Journal of structural biology最新文献

{"title":"Miffi: Improving the accuracy of CNN-based cryo-EM micrograph filtering with fine-tuning and Fourier space information","authors":"Da Xu,&nbsp;Nozomi Ando","doi":"10.1016/j.jsb.2024.108072","DOIUrl":"10.1016/j.jsb.2024.108072","url":null,"abstract":"<div><p>Efficient and high-accuracy filtering of cryo-electron microscopy (cryo-EM) micrographs is an emerging challenge with the growing speed of data collection and sizes of datasets. Convolutional neural networks (CNNs) are machine learning models that have been proven successful in many computer vision tasks, and have been previously applied to cryo-EM micrograph filtering. In this work, we demonstrate that two strategies, fine-tuning models from pretrained weights and including the power spectrum of micrographs as input, can greatly improve the attainable prediction accuracy of CNN models. The resulting software package, Miffi, is open-source and freely available for public use (<span>https://github.com/ando-lab/miffi</span><svg><path></path></svg>).</p></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"216 2","pages":"Article 108072"},"PeriodicalIF":3.0,"publicationDate":"2024-02-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140021986","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}

{"title":"Comprehensive structural overview of the C-terminal ligand-binding domains of the TetR family regulators","authors":"Jakub Filipek ,&nbsp;Katarzyna Chalaskiewicz ,&nbsp;Aleksandra Kosmider ,&nbsp;Maciej Nielipinski ,&nbsp;Agnieszka Michalak ,&nbsp;Maria Bednarkiewicz ,&nbsp;Mieszko Goslawski-Zeligowski ,&nbsp;Filip Prucnal ,&nbsp;Bartosz Sekula ,&nbsp;Agnieszka J. Pietrzyk-Brzezinska","doi":"10.1016/j.jsb.2024.108071","DOIUrl":"10.1016/j.jsb.2024.108071","url":null,"abstract":"<div><p>TetR family regulators (TFRs) represent a large group of one-component bacterial signal transduction systems which recognize environmental signals, like the presence of antibiotics or other bactericidal compounds, and trigger the cell response by regulating the expression of genes that secure bacterial survival in harsh environmental conditions. TFRs act as homodimers, each protomer is composed of a conserved DNA-binding N-terminal domain (NTD) and a variable ligand-binding C-terminal domain (CTD). Currently, there are about 500 structures of TFRs available in the Protein Data Bank and one-fourth of them represent the structures of TFR-ligand complexes. In this review, we summarized information on the ligands interacting with TFRs and based on structural data, we compared the CTDs of the TFR family members, as well as their ligand-binding cavities. Additionally, we divided the whole TFR family, including more than half of a million sequences, into subfamilies according to calculated multiple sequence alignment and phylogenetic tree. We also highlighted structural elements characteristic of some of the subfamilies. The presented comprehensive overview of the TFR CTDs provides good bases and future directions for further studies on TFRs that are not only important targets for battling multidrug resistance but also good candidates for many biotechnological approaches, like TFR-based biosensors.</p></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"216 2","pages":"Article 108071"},"PeriodicalIF":3.0,"publicationDate":"2024-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S104784772400011X/pdfft?md5=7a66a16b64c4f9dc5fdbc218ff7cf207&pid=1-s2.0-S104784772400011X-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139944182","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}

{"title":"The structural biology of type III CRISPR-Cas systems","authors":"Xuzichao Li ,&nbsp;Jie Han ,&nbsp;Jie Yang ,&nbsp;Heng Zhang","doi":"10.1016/j.jsb.2024.108070","DOIUrl":"10.1016/j.jsb.2024.108070","url":null,"abstract":"<div><p>CRISPR-Cas system is an RNA-guided adaptive immune system widespread in bacteria and archaea. Among them, type III CRISPR-Cas systems are the most ancient throughout the CRISPR-Cas family, proving anti-phage defense through a crRNA-guided RNA targeting manner and possessing multiple enzymatic activities. Type III CRISPR-Cas systems comprise four typical members (type III-A to III-D) and two atypical members (type III-E and type III-F), providing immune defense through distinct mechanisms. Here, we delve into structural studies conducted on three well-characterized members: the type III-A, III-B, and III-E systems, provide an overview of the structural insights into the crRNA-guided target RNA cleavage, self/non-self discrimination, and the target RNA-dependent regulation of enzymatic subunits in the effector complex.</p></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"216 1","pages":"Article 108070"},"PeriodicalIF":3.0,"publicationDate":"2024-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139940144","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}

{"title":"Obituary Luis Bachmann","authors":"Helmut Plattner,&nbsp;Wolfgang Baumeister","doi":"10.1016/j.jsb.2024.108069","DOIUrl":"10.1016/j.jsb.2024.108069","url":null,"abstract":"","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"216 2","pages":"Article 108069"},"PeriodicalIF":3.0,"publicationDate":"2024-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139922824","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}

{"title":"ColabSeg: An interactive tool for editing, processing, and visualizing membrane segmentations from cryo-ET data","authors":"Marc Siggel ,&nbsp;Rasmus K. Jensen ,&nbsp;Valentin J. Maurer ,&nbsp;Julia Mahamid ,&nbsp;Jan Kosinski","doi":"10.1016/j.jsb.2024.108067","DOIUrl":"10.1016/j.jsb.2024.108067","url":null,"abstract":"<div><p>Cellular cryo-electron tomography (cryo-ET) has emerged as a key method to unravel the spatial and structural complexity of cells in their near-native state at unprecedented molecular resolution. To enable quantitative analysis of the complex shapes and morphologies of lipid membranes, the noisy three-dimensional (3D) volumes must be segmented. Despite recent advances, this task often requires considerable user intervention to curate the resulting segmentations. Here, we present ColabSeg, a Python-based tool for processing, visualizing, editing, and fitting membrane segmentations from cryo-ET data for downstream analysis. ColabSeg makes many well-established algorithms for point-cloud processing easily available to the broad community of structural biologists for applications in cryo-ET through its graphical user interface (GUI). We demonstrate the usefulness of the tool with a range of use cases and biological examples. Finally, for a large <em>Mycoplasma pneumoniae</em> dataset of 50 tomograms, we show how ColabSeg enables high-throughput membrane segmentation, which can be used as valuable training data for fully automated convolutional neural network (CNN)-based segmentation.</p></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"216 2","pages":"Article 108067"},"PeriodicalIF":3.0,"publicationDate":"2024-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1047847724000078/pdfft?md5=c9c0c144f4c61f0c5ff3e9147ffe9c17&pid=1-s2.0-S1047847724000078-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139898077","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}

{"title":"A strategic approach for efficient cryo-EM grid optimization using design of experiments","authors":"Rose Marie Haynes ,&nbsp;Janette Myers ,&nbsp;Claudia S. López ,&nbsp;James Evans ,&nbsp;Omar Davulcu ,&nbsp;Craig Yoshioka","doi":"10.1016/j.jsb.2024.108068","DOIUrl":"10.1016/j.jsb.2024.108068","url":null,"abstract":"<div><div>In recent years, cryo-electron microscopy (cryo-EM) has become a practical and effective method of determining structures at previously unattainable resolutions due to advances in detection, automation, and data processing. However, sample preparation remains a major bottleneck in the cryo-EM workflow. Even after the arduous process of biochemical sample optimization, it often takes several iterations of grid vitrification and screening to determine the optimal grid freezing parameters that yield suitable ice thickness and particle distribution for data collection. Since a high-quality sample is imperative for high-resolution structure determination, grid optimization is a vital step. For researchers who rely on cryo-EM facilities for grid screening, each iteration of this optimization process may delay research progress by a matter of months. Therefore, a more strategic and efficient approach should be taken to ensure that the grid optimization process can be completed in as few iterations as possible. Here, we present an implementation of Design of Experiments (DOE) to expedite and strategize the grid optimization process. A Fractional Factorial Design (FFD) guides the determination of a limited set of experimental conditions which can model the full parameter space of interest. Grids are frozen with these conditions and screened for particle distribution and ice thickness. Quantitative scores are assigned to each of these grid characteristics based on a qualitative rubric. Input conditions and response scores are used to generate a least-squares regression model of the parameter space in JMP, which is used to determine the conditions which should, in theory, yield optimal grids. Upon testing this approach on apoferritin and L-glutamate dehydrogenase on both the Vitrobot Mark IV and the Leica GP2 plunge freezers, the resulting grid conditions reliably yielded grids with high-quality ice and particle distribution that were suitable for collecting large overnight datasets on a Krios. We conclude that a DOE-based approach is a cost-effective and time-saving tool for cryo-EM grid preparation.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"217 1","pages":"Article 108068"},"PeriodicalIF":3.0,"publicationDate":"2024-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139746779","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}

{"title":"Control of crystal growth during coccolith formation by the coccolithophore Gephyrocapsa oceanica","authors":"Alexander Triccas ,&nbsp;Fraser Laidlaw ,&nbsp;Martin R. Singleton ,&nbsp;Fabio Nudelman","doi":"10.1016/j.jsb.2024.108066","DOIUrl":"10.1016/j.jsb.2024.108066","url":null,"abstract":"<div><p>Coccolithophores are marine phytoplankton that produce calcite mineral scales called coccoliths. Many stages in the synthesis of these structures are still unresolved, making it difficult to accurately quantify the energetic costs involved in calcification, required to determine the response coccolith mineralization will have to rising ocean acidification and temperature created by an increase in global CO2 concentrations. To clarify this, an improved understanding of how coccolithophores control the fundamental processes of crystallization, including nucleation, growth, and morphology, is needed. Here, we study how crystal growth and morphology is controlled in the coccolithophore <em>Gephyrocapsa oceanica</em> by imaging coccoliths at various stages of maturity using cryo-transmission electron microscopy (cryoTEM), scanning electron microscopy (SEM) and focused ion beam SEM (FIB-SEM). We reveal that coccolith units tightly interlock with each other due to the non-vertical alignment of the two-layered tube element, causing these mineral units to extend over the adjacent crystals. In specific directions, the growth of the coccolith tube seems to be impacted by the physical constraint created by the close association of neighbouring units around the ring, influencing the overall morphology and organization of the crystals that develop. Our findings contribute to the overall understanding of how biological systems can manipulate crystallization to produce functional mineralized tissues.</p></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"216 1","pages":"Article 108066"},"PeriodicalIF":3.0,"publicationDate":"2024-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1047847724000066/pdfft?md5=e650e944fc9dfcf785c724a2072652d9&pid=1-s2.0-S1047847724000066-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139729869","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}

{"title":"Crystal structures of the fatty acid biosynthesis initiation enzymes in Bacillus subtilis","authors":"Christopher D. Radka ,&nbsp;Charles O. Rock","doi":"10.1016/j.jsb.2024.108065","DOIUrl":"10.1016/j.jsb.2024.108065","url":null,"abstract":"<div><p>Bacteria use the fatty acid composition of membrane lipids to maintain homeostasis of the bilayer. β-Ketoacyl-ACP synthase III (FabH) initiates fatty acid biosynthesis and is the primary determinant of the fatty acid composition. FabH condenses malonyl-acyl carrier protein with an acyl-Coenzyme A primer to form β -ketoacyl-acyl carrier protein which is used to make substrates for lipid synthesis. The acyl-Coenzyme A primer determines whether an acyl chain in the membrane has iso, anteiso, or no branching (straight chain) and biophysical properties of the membrane. The soil bacterium <em>Bacillus subtilis</em> encodes two copies of FabH (<em>Bs</em>FabHA and <em>Bs</em>FabHB), and here we solve their crystal structures. The substrate-free 1.85 Å and 2.40 Å structures of <em>Bs</em>FabHA and <em>Bs</em>FabHB show both enzymes have similar residues that line the active site but differ in the architecture surrounding the catalytic residues and oxyanion hole. Branching in the <em>Bs</em>FabHB active site may better accommodate the structure of an iso-branched acyl-Coenzyme A molecule and thus confer superior utilization to <em>Bs</em>FabHA for this primer type. The 2.02 Å structure of <em>Bs</em>FabHA•Coenzyme A shows how the active site architecture changes after binding the first substrate. The other notable difference is an amino acid insertion in <em>Bs</em>FabHB that extends a cap that covers the dimer interface. The cap topology is diverse across FabH structures and appears to be a distinguishing feature. FabH enzymes have variable sensitivity to natural product inhibitors and the availability of crystal structures help clarify how nature designs antimicrobials that differentially target FabH homologs.</p></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"216 1","pages":"Article 108065"},"PeriodicalIF":3.0,"publicationDate":"2024-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1047847724000054/pdfft?md5=241a6f10088e07721d7498722a671e26&pid=1-s2.0-S1047847724000054-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139678482","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}

{"title":"Characterization of a new extra-axonemal structure in the Giardia intestinalis flagella","authors":"Raphael Verdan ,&nbsp;Beatriz Patricio ,&nbsp;Gilberto Weismuller ,&nbsp;Kildare Miranda ,&nbsp;Wanderley de Souza ,&nbsp;Marlene Benchimol ,&nbsp;Ana Paula Gadelha","doi":"10.1016/j.jsb.2024.108064","DOIUrl":"10.1016/j.jsb.2024.108064","url":null,"abstract":"<div><p>The inner structure of the flagella of <span><em>Giardia</em><em> intestinalis</em></span><span> is similar to that of other organisms, consisting of nine pairs of outer microtubules and a central pair containing radial spokes. Although the 9+2 axonemal structure is conserved, it is not clear whether subregions, including the transition zone, are present in the flagella of this parasite. </span><em>Giardia</em><span> axonemes<span> originate from basal bodies and have a lengthy cytosolic portion before becoming active flagella. The region of the emergence of the flagellum is not accompanied by any membrane specialization, as seen in other protozoa. Although </span></span><em>Giardia</em> is an intriguing model of study, few works focused on the ultrastructural analysis of the flagella of this parasite. Here, we analyzed the externalization region of the <em>G. intestinalis</em><span> flagella using ultra-high resolution scanning microscopy (with electrons and ions), atomic force microscopy<span> in liquid medium, freeze fracture, and electron tomography. Our data show that this region possesses a distinctive morphological feature – it extends outward and takes on a ring-like shape. When the plasma membrane is removed, a structure surrounding the axoneme becomes visible in this region. This new extra-axonemal structure is observed in all pairs of flagella of trophozoites and remains attached to the axoneme even when the interconnections between the axonemal microtubules are disrupted. High-resolution scanning electron microscopy provided insights into the arrangement of this structure, contributing to the characterization of the externalization region of the flagella of this parasite.</span></span></p></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"216 1","pages":"Article 108064"},"PeriodicalIF":3.0,"publicationDate":"2024-01-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139570592","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}

{"title":"A strained N-capping motif in α-helices of βαβ-units","authors":"Anton M. Kargatov","doi":"10.1016/j.jsb.2024.108063","DOIUrl":"10.1016/j.jsb.2024.108063","url":null,"abstract":"<div><p>A novel helical N-capping motif has been considered. It occurs in the βα-arches of right-handed βαβ-units and contains an N-cap residue in a sterically strained conformation. Moreover, this amino acid position contains almost no glycines, that could relieve strain. It was shown that the N-cap adopts this conformation as a result of the unusual convergence between the second and third amino acid positions of the α-helix (counting from the N-cap) and the second position of the preceding β-strand. This is achieved by the presence of glycines in the specified positions (i.e. positions <em>i</em> – 2, <em>i</em> + 2 and <em>i</em> + 3, if N-cap is <em>i</em>). The N-cap conformation is stabilized by a hydrogen bond between the backbone amide group in the second position of the α-helix and the carbonyl group in the first position of the β-strand. The occurrence of similar N-capping motifs in different types of βαβ-units was compared and their structural differences caused by the influence of the environment were described. Study results may be useful for protein design and ab initio prediction of the 3D protein structure.</p></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"216 1","pages":"Article 108063"},"PeriodicalIF":3.0,"publicationDate":"2024-01-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139509702","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}