Journal of structural biology最新文献

{"title":"Building alternative splicing and evolution-aware sequence-structure maps for protein repeats","authors":"Antoine Szatkownik ,&nbsp;Diego Javier Zea ,&nbsp;Hugues Richard ,&nbsp;Elodie Laine","doi":"10.1016/j.jsb.2023.107997","DOIUrl":"10.1016/j.jsb.2023.107997","url":null,"abstract":"<div><p>Alternative splicing of repeats in proteins provides a mechanism for rewiring and fine-tuning protein interaction networks. In this work, we developed a robust and versatile method, ASPRING, to identify alternatively spliced protein repeats from gene annotations. ASPRING leverages evolutionary meaningful alternative splicing-aware hierarchical graphs to provide maps between protein repeats sequences and 3D structures. We re-think the definition of repeats by explicitly accounting for transcript diversity across several genes/species. Using a stringent sequence-based similarity criterion, we detected over 5,000 evolutionary conserved repeats by screening virtually all human protein-coding genes and their orthologs across a dozen species. Through a joint analysis of their sequences and structures, we extracted specificity-determining sequence signatures and assessed their implication in experimentally resolved and modelled protein interactions. Our findings demonstrate the widespread alternative usage of protein repeats in modulating protein interactions and open avenues for targeting repeat-mediated interactions.</p></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10273043","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":"Cell recognition based on atomic force microscopy and modified residual neural network","authors":"Junxi Wang ,&nbsp;Mingyan Gao ,&nbsp;Lixin Yang ,&nbsp;Yuxi Huang ,&nbsp;Jiahe Wang ,&nbsp;Bowei Wang ,&nbsp;Guicai Song ,&nbsp;Zuobin Wang","doi":"10.1016/j.jsb.2023.107991","DOIUrl":"10.1016/j.jsb.2023.107991","url":null,"abstract":"<div><p><span>Cell recognition methods are in high demand in cell biology and medicine, and the method based on atomic force microscopy (AFM) shows a great value in application. The difference in mechanical properties or morphology of cells has been frequently used to detect whether cells are cancerous, but this detection method cannot be a general means for cancer cell detection, and the traditional artificial feature extraction method also has its limitations. In this work, we proposed an analytic method based on the physical properties of cells and deep learning method for recognizing cell types. The residual neural network used for recognition was modified by multi-scale convolutional fusion, attention mechanism and depthwise separable convolution, so as to optimize feature extraction and reduce operation costs. In the method, the collected cells were imaged by AFM, and the processed images were analyzed by the optimized convolutional neural network. The recognition results of two groups of cells (HL-7702 and SMMC-7721, SGC-7901 and GES-1) by this method show that the recognition rate of dataset with the combination of cell surface morphology, adhesion and </span>Young's modulus is higher, and the recognition rate of the dataset with optimal resolution is higher. Our study indicated that the recognition of physical properties of cells using deep learning technology can serve as a universal and effective method for the automated analysis of cell information.</p></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10217487","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":"Double-headed binding of myosin II to F-actin shows the effect of strain on head structure","authors":"Alimohammad Hojjatian ,&nbsp;Dianne W. Taylor ,&nbsp;Nadia Daneshparvar ,&nbsp;Patricia M. Fagnant ,&nbsp;Kathleen M. Trybus ,&nbsp;Kenneth A. Taylor","doi":"10.1016/j.jsb.2023.107995","DOIUrl":"10.1016/j.jsb.2023.107995","url":null,"abstract":"<div><p>Force production in muscle is achieved through the interaction of myosin and actin. Strong binding states in active muscle are associated with Mg·ADP bound to the active site; release of Mg·ADP allows rebinding of ATP and dissociation from actin. Thus, Mg·ADP binding is positioned for adaptation as a force sensor. Mechanical loads on the lever arm can affect the ability of myosin to release Mg·ADP but exactly how this is done is poorly defined. Here we use F-actin decorated with double-headed smooth muscle myosin fragments in the presence of Mg·ADP to visualize the effect of internally supplied tension on the paired lever arms using cryoEM. The interaction of the paired heads with two adjacent actin subunits is predicted to place one lever arm under positive and the other under negative strain. The converter domain is believed to be the most flexible domain within myosin head. Our results, instead, point to the segment of heavy chain between the essential and regulatory light chains as the location of the largest structural change. Moreover, our results suggest no large changes in the myosin coiled coil tail as the locus of strain relief when both heads bind F-actin. The method would be adaptable to double-headed members of the myosin family. We anticipate that the study of actin-myosin interaction using double-headed fragments enables visualization of domains that are typically noisy in decoration with single-headed fragments.</p></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10544818/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10215427","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":"Identification and evaluation of potential inhibitor molecules against TcyA from Candidatus Liberibacter asiaticus","authors":"Sapna Lonare ,&nbsp;Monica Sharma ,&nbsp;Vikram Dalal ,&nbsp;Mrugendra Gubyad ,&nbsp;Pranav Kumar ,&nbsp;Deena Nath Gupta ,&nbsp;Akshay Pareek ,&nbsp;Shailly Tomar ,&nbsp;Dilip Kumar Ghosh ,&nbsp;Pravindra Kumar ,&nbsp;Ashwani Kumar Sharma","doi":"10.1016/j.jsb.2023.107992","DOIUrl":"10.1016/j.jsb.2023.107992","url":null,"abstract":"<div><p>Of the two putative amino acid binding periplasmic receptors of ABC transporter family in <em>Candidatus</em> Liberibacter asiaticus (CLas), cystine binding receptor (CLasTcyA) has been shown to mainly express in phloem of citrus plant and is a target for inhibitor development. The crystal structure of CLasTcyA in complex with substrates has been reported earlier. The present work reports the identification and evaluation of potential candidates for their inhibitory potential against CLasTcyA. Among many compounds, selected through virtual screening, and MD simulation, pimozide, clidinium, sulfasalazine and folic acid showed significantly higher affinities and stability in complex with CLasTcyA. The SPR studies with CLasTcyA revealed significantly higher binding affinities for pimozide and clidinium (Kd, 2.73 nM and 70 nM, respectively) as compared to cystine (Kd, 1.26 µM). The higher binding affinities could be attributed to significantly increased number of interactions in the binding pocket as evident from the crystal structures of CLasTcyA in complex with pimozide and clidinium as compared to cystine. The CLasTcyA possess relatively large binding pocket where bulkier inhibitors fit quite well. <em>In planta</em> studies, carried out to assess the effect of inhibitors on HLB infected Mosambi plants, showed significant reduction in CLas titre in plants treated with inhibitors as compared to control plants. The results showed that pimozide exhibited higher efficiency as compared to clidinium in reducing CLas titre in treated plants. Our results showed that the inhibitor development against critical proteins like CLasTcyA can be an important strategy in management of HLB.</p></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10218757","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":"The repetitive structure of DNA clamps: An overlooked protein tandem repeat","authors":"Paula Nazarena Arrías ,&nbsp;Alexander Miguel Monzon ,&nbsp;Damiano Clementel ,&nbsp;Soroush Mozaffari ,&nbsp;Damiano Piovesan ,&nbsp;Andrey V. Kajava ,&nbsp;Silvio C.E. Tosatto","doi":"10.1016/j.jsb.2023.108001","DOIUrl":"10.1016/j.jsb.2023.108001","url":null,"abstract":"<div><p>Structured tandem repeats proteins (STRPs) are a specific kind of tandem repeat proteins characterized by a modular and repetitive three-dimensional structure arrangement. The majority of STRPs adopt solenoid structures, but with the increasing availability of experimental structures and high-quality predicted structural models, more STRP folds can be characterized. Here, we describe “Box repeats”, an overlooked STRP fold present in the DNA sliding clamp processivity factors, which has eluded classification although structural data has been available since the late 1990s. Each Box repeat is a β⍺βββ module of about 60 residues, which forms a class V “beads-on-a-string” type STRP. The number of repeats present in processivity factors is organism dependent. Monomers of PCNA proteins in both Archaea and Eukarya have 4 repeats, while the monomers of bacterial beta-sliding clamps have 6 repeats. This new repeat fold has been added to the RepeatsDB database, which now provides structural annotation for 66 Box repeat proteins belonging to different organisms, including viruses.</p></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10218805","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":"The role of tandem repeats in bacterial functional amyloids","authors":"Alicja W. Nowakowska ,&nbsp;Jakub W. Wojciechowski ,&nbsp;Natalia Szulc ,&nbsp;Malgorzata Kotulska","doi":"10.1016/j.jsb.2023.108002","DOIUrl":"10.1016/j.jsb.2023.108002","url":null,"abstract":"<div><p>Repetitivity and modularity of proteins are two related notions incorporated into multiple evolutionary concepts. We discuss whether they may also be essential for functional amyloids. Amyloids are proteins that create very regular and usually highly insoluble fibrils, which are often associated with neurodegeneration. However, recent discoveries showed that amyloid structure of a protein could also be beneficial and desired, e.g., to promote cell adhesion. Functional amyloids are proteins which differ in their characteristics from pathological amyloids, so that the fibril formation could be more under control of an organism. We propose that repeats in the sequence could regulate the aggregation propensity of these proteins. The inclusion of multiple symmetric interactions, due to the presence of the repeats, could be supporting and strengthening the desirable structural properties of functional amyloids. Our results show that tandem repeats in bacterial functional amyloids have a distinct characteristic. The pattern of repeats supports the appropriate level of fibril formation and better controllability of fibril stability. The repeats tend to be more imperfect, which attenuates excessive aggregation propensity. Their desired structure and function are also reinforced by their amino acid profile. Although in the study we focused on bacterial functional amyloids, due to their importance in biofilm formation, we propose that similar mechanisms could be employed in other functional amyloids which are designed by evolution to aggregate in a desirable manner, but not necessarily in pathological amyloids.</p></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10225681","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":"Biological light-weight materials: The endoskeletons of cephalopod mollusks","authors":"Erika Griesshaber ,&nbsp;Antonio G. Checa ,&nbsp;Carmen Salas ,&nbsp;René Hoffmann ,&nbsp;Xiaofei Yin ,&nbsp;Rolf Neuser ,&nbsp;U. Rupp ,&nbsp;Wolfgang W. Schmahl","doi":"10.1016/j.jsb.2023.107988","DOIUrl":"10.1016/j.jsb.2023.107988","url":null,"abstract":"<div><p><span>Structural biological hard tissues fulfill diverse tasks: protection, defence, locomotion, structural support, reinforcement, buoyancy. The cephalopod mollusk </span><em>Spirula spirula</em> has a planspiral, endogastrically coiled, chambered, endoskeleton consisting of the main elements: shell-wall, septum, adapical-ridge, siphuncular-tube. The cephalopod mollusk <span><em>Sepia officinalis</em></span> has an oval, flattened, layered-cellular endoskeleton, formed of the main elements: dorsal-shield, wall/pillar, septum, siphuncular-zone. Both endoskeletons are light-weight buoyancy devices that enable transit through marine environments: vertical (<em>S. spirula</em>), horizontal (<em>S. officinalis</em>). Each skeletal element of the phragmocones has a specific morphology, component structure and organization. The conjunction of the different structural and compositional characteristics renders the evolved nature of the endoskeletons and facilitates for <em>Spirula</em> frequent migration from deep to shallow water and for <em>Sepia</em> coverage over large horizontal distances, without damage of the buoyancy device.</p><p>Based on Electron-Backscatter-Diffraction (EBSD) measurements and TEM, FE-SEM, laser-confocal-microscopy imaging we highlight for each skeletal element of the endoskeleton its specific mineral/biopolymer hybrid nature and constituent arrangement. We demonstrate that a variety of crystal morphologies and biopolymer assemblies are needed for enabling the endoskeleton to act as a buoyancy device. We show that all organic components of the endoskeletons have the structure of cholesteric-liquid-crystals and indicate which feature of the skeletal element yields the necessary mechanical property to enable the endoskeleton to fulfill its function. We juxtapose structural, microstructural, texture characteristics and benefits of coiled and planar endoskeletons and discuss how morphometry tunes structural biomaterial function. Both mollusks use their endoskeleton for buoyancy regulation, live and move, however, in distinct marine environments.</p></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10272529","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":"Locating cellular contents during cryoFIB milling using cellular secondary-electron imaging","authors":"Chao Lin ,&nbsp;Li Zhang ,&nbsp;Ziying Zhang ,&nbsp;Yifeng Jiang ,&nbsp;Xueming Li","doi":"10.1016/j.jsb.2023.108005","DOIUrl":"10.1016/j.jsb.2023.108005","url":null,"abstract":"<div><p>Cryo-electron tomography (cryoET) is a powerful technology that allows <em>in-situ</em> observation of the molecular structure of tissues and cells. Cryo-focused ion beam (cryoFIB) milling plays an important role in the preparation of high-quality thin lamellar samples for cryoET studies, thus, promoting the rapid development of cryoET in recent years. However, locating the regions of interest in a large cell or tissue during cryoFIB milling remains a major challenge limiting cryoET applications on arbitrary biological samples. Here, we report an on-the-fly localization method based on cellular secondary electron imaging (CSEI), which is derived from a basic imaging function of the cryoFIB instruments and enables high-contrast imaging of the cellular contents of frozen-hydrated biological samples. Moreover, CSEI does not require fluorescent labels and additional devices. The present study discusses the imaging principles and settings for optimizing CSEI. Tests on several commercially available cryoFIB instruments demonstrated that CSEI was feasible on mainstream instruments to observe all types of cellular contents and reliable under different milling conditions. We established a simple milling-localization workflow and tested it using the basal body of <em>Chlamydomonas reinhardtii</em>.</p></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10568126","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":"New protein families with hendecad coiled coils in the proteome of life","authors":"Mikel Martinez-Goikoetxea,&nbsp;Andrei N. Lupas","doi":"10.1016/j.jsb.2023.108007","DOIUrl":"10.1016/j.jsb.2023.108007","url":null,"abstract":"<div><p>Coiled coils are a widespread and well understood protein fold. Their short and simple repeats underpin considerable structural and functional diversity. The vast majority of coiled coils consist of 7-residue (heptad) sequence repeats, but in essence most combinations of 3- and 4-residue segments, each starting with a residue of the hydrophobic core, are compatible with coiled-coil structure. The most frequent among these other repeat patterns are 11-residue (hendecad, 3 + 4 + 4) repeats. Hendecads are frequently found in low copy number, interspersed between heptads, but some proteins consist largely or entirely of hendecad repeats. Here we describe the first large-scale survey of these proteins in the proteome of life. For this, we scanned the protein sequence database for sequences with 11-residue periodicity that lacked β-strand prediction. We then clustered these by pairwise similarity to construct a map of potential hendecad coiled-coil families. Here we discuss these according to their structural properties, their potential cellular roles, and the evolutionary mechanisms shaping their diversity. We note in particular the continuous amplification of hendecads, both within existing proteins and <em>de novo</em> from previously non-coding sequence, as a powerful mechanism in the genesis of new coiled-coil forms.</p></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10218019","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":"Focused classifications and refinements in high-resolution single particle cryo-EM analysis","authors":"Charles Barchet,&nbsp;Léo Fréchin,&nbsp;Samuel Holvec,&nbsp;Isabelle Hazemann,&nbsp;Ottilie von Loeffelholz,&nbsp;Bruno P. Klaholz","doi":"10.1016/j.jsb.2023.108015","DOIUrl":"10.1016/j.jsb.2023.108015","url":null,"abstract":"<div><p>Recent advances in cryo electron microscopy (cryo-EM) and image processing provide new opportunities to analyse drug targets at high resolution. However, structural heterogeneity limits resolution in many practical cases, hence restricting the level at which structural details can be analysed and drug design be performed. As structural disorder is not spread throughout the entire structure of a given macromolecular complex but instead is found in certain regions that move with respect to others and covering molecular scales from domain conformational changes up to the level of side chain conformations in ligand binding pockets, it is possible to focus the attention on those regions and the associated relative movements. Here we show how the usage of focused classifications and refinements provide insights into global conformational arrangements, exemplified on the human ribosome and on the cannabinoid G protein coupled receptor (GPCR), and how they can improve the local map resolution from an essentially disordered region to the 3–4 Å and finally to the 2 Å resolution range. A systematic analysis with variable spherical masks during focused refinement is presented showing that the choice of an optimal mask size helps refining to high resolution. This study covers several practical approaches on 4 examples illustrating how important mask size &amp; shape and including neighbouring structural elements are for a focused analysis of a macromolecular complex. Such methods will be crucial for cryo-EM structure-based drug design of various medical targets and are applicable to single particle cryo-EM and electron tomography data.</p></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10131345","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}