomicroscopy (cryo-EM) has recently allowed determination of near-atomic resolution structures of membrane proteins and protein complexes embedded in lipid vesicles. However, particle selection from electron micrographs of these vesicles can be challenging due to the strong signal contributed from the lipid bilayer. This challenge often requires iterative and laborious particle selection workflows to generate a dataset of high-quality particle images for subsequent analysis. Here we present Vesicle Picker, an open-source program built on the Segment Anything model. Vesicle Picker enables automatic identification of vesicles in cryo-EM micrographs with high recall and precision. It then exhaustively selects all potential particle locations, either at the perimeter or uniformly over the surface of the projection of the vesicle. The program is designed to interface with cryoSPARC, which performs both upstream micrograph processing and downstream single particle image analysis. We demonstrate Vesicle Picker’s utility by determining a high-resolution map of the vacuolar-type ATPase from micrographs of native synaptic vesicles (SVs) and identifying an additional protein or protein complex in the SV membrane.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"216 4","pages":"Article 108148"},"PeriodicalIF":3.0,"publicationDate":"2024-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142558096","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