Journal of Structural Biology: X最新文献_第10页

SIMPLE 3.0. Stream single-particle cryo-EM analysis in real time 简单的3.0。实时流单粒子低温电镜分析

IF 2.9

Journal of Structural Biology: X Pub Date : 2020-01-01 DOI: 10.1016/j.yjsbx.2020.100040

Joseph Caesar , Cyril F. Reboul , Chiara Machello , Simon Kiesewetter , Molly L. Tang , Justin C. Deme , Steven Johnson , Dominika Elmlund , Susan M. Lea , Hans Elmlund

{"title":"SIMPLE 3.0. Stream single-particle cryo-EM analysis in real time","authors":"Joseph Caesar , Cyril F. Reboul , Chiara Machello , Simon Kiesewetter , Molly L. Tang , Justin C. Deme , Steven Johnson , Dominika Elmlund , Susan M. Lea , Hans Elmlund","doi":"10.1016/j.yjsbx.2020.100040","DOIUrl":"10.1016/j.yjsbx.2020.100040","url":null,"abstract":"<div><p>We here introduce the third major release of the SIMPLE (Single-particle IMage Processing Linux Engine) open-source software package for analysis of cryogenic transmission electron microscopy (cryo-EM) movies of single-particles (Single-Particle Analysis, SPA). Development of SIMPLE 3.0 has been focused on real-time data processing using minimal CPU computing resources to allow easy and cost-efficient scaling of processing as data rates escalate. Our stream SPA tool implements the steps of anisotropic motion correction and CTF estimation, rapid template-based particle identification and 2D clustering with automatic class rejection. SIMPLE 3.0 additionally features an easy-to-use web-based graphical user interface (GUI) that can be run on any device (workstation, laptop, tablet or phone) and supports a remote multi-user environment over the network. The new project-based execution model automatically records the executed workflow and represents it as a flow diagram in the GUI. This facilitates meta-data handling and greatly simplifies usage. Using SIMPLE 3.0, it is possible to automatically obtain a clean SP data set amenable to high-resolution 3D reconstruction directly upon completion of the data acquisition, without the need for extensive image processing post collection. Only minimal standard CPU computing resources are required to keep up with a rate of ∼300 Gatan K3 direct electron detector movies per hour. SIMPLE 3.0 is available for download from simplecryoem.com.</p></div>","PeriodicalId":17238,"journal":{"name":"Journal of Structural Biology: X","volume":"4 ","pages":"Article 100040"},"PeriodicalIF":2.9,"publicationDate":"2020-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.yjsbx.2020.100040","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38351940","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: 8

Structures and dynamics of the novel S1/S2 protease cleavage site loop of the SARS-CoV-2 spike glycoprotein 新型SARS-CoV-2刺突糖蛋白S1/S2蛋白酶裂解位点环的结构和动力学

IF 2.9

Journal of Structural Biology: X Pub Date : 2020-01-01 DOI: 10.1016/j.yjsbx.2020.100038

Thomas Lemmin , David Kalbermatter , Daniel Harder , Philippe Plattet , Dimitrios Fotiadis

{"title":"Structures and dynamics of the novel S1/S2 protease cleavage site loop of the SARS-CoV-2 spike glycoprotein","authors":"Thomas Lemmin , David Kalbermatter , Daniel Harder , Philippe Plattet , Dimitrios Fotiadis","doi":"10.1016/j.yjsbx.2020.100038","DOIUrl":"10.1016/j.yjsbx.2020.100038","url":null,"abstract":"<div><p>At the end of 2019, a new highly virulent coronavirus known under the name SARS-CoV-2 emerged as a human pathogen. One key feature of SARS-CoV-2 is the presence of an enigmatic insertion in the spike glycoprotein gene representing a novel multibasic S1/S2 protease cleavage site. The proteolytic cleavage of the spike at this site is essential for viral entry into host cells. However, it has been systematically abrogated in structural studies in order to stabilize the spike in the prefusion state. In this study, multi-microsecond molecular dynamics simulations and <em>ab initio</em> modeling were leveraged to gain insights into the structures and dynamics of the loop containing the S1/S2 protease cleavage site. They unveiled distinct conformations, formations of short helices and interactions of the loop with neighboring glycans that could potentially regulate the accessibility of the cleavage site to proteases and its processing. In most conformations, this loop protrudes from the spike, thus representing an attractive SARS-CoV-2 specific therapeutic target.</p></div>","PeriodicalId":17238,"journal":{"name":"Journal of Structural Biology: X","volume":"4 ","pages":"Article 100038"},"PeriodicalIF":2.9,"publicationDate":"2020-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.yjsbx.2020.100038","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38476957","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: 37

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":"4 ","pages":"Article 100023"},"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

{"title":"Cryo-electron microscopic and X-ray crystallographic analysis of the light-driven proton pump proteorhodopsin reveals a pentameric assembly","authors":"Stephan Hirschi, David Kalbermatter, Zöhre Ucurum, Dimitrios Fotiadis","doi":"10.1016/j.yjsbx.2020.100024","DOIUrl":"10.1016/j.yjsbx.2020.100024","url":null,"abstract":"<div><p>The green-light absorbing proteorhodopsin (GPR) is the prototype of bacterial light-driven proton pumps. It has been the focus of continuous research since its discovery 20 years ago and has sparked the development and application of various biophysical techniques. However, a certain controversy and ambiguity about the oligomeric assembly of GPR still remains. We present here the first tag-free purification of pentameric GPR. The combination of ion exchange and size exclusion chromatography yields homogeneous and highly pure untagged pentamers from GPR overexpressing <em>Escherichia coli</em>. The presented purification procedure provides native-like protein and excludes the need for affinity purification tags. Importantly, three-dimensional protein crystals of GPR were successfully grown and analyzed by X-ray crystallography. These results together with data from single particle cryo-electron microscopy provide direct evidence for the pentameric stoichiometry of purified GPR.</p></div>","PeriodicalId":17238,"journal":{"name":"Journal of Structural Biology: X","volume":"4 ","pages":"Article 100024"},"PeriodicalIF":2.9,"publicationDate":"2020-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.yjsbx.2020.100024","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38137187","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

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":"4 ","pages":"Article 100018"},"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

Specificity in PDZ-peptide interaction networks: Computational analysis and review pdz -肽相互作用网络的特异性:计算分析和回顾

IF 2.9

Journal of Structural Biology: X Pub Date : 2020-01-01 DOI: 10.1016/j.yjsbx.2020.100022

Jeanine F. Amacher , Lionel Brooks 3rd , Thomas H. Hampton , Dean R. Madden

{"title":"Specificity in PDZ-peptide interaction networks: Computational analysis and review","authors":"Jeanine F. Amacher , Lionel Brooks 3rd , Thomas H. Hampton , Dean R. Madden","doi":"10.1016/j.yjsbx.2020.100022","DOIUrl":"10.1016/j.yjsbx.2020.100022","url":null,"abstract":"<div><p>Globular PDZ domains typically serve as protein–protein interaction modules that regulate a wide variety of cellular functions via recognition of short linear motifs (SLiMs). Often, PDZ mediated-interactions are essential components of macromolecular complexes, and disruption affects the entire scaffold. Due to their roles as linchpins in trafficking and signaling pathways, PDZ domains are attractive targets: both for controlling viral pathogens, which bind PDZ domains and hijack cellular machinery, as well as for developing therapies to combat human disease. However, successful therapeutic interventions that avoid off-target effects are a challenge, because each PDZ domain interacts with a number of cellular targets, and specific binding preferences can be difficult to decipher. Over twenty-five years of research has produced a wealth of data on the stereochemical preferences of individual PDZ proteins and their binding partners. Currently the field lacks a central repository for this information. Here, we provide this important resource and provide a manually curated, comprehensive list of the 271 human PDZ domains. We use individual domain, as well as recent genomic and proteomic, data in order to gain a holistic view of PDZ domains and interaction networks, arguing this knowledge is critical to optimize targeting selectivity and to benefit human health.</p></div>","PeriodicalId":17238,"journal":{"name":"Journal of Structural Biology: X","volume":"4 ","pages":"Article 100022"},"PeriodicalIF":2.9,"publicationDate":"2020-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.yjsbx.2020.100022","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37833891","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: 30

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":"4 ","pages":"Article 100034"},"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

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

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":"4 ","pages":"Article 100027"},"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