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

Reconstruction of Average Subtracted Tubular Regions (RASTR) enables structure determination of tubular filaments by cryo-EM 平均减去管状区域(RASTR)的重建使管状细丝的结构通过低温电镜测定

IF 2.9

Journal of Structural Biology: X Pub Date : 2020-01-01 DOI: 10.1016/j.yjsbx.2020.100023

Peter S. Randolph , Scott M. Stagg

{"title":"Reconstruction of Average Subtracted Tubular Regions (RASTR) enables structure determination of tubular filaments by cryo-EM","authors":"Peter S. Randolph , Scott M. Stagg","doi":"10.1016/j.yjsbx.2020.100023","DOIUrl":"10.1016/j.yjsbx.2020.100023","url":null,"abstract":"<div><p>As the field of electron microscopy advances, the increasing complexity of samples being produced demand more involved processing methods. In this study, we have developed a new processing method for generating 3D reconstructions of tubular structures. Tubular biomolecules are common throughout many cellular processes and are appealing targets for biophysical research. Processing of tubules with helical symmetry is relatively straightforward for electron microscopy if the helical parameters are known, but tubular structures that deviate from helical symmetry (asymmetrical components, local but no global order, etc) present myriad issues. Here we present a new processing technique called Reconstruction of Average Subtracted Tubular Regions (RASTR), which was developed to reconstruct tubular structures without applying symmetry. We explain the RASTR approach and quantify its performance using three examples: a simulated symmetrical tubular filament, a symmetrical tubular filament from cryo-EM data, and a membrane tubule coated with locally ordered but not globally ordered proteins.</p></div>","PeriodicalId":17238,"journal":{"name":"Journal of Structural Biology: X","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2020-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.yjsbx.2020.100023","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38137186","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: 1

Cryo-electron microscopic and X-ray crystallographic analysis of the light-driven proton pump proteorhodopsin reveals a pentameric assembly 低温电子显微镜和x射线晶体学分析的光驱动质子泵变形紫红质揭示了一个五聚体组装

IF 2.9

Journal of Structural Biology: X Pub Date : 2020-01-01 DOI: 10.1016/j.yjsbx.2020.100024

Stephan Hirschi, David Kalbermatter, Zöhre Ucurum, Dimitrios Fotiadis

引用次数: 4

Structural basis for differentiation between two classes of thiolase: Degradative vs biosynthetic thiolase 区分两类硫醇酶的结构基础:降解型与生物合成型硫醇酶

IF 2.9

Journal of Structural Biology: X Pub Date : 2020-01-01 DOI: 10.1016/j.yjsbx.2019.100018

Sukritee Bhaskar , David L. Steer , Ruchi Anand , Santosh Panjikar

{"title":"Structural basis for differentiation between two classes of thiolase: Degradative vs biosynthetic thiolase","authors":"Sukritee Bhaskar , David L. Steer , Ruchi Anand , Santosh Panjikar","doi":"10.1016/j.yjsbx.2019.100018","DOIUrl":"10.1016/j.yjsbx.2019.100018","url":null,"abstract":"<div><p>Thiolases are a well characterized family of enzymes with two distinct categories: degradative, β-ketoadipyl-CoA thiolases and biosynthetic, acetoacetyl-CoA thiolases. Both classes share an identical catalytic triad but catalyze reactions in opposite directions. Moreover, it is established that in contrast to the biosynthetic thiolases the degradative thiolases can accept substrates with broad chain lengths. Hitherto, no residue or structural pattern has been recognized that might help to discern the two thiolases, here we exploit, a tetrameric degradative thiolase from <em>Pseudomonas putida</em> KT2440 annotated as PcaF, as a model system to understand features which distinguishes the two classes using structural studies and bioinformatics analyses. Degradative thiolases have different active site architecture when compared to biosynthetic thiolases, demonstrating the dissimilar chemical nature of the active site architecture. Both thiolases deploy different “anchoring residues” to tether the large Coenzyme A (CoA) or CoA derivatives. Interestingly, the H356 of the catalytic triad in PcaF is directly involved in tethering the CoA/CoA derivatives into the active site and we were able to trap a gridlocked thiolase structure of the H356A mutant, where the CoA was found to be covalently linked to the catalytic cysteine residue, inhibiting the overall reaction. Further, X-ray structures with two long chain CoA derivatives, hexanal-CoA and octanal-CoA helped in delineating the long tunnel of 235 Å<sup>2</sup> surface area in PcaF and led to identification of a unique covering loop exclusive to degradative thiolases that plays an active role in determining the tunnel length and the nature of the binding substrate.</p></div>","PeriodicalId":17238,"journal":{"name":"Journal of Structural Biology: X","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2020-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.yjsbx.2019.100018","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38137266","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: 7

On the complementarity of X-ray and NMR data 论x射线和核磁共振数据的互补性

IF 2.9

Journal of Structural Biology: X Pub Date : 2020-01-01 DOI: 10.1016/j.yjsbx.2020.100019

Antonio Schirò , Azzurra Carlon , Giacomo Parigi , Garib Murshudov , Vito Calderone , Enrico Ravera , Claudio Luchinat

引用次数: 7

An allosteric pocket for inhibition of bacterial Enzyme I identified by NMR-based fragment screening 通过核磁共振片段筛选鉴定出抑制细菌酶I的变构口袋

IF 2.9

Journal of Structural Biology: X Pub Date : 2020-01-01 DOI: 10.1016/j.yjsbx.2020.100034

Trang T. Nguyen , Vincenzo Venditti

{"title":"An allosteric pocket for inhibition of bacterial Enzyme I identified by NMR-based fragment screening","authors":"Trang T. Nguyen , Vincenzo Venditti","doi":"10.1016/j.yjsbx.2020.100034","DOIUrl":"10.1016/j.yjsbx.2020.100034","url":null,"abstract":"<div><p>Enzyme I (EI), which is the key enzyme to activate the bacterial phosphotransferase system, plays an important role in the regulation of several metabolic pathways and controls the biology of bacterial cells at multiple levels. The conservation and ubiquity of EI among different types of bacteria makes the enzyme a potential target for antimicrobial research. Here, we use NMR-based fragment screening to identify novel inhibitors of EI. We identify three molecular fragments that allosterically inhibit the phosphoryl transfer reaction catalyzed by EI by interacting with the enzyme at a surface pocket located more than 10 Å away from the substrate binding site. Interestingly, although the three molecules share the same binding pocket, we observe that two of the discovered EI ligands act as competitive inhibitors while the third ligand acts as a mixed inhibitor. Characterization of the EI-inhibitor complexes by NMR and Molecular Dynamics simulations reveals key interactions that perturb the fold of the active site and provides structural foundation for the different inhibitory activity of the identified molecular fragments. In particular, we show that contacts between the inhibitor and the side-chain of V292 are crucial to destabilize binding of the substrate to EI. In contrast, mixed inhibition is caused by additional contacts between the inhibitor and ⍺-helix 2 that perturb the active site structure and turnover in an allosteric manner. We expect our results to provide the basis for the development of second generation allosteric inhibitors of increased potency and to suggest novel molecular strategies to combat drug-resistant infections.</p></div>","PeriodicalId":17238,"journal":{"name":"Journal of Structural Biology: X","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2020-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.yjsbx.2020.100034","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38218713","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

Molecular assemblies built with the artificial protein Pizza 用人造蛋白披萨构建的分子组装

IF 2.9

Journal of Structural Biology: X Pub Date : 2020-01-01 DOI: 10.1016/j.yjsbx.2020.100027

Jeroen P.M. Vrancken , Jana Aupič , Christine Addy , Roman Jerala , Jeremy R.H. Tame , Arnout R.D. Voet

{"title":"Molecular assemblies built with the artificial protein Pizza","authors":"Jeroen P.M. Vrancken , Jana Aupič , Christine Addy , Roman Jerala , Jeremy R.H. Tame , Arnout R.D. Voet","doi":"10.1016/j.yjsbx.2020.100027","DOIUrl":"10.1016/j.yjsbx.2020.100027","url":null,"abstract":"<div><p>Recently an artificial protein named Pizza6 was reported, which possesses six identical tandem repeats and adopts a monomeric <span><math><mrow><mi>β</mi></mrow></math></span>-propeller fold with sixfold structural symmetry. Pizza2, a truncated form that consists of a double tandem repeat, self-assembles into a trimer reconstructing the same propeller architecture as Pizza6. The ability of pizza proteins to self-assemble to form complete propellers makes them interesting building blocks to engineer larger symmetrical protein complexes such as symmetric nanoparticles. Here we have explored the self-assembly of Pizza2 fused to homo-oligomerizing peptides. In total, we engineered five different fusion proteins, of which three appeared to assemble successfully into larger complexes. Further characterization of these proteins showed one monodisperse designer protein with a structure close to the intended design. This protein was further fused to eGFP to investigate functionalization of the nanoparticle. The fusion protein was stable and could be expressed in high yield, showing that Pizza-based nanoparticles may be further decorated with functional domains</p></div>","PeriodicalId":17238,"journal":{"name":"Journal of Structural Biology: X","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2020-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.yjsbx.2020.100027","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38137189","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: 7

A Monte Carlo framework for missing wedge restoration and noise removal in cryo-electron tomography 低温电子断层扫描中缺失楔形恢复和噪声去除的蒙特卡罗框架

IF 2.9

Journal of Structural Biology: X Pub Date : 2020-01-01 DOI: 10.1016/j.yjsbx.2019.100013

Emmanuel Moebel, Charles Kervrann

引用次数: 14

Cryo-EM structure of the prefusion state of canine distemper virus fusion protein ectodomain 犬瘟热病毒融合蛋白外结构域融合前状态的低温电镜结构

IF 2.9

Journal of Structural Biology: X Pub Date : 2020-01-01 DOI: 10.1016/j.yjsbx.2020.100021

David Kalbermatter , Neeta Shrestha , Flavio M. Gall , Marianne Wyss , Rainer Riedl , Philippe Plattet , Dimitrios Fotiadis

{"title":"Cryo-EM structure of the prefusion state of canine distemper virus fusion protein ectodomain","authors":"David Kalbermatter , Neeta Shrestha , Flavio M. Gall , Marianne Wyss , Rainer Riedl , Philippe Plattet , Dimitrios Fotiadis","doi":"10.1016/j.yjsbx.2020.100021","DOIUrl":"10.1016/j.yjsbx.2020.100021","url":null,"abstract":"<div><p>Measles virus (MeV) and canine distemper virus (CDV), two members of the <em>Morbillivirus</em> genus, are still causing important global diseases of humans and animals, respectively. To enter target cells, morbilliviruses rely on an envelope-anchored machinery, which is composed of two interacting glycoproteins: a tetrameric receptor binding (H) protein and a trimeric fusion (F) protein. To execute membrane fusion, the F protein initially adopts a metastable, prefusion state that refolds into a highly stable postfusion conformation as the result of a finely coordinated activation process mediated by the H protein. Here, we employed cryo-electron microscopy (cryo-EM) and single particle reconstruction to elucidate the structure of the prefusion state of the CDV F protein ectodomain (solF) at 4.3 Å resolution. Stabilization of the prefusion solF trimer was achieved by fusing the GCNt trimerization sequence at the C-terminal protein region, and expressing and purifying the recombinant protein in the presence of a morbilliviral fusion inhibitor class compound. The three-dimensional cryo-EM map of prefusion CDV solF in complex with the inhibitor clearly shows density for the ligand at the protein binding site suggesting common mechanisms of membrane fusion activation and inhibition employed by different morbillivirus members.</p></div>","PeriodicalId":17238,"journal":{"name":"Journal of Structural Biology: X","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2020-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.yjsbx.2020.100021","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38137185","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: 3

Sub-2 Angstrom resolution structure determination using single-particle cryo-EM at 200 keV 在200 keV下使用单粒子低温电镜进行亚2埃分辨率结构测定

IF 2.9

Journal of Structural Biology: X Pub Date : 2020-01-01 DOI: 10.1016/j.yjsbx.2020.100020

Mengyu Wu , Gabriel C. Lander , Mark A. Herzik Jr.

{"title":"Sub-2 Angstrom resolution structure determination using single-particle cryo-EM at 200 keV","authors":"Mengyu Wu , Gabriel C. Lander , Mark A. Herzik Jr.","doi":"10.1016/j.yjsbx.2020.100020","DOIUrl":"10.1016/j.yjsbx.2020.100020","url":null,"abstract":"<div><p>Although the advent of direct electron detectors (DEDs) and software developments have enabled the routine use of single-particle cryogenic electron microscopy (cryo-EM) for structure determination of well-behaved specimens to high-resolution, there nonetheless remains a discrepancy between the resolutions attained for biological specimens and the information limits of modern transmission electron microscopes (TEMs). Instruments operating at 300 kV equipped with DEDs are the current paradigm for high-resolution single-particle cryo-EM, while 200 kV TEMs remain comparatively underutilized for purposes beyond sample screening. Here, we expand upon our prior work and demonstrate that one such 200 kV microscope, the Talos Arctica, equipped with a K2 DED is capable of determining structures of macromolecules to as high as ∼1.7 Å resolution. At this resolution, ordered water molecules are readily assigned and holes in aromatic residues can be clearly distinguished in the reconstructions. This work emphasizes the utility of 200 kV electrons for high-resolution single-particle cryo-EM and applications such as structure-based drug design.</p></div>","PeriodicalId":17238,"journal":{"name":"Journal of Structural Biology: X","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2020-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.yjsbx.2020.100020","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38137268","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: 35

Improvements on marker-free images alignment for electron tomography 电子断层扫描无标记图像对准的改进

IF 2.9

Journal of Structural Biology: X Pub Date : 2020-01-01 DOI: 10.1016/j.yjsbx.2020.100037

C.O.S. Sorzano , F. de Isidro-Gómez , E. Fernández-Giménez , D. Herreros , S. Marco , J.M. Carazo , C. Messaoudi

{"title":"Improvements on marker-free images alignment for electron tomography","authors":"C.O.S. Sorzano , F. de Isidro-Gómez , E. Fernández-Giménez , D. Herreros , S. Marco , J.M. Carazo , C. Messaoudi","doi":"10.1016/j.yjsbx.2020.100037","DOIUrl":"10.1016/j.yjsbx.2020.100037","url":null,"abstract":"<div><p>Electron tomography is a technique to obtain three-dimensional structural information of samples. However, the technique is limited by shifts occurring during acquisition that need to be corrected before the reconstruction process. In 2009, we proposed an approach for post-acquisition alignment of tilt series images. This approach was marker-free, based on patch tracking and integrated in free software. Here, we present improvements to the method to make it more reliable, stable and accurate. In addition, we modified the image formation model underlying the alignment procedure to include different deformations occurring during acquisition. We propose a new way to correct these computed deformations to obtain reconstructions with reduced artifacts. The new approach has demonstrated to improve the quality of the final 3D reconstruction, giving access to better defined structures for different transmission electron tomography methods: resin embedded STEM-tomography and cryo-TEM tomography. The method is freely available in TomoJ software.</p></div>","PeriodicalId":17238,"journal":{"name":"Journal of Structural Biology: X","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2020-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.yjsbx.2020.100037","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38461302","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