Journal of Structural Biology: X最新文献_第9页

In situ structural analysis of the flagellum attachment zone in Trypanosoma brucei using cryo-scanning transmission electron tomography 应用冷冻扫描透射电子断层扫描技术对布氏锥虫鞭毛附着区的原位结构分析

IF 2.9

Journal of Structural Biology: X Pub Date : 2020-01-01 DOI: 10.1016/j.yjsbx.2020.100033

Sylvain Trépout

{"title":"In situ structural analysis of the flagellum attachment zone in Trypanosoma brucei using cryo-scanning transmission electron tomography","authors":"Sylvain Trépout","doi":"10.1016/j.yjsbx.2020.100033","DOIUrl":"https://doi.org/10.1016/j.yjsbx.2020.100033","url":null,"abstract":"<div><p>The flagellum of <em>Trypanosoma brucei</em> is a 20 µm-long organelle responsible for locomotion and cell morphogenesis. The flagellum attachment zone (FAZ) is a multi-protein complex whose function is to attach the flagellum to the cell body but also to guide cytokinesis. Cryo-transmission electron microscopy is a tool of choice to access the structure of the FAZ in a close-to-native state. However, because of the large dimension of the cell body, the whole FAZ cannot be structurally studied <em>in situ</em> at the nanometre scale in 3D using classical transmission electron microscopy approaches. In the present work, cryo-scanning transmission electron tomography, a new method capable of investigating cryo-fixed thick biological samples, has been used to study whole <em>T. brucei</em> cells at the bloodstream stage. The method has been used to visualise and characterise the structure and organisation of the FAZ filament. It is composed of an array of cytoplasmic stick-like structures. These sticks are heterogeneously distributed between the posterior part and the anterior tip of the cell. This cryo-STET investigation provides new insights into the structure of the FAZ filament. In combination with protein structure predictions, this work proposes a new model for the elongation of the FAZ.</p></div>","PeriodicalId":17238,"journal":{"name":"Journal of Structural Biology: X","volume":"4 ","pages":"Article 100033"},"PeriodicalIF":2.9,"publicationDate":"2020-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.yjsbx.2020.100033","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72113477","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 9

Specificity and regulation of phosphotyrosine signaling through SH2 domains 磷酸化酪氨酸信号通过SH2结构域的特异性和调控

IF 2.9

Journal of Structural Biology: X Pub Date : 2020-01-01 DOI: 10.1016/j.yjsbx.2020.100026

Michelangelo Marasco , Teresa Carlomagno

引用次数: 17

Essential role of calcium in extending RTX adhesins to their target 钙在将RTX粘连蛋白延伸到其靶标中的重要作用

IF 2.9

Journal of Structural Biology: X Pub Date : 2020-01-01 DOI: 10.1016/j.yjsbx.2020.100036

Tyler D.R. Vance , Qilu Ye, Brigid Conroy, Peter L. Davies

{"title":"Essential role of calcium in extending RTX adhesins to their target","authors":"Tyler D.R. Vance , Qilu Ye, Brigid Conroy, Peter L. Davies","doi":"10.1016/j.yjsbx.2020.100036","DOIUrl":"10.1016/j.yjsbx.2020.100036","url":null,"abstract":"<div><p>RTX adhesins are long, multi-domain proteins present on the outer membrane of many Gram-negative bacteria. From this vantage point, adhesins use their distal ligand-binding domains for surface attachment leading to biofilm formation. To expand the reach of the ligand-binding domains, RTX adhesins maintain a central extender region of multiple tandem repeats, which makes up most of the proteins’ large molecular weight. Alignments of the 10-15-kDa extender domains show low sequence identity between adhesins. Here we have produced and structurally characterized protein constructs of four tandem repeats (tetra-tandemers) from two different RTX adhesins. In comparing the tetra-tandemers to each other and already solved structures from <em>Marinomonas primoryensis</em> and <em>Salmonella enterica</em>, the extender domains fold as diverse beta-sandwich structures with widely differing calcium contents. However, all the tetra-tandemers have at least one calcium ion coordinated in the linker region between beta-sandwich domains whose role appears to be the rigidification of the extender region to help the adhesin extend its reach.</p></div>","PeriodicalId":17238,"journal":{"name":"Journal of Structural Biology: X","volume":"4 ","pages":"Article 100036"},"PeriodicalIF":2.9,"publicationDate":"2020-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.yjsbx.2020.100036","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38426633","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 4

High resolution CryoEM structure of the ring-shaped virulence factor EspB from Mycobacterium tuberculosis 结核分枝杆菌环状毒力因子EspB的高分辨率CryoEM结构

IF 2.9

Journal of Structural Biology: X Pub Date : 2020-01-01 DOI: 10.1016/j.yjsbx.2020.100029

Jérémie Piton , Florence Pojer , Soichi Wakatsuki , Cornelius Gati , Stewart T. Cole

{"title":"High resolution CryoEM structure of the ring-shaped virulence factor EspB from Mycobacterium tuberculosis","authors":"Jérémie Piton , Florence Pojer , Soichi Wakatsuki , Cornelius Gati , Stewart T. Cole","doi":"10.1016/j.yjsbx.2020.100029","DOIUrl":"https://doi.org/10.1016/j.yjsbx.2020.100029","url":null,"abstract":"<div><p>The EspB protein of <em>Mycobacterium tuberculosis</em> is a 60 kDa virulence factor, implicated in conjugation and exported by the ESX-1 system of which it may also be a component. Previous attempts to obtain high-resolution maps of EspB by cryo-electron microscopic examination of single particles have been thwarted by severe orientation bias of the particles. This was overcome by using detergent as a surfactant thereby allowing reconstruction of the EspB structure at 3.37 Å resolution. The final structure revealed the N-terminal domain of EspB to be organized as a cylindrical heptamer with dimensions of 90 Å x 90 Å and a central channel of 45 Å diameter whereas the C-terminal domain was unstructured. New atomic insight was obtained into the helical packing required for protomer interactions and the overall electrostatic potential. The external surface is electronegatively charged while the channel is lined with electropositive patches. EspB thus has many features of a pore-like transport protein that might allow the passage of an ESX-1 substrate such as the 35 Å diameter EsxA-EsxB heterodimer or B-form DNA consistent with its proposed role in DNA uptake.</p></div>","PeriodicalId":17238,"journal":{"name":"Journal of Structural Biology: X","volume":"4 ","pages":"Article 100029"},"PeriodicalIF":2.9,"publicationDate":"2020-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.yjsbx.2020.100029","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72076018","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 17

In crystallo-screening for discovery of human norovirus 3C-like protease inhibitors 人诺如病毒3C样蛋白酶抑制剂的晶体内筛选

IF 2.9

Journal of Structural Biology: X Pub Date : 2020-01-01 DOI: 10.1016/j.yjsbx.2020.100031

Jingxu Guo , Alice Douangamath , Weixiao Song , Alun R. Coker , A.W. Edith Chan , Steve P. Wood , Jonathan B. Cooper , Efrat Resnick , Nir London , Frank von Delft

{"title":"In crystallo-screening for discovery of human norovirus 3C-like protease inhibitors","authors":"Jingxu Guo , Alice Douangamath , Weixiao Song , Alun R. Coker , A.W. Edith Chan , Steve P. Wood , Jonathan B. Cooper , Efrat Resnick , Nir London , Frank von Delft","doi":"10.1016/j.yjsbx.2020.100031","DOIUrl":"https://doi.org/10.1016/j.yjsbx.2020.100031","url":null,"abstract":"<div><p>Outbreaks of human epidemic nonbacterial gastroenteritis are mainly caused by noroviruses. Viral replication requires a 3C-like cysteine protease (3CL<sup>pro</sup>) which processes the 200 kDa viral polyprotein into six functional proteins. The 3CL<sup>pro</sup> has attracted much interest due to its potential as a target for antiviral drugs. A system for growing high-quality crystals of native Southampton norovirus 3CL<sup>pro</sup> (SV3CP) has been established, allowing the ligand-free crystal structure to be determined to 1.3 Å in a tetrameric state. This also allowed crystal-based fragment screening to be performed with various compound libraries, ultimately to guide drug discovery for SV3CP. A total of 19 fragments were found to bind to the protease out of the 844 which were screened. Two of the hits were located at the active site of SV3CP and showed good inhibitory activity in kinetic assays. Another 5 were found at the enzyme’s putative RNA-binding site and a further 11 were located in the symmetric central cavity of the tetramer.</p></div>","PeriodicalId":17238,"journal":{"name":"Journal of Structural Biology: X","volume":"4 ","pages":"Article 100031"},"PeriodicalIF":2.9,"publicationDate":"2020-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.yjsbx.2020.100031","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72076019","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2

Measurement of local resolution in electron tomography 电子断层扫描局部分辨率的测量

IF 2.9

Journal of Structural Biology: X Pub Date : 2020-01-01 DOI: 10.1016/j.yjsbx.2019.100016

J.L. Vilas , J. Oton , C. Messaoudi , R. Melero , P. Conesa , E. Ramirez-Aportela , J. Mota , M. Martinez , A. Jimenez , R. Marabini , J.M. Carazo , J. Vargas , C.O.S. Sorzano

{"title":"Measurement of local resolution in electron tomography","authors":"J.L. Vilas , J. Oton , C. Messaoudi , R. Melero , P. Conesa , E. Ramirez-Aportela , J. Mota , M. Martinez , A. Jimenez , R. Marabini , J.M. Carazo , J. Vargas , C.O.S. Sorzano","doi":"10.1016/j.yjsbx.2019.100016","DOIUrl":"10.1016/j.yjsbx.2019.100016","url":null,"abstract":"<div><p>Resolution (global and local) is one of the most reported metrics of quality measurement in Single Particle Analysis (SPA). However, in electron tomography, the situation is different and its computation is not straightforward. Typically, resolution estimation is global and, therefore, reduces the assessment of a whole tomogram to a single number. However, it is known that tomogram quality is spatially variant. Still, up to our knowledge, a method to estimate local quality metrics in tomography is lacking. This work introduces <em>MonoTomo</em>, a method developed to estimate locally in a tomogram the highest reliable frequency component, expressed as a form of local resolution. The fundamentals lie in a local analysis of the density map via monogenic signals, which, in analogy to <em>MonoRes</em>, allows for local estimations. Results with experimental data show that the local resolution range that MonoTomo casts agrees with reported resolution values for experimental data sets, with the advantage of providing a local estimation. A range of applications of <em>MonoTomo</em> are suggested for further exploration.</p></div>","PeriodicalId":17238,"journal":{"name":"Journal of Structural Biology: X","volume":"4 ","pages":"Article 100016"},"PeriodicalIF":2.9,"publicationDate":"2020-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.yjsbx.2019.100016","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38137262","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 11

Small angle X-ray scattering and molecular dynamic simulations provide molecular insight for stability of recombinant human transferrin 小角度x射线散射和分子动力学模拟为重组人转铁蛋白的稳定性提供了分子视角

IF 2.9

Journal of Structural Biology: X Pub Date : 2020-01-01 DOI: 10.1016/j.yjsbx.2019.100017

Alina Kulakova , Sowmya Indrakumar , Pernille Sønderby , Lorenzo Gentiluomo , Werner Streicher , Dierk Roessner , Wolfgang Frieß , Günther H.J. Peters , Pernille Harris

{"title":"Small angle X-ray scattering and molecular dynamic simulations provide molecular insight for stability of recombinant human transferrin","authors":"Alina Kulakova , Sowmya Indrakumar , Pernille Sønderby , Lorenzo Gentiluomo , Werner Streicher , Dierk Roessner , Wolfgang Frieß , Günther H.J. Peters , Pernille Harris","doi":"10.1016/j.yjsbx.2019.100017","DOIUrl":"10.1016/j.yjsbx.2019.100017","url":null,"abstract":"<div><p>Transferrin is an attractive candidate for drug delivery due to its ability to cross the blood brain barrier. However, in order to be able to use it for therapeutic purposes, it is important to investigate how its stability depends on different formulation conditions. Combining high-throughput thermal and chemical denaturation studies with small angle X-ray scattering (SAXS) and molecular dynamics (MD) simulations, it was possible to connect the stability of transferrin with its conformational changes. Lowering pH induces opening of the transferrin N-lobe, which results in a negative effect on the stability. Presence of NaCl or arginine at low pH enhances the opening and has a negative impact on the overall protein stability.</p></div><div><h3>Statement of Significance</h3><p>Protein-based therapeutics have become an essential part of medical treatment. They are highly specific, have high affinity and fewer off-target effects. However, stabilization of proteins is critical, time-consuming, and expensive, and it is not yet possible to predict the behavior of proteins under different conditions. The current work is focused on a molecular understanding of the stability of human serum transferrin; a protein which is abundant in blood serum, may pass the blood brain barrier and therefore with high potential in drug delivery. Combination of high throughput unfolding techniques and structural studies, using small angle X-ray scattering and molecular dynamic simulations, allows us to understand the behavior of transferrin on a molecular level.</p></div>","PeriodicalId":17238,"journal":{"name":"Journal of Structural Biology: X","volume":"4 ","pages":"Article 100017"},"PeriodicalIF":2.9,"publicationDate":"2020-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.yjsbx.2019.100017","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38137264","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 10

Structural insights into human Arginase-1 pH dependence and its inhibition by the small molecule inhibitor CB-1158 人精氨酸酶-1 pH依赖性的结构研究及其小分子抑制剂CB-1158的抑制作用

IF 2.9

Journal of Structural Biology: X Pub Date : 2020-01-01 DOI: 10.1016/j.yjsbx.2019.100014

Yvonne Grobben, Joost C.M. Uitdehaag, Nicole Willemsen-Seegers, Werner W.A. Tabak, Jos de Man, Rogier C. Buijsman, Guido J.R. Zaman

{"title":"Structural insights into human Arginase-1 pH dependence and its inhibition by the small molecule inhibitor CB-1158","authors":"Yvonne Grobben, Joost C.M. Uitdehaag, Nicole Willemsen-Seegers, Werner W.A. Tabak, Jos de Man, Rogier C. Buijsman, Guido J.R. Zaman","doi":"10.1016/j.yjsbx.2019.100014","DOIUrl":"10.1016/j.yjsbx.2019.100014","url":null,"abstract":"<div><p>Arginase-1 is a manganese-dependent metalloenzyme that catalyzes the hydrolysis of L-arginine into L-ornithine and urea. Arginase-1 is abundantly expressed by tumor-infiltrating myeloid cells that promote tumor immunosuppression, which is relieved by inhibition of Arginase-1. We have characterized the potencies of the Arginase-1 reference inhibitors (2<em>S</em>)-2-amino-6-boronohexanoic acid (ABH) and <em>N</em><sup>ω</sup>-hydroxy-nor-L-arginine (nor-NOHA), and studied their pH-dependence and binding kinetics. To gain a better understanding of the structural changes underlying the high pH optimum of Arginase-1 and its pH-dependent inhibition, we determined the crystal structure of the human Arginase-1/ABH complex at pH 7.0 and 9.0. These structures revealed that at increased pH, the manganese cluster assumes a more symmetrical coordination structure, which presumably contributes to its increase in catalytic activity. Furthermore, we show that binding of ABH involves the presence of a sodium ion close to the manganese cluster. We also studied the investigational new drug CB-1158 (INCB001158). This inhibitor has a low-nanomolar potency at pH 7.4 and increases the thermal stability of Arginase-1 more than ABH and nor-NOHA. Moreover, CB-1158 displays slow association and dissociation kinetics at both pH 9.5 and 7.4, as indicated by surface plasmon resonance. The potent character of CB-1158 is presumably due to its increased rigidity compared to ABH as well as the formation of an additional hydrogen-bond network as observed by resolution of the Arginase-1/CB-1158 crystal structure.</p></div>","PeriodicalId":17238,"journal":{"name":"Journal of Structural Biology: X","volume":"4 ","pages":"Article 100014"},"PeriodicalIF":2.9,"publicationDate":"2020-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.yjsbx.2019.100014","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38137863","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 25

A guided approach for subtomogram averaging of challenging macromolecular assemblies 具有挑战性的大分子组合的亚层析图平均的引导方法

IF 2.9

Journal of Structural Biology: X Pub Date : 2020-01-01 DOI: 10.1016/j.yjsbx.2020.100041

Benjamin Basanta , Saikat Chowdhury , Gabriel C. Lander , Danielle A. Grotjahn

引用次数: 7

A complex between the Zika virion and the Fab of a broadly cross-reactive neutralizing monoclonal antibody revealed by cryo-EM and single particle analysis at 4.1 Å resolution 通过低温电镜和单颗粒分析，以4.1 Å分辨率发现了寨卡病毒粒子和广泛交叉反应中和单克隆抗体Fab之间的复合物

IF 2.9

Journal of Structural Biology: X Pub Date : 2020-01-01 DOI: 10.1016/j.yjsbx.2020.100028

Anu Tyagi , Tofayel Ahmed , Jian Shi , Shashi Bhushan

{"title":"A complex between the Zika virion and the Fab of a broadly cross-reactive neutralizing monoclonal antibody revealed by cryo-EM and single particle analysis at 4.1 Å resolution","authors":"Anu Tyagi , Tofayel Ahmed , Jian Shi , Shashi Bhushan","doi":"10.1016/j.yjsbx.2020.100028","DOIUrl":"10.1016/j.yjsbx.2020.100028","url":null,"abstract":"<div><p>Zika virus (ZIKV) recently emerged as a major public health concern because it can cause fetal microcephaly and neurological disease such as the Guillain-Barré syndrome. A particularly potent class of broadly neutralizing antibodies (nAbs) targets a quaternary epitope located at the interface of two envelope proteins monomers, exposed at the surface of the mature virion. This “E-dimer-dependent epitope” (EDE), comprises the fusion loop of one monomer at the tip of domain II of E and a portion of the domains I and III of the adjacent monomer. Since this epitope largely overlaps with the binding site of the precursor membrane protein (prM) during Zika virion maturation, its molecular surface is evolutionary conserved in flaviviruses such as Dengue and Zika viruses, and can elicit antibodies that broadly neutralize various ZIKV strains. Here, we present a cryo-EM reconstruction at 4.1 Å resolution of the virion bound to the antigen binding fragment (Fab) of an antibody that targets this mutationally-constrained quaternary epitope. The Fab incompletely covers the surface of the virion as it does not bind next to its 5-fold icosahedral axes. The structure reveals details of the binding mode of this potent neutralizing class of antibodies and can inform the design of immunogens and vaccines targeting this conserved epitope.</p></div>","PeriodicalId":17238,"journal":{"name":"Journal of Structural Biology: X","volume":"4 ","pages":"Article 100028"},"PeriodicalIF":2.9,"publicationDate":"2020-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.yjsbx.2020.100028","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38137190","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 5