Journal of structural biology最新文献_第8页

Insight into structural biophysics from solution X-ray scattering 从溶液X射线散射透视结构生物物理学。

IF 3 3区生物学

Journal of structural biology Pub Date : 2023-09-22 DOI: 10.1016/j.jsb.2023.108029

Uri Raviv , Roi Asor , Asaf Shemesh , Avi Ginsburg , Tal Ben-Nun , Yaelle Schilt , Yehonatan Levartovsky , Israel Ringel

{"title":"Insight into structural biophysics from solution X-ray scattering","authors":"Uri Raviv , Roi Asor , Asaf Shemesh , Avi Ginsburg , Tal Ben-Nun , Yaelle Schilt , Yehonatan Levartovsky , Israel Ringel","doi":"10.1016/j.jsb.2023.108029","DOIUrl":"10.1016/j.jsb.2023.108029","url":null,"abstract":"<div><p>The current challenges of structural biophysics include determining the structure of large self-assembled complexes, resolving the structure of ensembles of complex structures and their mass fraction, and unraveling the dynamic pathways and mechanisms leading to the formation of complex structures from their subunits. Modern synchrotron solution X-ray scattering data enable simultaneous high-spatial and high-temporal structural data required to address the current challenges of structural biophysics. These data are complementary to crystallography, NMR, and cryo-TEM data. However, the analysis of solution scattering data is challenging; hence many different analysis tools, listed in the SAS Portal (http://smallangle.org/), were developed. In this review, we start by briefly summarizing classical X-ray scattering analyses providing insight into fundamental structural and interaction parameters. We then describe recent developments, integrating simulations, theory, and advanced X-ray scattering modeling, providing unique insights into the structure, energetics, and dynamics of self-assembled complexes. The structural information is essential for understanding the underlying physical chemistry principles leading to self-assembled supramolecular architectures and computational structural refinement.</p></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2023-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41141716","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}

引用次数: 1

Domain crossover in the reductase subunit of NADPH-dependent assimilatory sulfite reductase NADPH依赖性同化亚硫酸还原酶还原酶亚基中的结构域交叉。

IF 3 3区生物学

Journal of structural biology Pub Date : 2023-09-12 DOI: 10.1016/j.jsb.2023.108028

Nidhi Walia , Daniel T. Murray , Yashika Garg , Huan He , Kevin L. Weiss , Gergely Nagy , M. Elizabeth Stroupe

{"title":"Domain crossover in the reductase subunit of NADPH-dependent assimilatory sulfite reductase","authors":"Nidhi Walia , Daniel T. Murray , Yashika Garg , Huan He , Kevin L. Weiss , Gergely Nagy , M. Elizabeth Stroupe","doi":"10.1016/j.jsb.2023.108028","DOIUrl":"10.1016/j.jsb.2023.108028","url":null,"abstract":"<div><p>NADPH-dependent assimilatory sulfite reductase (SiR) from <em>Escherichia coli</em> performs a six-electron reduction of sulfite to the bioavailable sulfide. SiR is composed of a flavoprotein (SiRFP) reductase subunit and a hemoprotein (SiRHP) oxidase subunit. There is no known high-resolution structure of SiR or SiRFP, thus we do not yet fully understand how the subunits interact to perform their chemistry. Here, we used small-angle neutron scattering to understand the impact of conformationally restricting the highly mobile SiRFP octamer into an electron accepting (closed) or electron donating (open) conformation, showing that SiR remains active, flexible, and asymmetric even with these conformational restrictions. From these scattering data, we model the first solution structure of SiRFP. Further, computational modeling of the N-terminal 52 amino acids that are responsible for SiRFP oligomerization suggests an eight-helical bundle tethers together the SiRFP subunits to form the SiR core. Finally, mass spectrometry analysis of the closed SiRFP variant show that SiRFP is capable of inter-molecular domain crossover, in which the electron donating domain from one polypeptide is able to interact directly with the electron accepting domain of another polypeptide. This structural characterization suggests that SiR performs its high-volume electron transfer through both inter- and intramolecular pathways between SiRFP domains and, thus, <em>cis</em> or <em>trans</em> transfer from reductase to oxidase subunits. Such highly redundant potential for electron transfer makes this system a potential target for designing synthetic enzymes.</p></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2023-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10232829","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}

引用次数: 0

A new algorithm for particle weighted subtraction to decrease signals from unwanted components in single particle analysis 一种新的粒子加权减法算法，用于减少单粒子分析中不需要的分量的信号。

IF 3 3区生物学

Journal of structural biology Pub Date : 2023-09-11 DOI: 10.1016/j.jsb.2023.108024

E. Fernández-Giménez , M.M. Martínez , R. Marabini , D. Strelak , R. Sánchez-García , J.M. Carazo , C.O.S. Sorzano

{"title":"A new algorithm for particle weighted subtraction to decrease signals from unwanted components in single particle analysis","authors":"E. Fernández-Giménez , M.M. Martínez , R. Marabini , D. Strelak , R. Sánchez-García , J.M. Carazo , C.O.S. Sorzano","doi":"10.1016/j.jsb.2023.108024","DOIUrl":"10.1016/j.jsb.2023.108024","url":null,"abstract":"<div><p>Single particle analysis (SPA) in cryo-electron microscopy (cryo-EM) is highly used to obtain the near-atomic structure of biological macromolecules. The current methods allow users to produce high-resolution maps from many samples. However, there are still challenging cases that require extra processing to obtain high resolution. This is the case when the macromolecule of the sample is composed of different components and we want to focus just on one of them. For example, if the macromolecule is composed of several flexible subunits and we are interested in a specific one, if it is embedded in a viral capsid environment, or if it has additional components to stabilize it, such as nanodiscs. The signal from these components, which in principle we are not interested in, can be removed from the particles using a projection subtraction method. Currently, there are two projection subtraction methods used in practice and both have some limitations. In fact, after evaluating their results, we consider that the problem is still open to new solutions, as they do not fully remove the signal of the components that are not of interest. Our aim is to develop a new and more precise projection subtraction method, improving the performance of state-of-the-art methods. We tested our algorithm with data from public databases and an in–house data set. In this work, we show that the performance of our algorithm improves the results obtained by others, including the localization of small ligands, such as drugs, whose binding location is unknown <em>a priori</em>.</p></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2023-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10285701","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}

引用次数: 0

Selective labeling of phosphatidylserine for cryo-TEM by a two-step immunogold method 两步免疫金法选择性标记冷冻透射电镜磷脂酰丝氨酸。

IF 3 3区生物学

Journal of structural biology Pub Date : 2023-09-09 DOI: 10.1016/j.jsb.2023.108025

Na'ama Koifman , Maayan Nir-Shapira, Yeshayahu Talmon

{"title":"Selective labeling of phosphatidylserine for cryo-TEM by a two-step immunogold method","authors":"Na'ama Koifman , Maayan Nir-Shapira, Yeshayahu Talmon","doi":"10.1016/j.jsb.2023.108025","DOIUrl":"10.1016/j.jsb.2023.108025","url":null,"abstract":"<div><p><span><span>Immunogold labeling in </span>transmission electron microscopy<span><span><span> (TEM) utilizes the high electron density of gold nanoparticles conjugated to proteins to identify specific antigens in biological samples. In this work we applied the concept of immunogold labeling for the labeling of negatively charged </span>phospholipids<span>, namely phosphatidylserine, by a simple protocol, performed entirely in the liquid-phase, from which cryo-TEM specimens can be directly prepared. Labeling included a two-step process using biotinylated annexin-V and gold-conjugated </span></span>streptavidin. We initially applied it on liposomal systems, demonstrating its specificity and selectivity, differentiating between 1,2-dioleoyl-</span></span><em>sn</em>-glycero-3-phosphocholine (DOPC) and 1,2-dioleoyl-<em>sn</em>-glycero-3-phospho-l-serine (DOPS) membranes. We also observed specific labeling on extracellular vesicle samples isolated from THP1 cells and from MDA-468 cells, which underwent stimulations. Finally, we compared the levels of annexin-V labeling on the cells vs. on their isolated EVs by flow cytometry and found a good correlation with the cryo-TEM results. This simple, yet effective labeling technique makes it possible to differentiate between negatively charged and non-negatively charged membranes, thus shillucidating their possible EV shedding mechanism.</p></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2023-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10181089","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}

引用次数: 0

Lipid nanodiscs as a template for high-resolution cryo-EM structures of peripheral membrane proteins 脂质纳米盘作为外周膜蛋白的高分辨率冷冻EM结构的模板。

IF 3 3区生物学

Journal of structural biology Pub Date : 2023-09-01 DOI: 10.1016/j.jsb.2023.107989

Kevin S. Cannon , Reta D. Sarsam , Tanita Tedamrongwanish , Kevin Zhang , Richard W. Baker

{"title":"Lipid nanodiscs as a template for high-resolution cryo-EM structures of peripheral membrane proteins","authors":"Kevin S. Cannon , Reta D. Sarsam , Tanita Tedamrongwanish , Kevin Zhang , Richard W. Baker","doi":"10.1016/j.jsb.2023.107989","DOIUrl":"10.1016/j.jsb.2023.107989","url":null,"abstract":"<div><p><span>Peripheral membrane proteins are ubiquitous throughout cell biology and are required for a variety of cellular processes such as </span>signal transduction<span><span>, membrane trafficking, and autophagy. Transient binding to the membrane has a profound impact on protein function, serving to induce conformational changes and alter biochemical and biophysical parameters by increasing the local concentration of factors and restricting diffusion to two dimensions. Despite the centrality of the membrane in serving as a template for cell biology, there are few reported high-resolution structures of peripheral membrane proteins bound to the membrane. We analyzed the utility of lipid nanodiscs to serve as a template for cryo-EM analysis of peripheral membrane proteins. We tested a variety of nanodiscs and we report a 3.3 Å structure of the AP2 </span>clathrin adaptor complex bound to a 17-nm nanodisc, with sufficient resolution to visualize a bound lipid head group. Our data demonstrate that lipid nanodiscs are amenable to high-resolution structure determination of peripheral membrane proteins and provide a framework for extending this analysis to other systems.</span></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":"10218308","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}

引用次数: 0

Why does the first protein repeat often become the only one? 为什么第一个重复的蛋白质经常成为唯一一个?

IF 3 3区生物学

Journal of structural biology Pub Date : 2023-09-01 DOI: 10.1016/j.jsb.2023.108014

Simona Manasra , Andrey V. Kajava

{"title":"Why does the first protein repeat often become the only one?","authors":"Simona Manasra , Andrey V. Kajava","doi":"10.1016/j.jsb.2023.108014","DOIUrl":"10.1016/j.jsb.2023.108014","url":null,"abstract":"<div><p>Proteins with two similar motifs in tandem are one of the most common cases of tandem repeat proteins. The question arises: why is the first emerged repeat frequently fixed in the process of evolution, despite the ample opportunities to continue its multiplication at the DNA level? To answer this question, we systematically analyzed the structure and function of these proteins. Our analysis showed that, in the vast majority of cases, the structural repetitive units have a two-fold (C2) internal symmetry. These closed structures provide an internal structural limitation for the subsequent growth of the repeat number. Frequently, the units “swap” their secondary structure elements with each other. Moreover, the duplicated domains, in contrast to other tandem repeat proteins, form binding sites for small molecules around the axis of C2 symmetry. Thus, the closure of the C2 structures and the emergence of new functional sites around the axis of C2 symmetry provide plausible explanations for why a repeat, once appeared, becomes fixed in the evolutionary process. We have placed these structures within the general structural classification of tandem repeat proteins, classifying them as either Class IV or V depending on the size of the repetitive unit.</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":"10219728","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}

引用次数: 0

Lipid composition modulates interactions of p7 viroporin during membrane insertion 脂质组成调节膜插入过程中p7病毒孔蛋白的相互作用

IF 3 3区生物学

Journal of structural biology Pub Date : 2023-09-01 DOI: 10.1016/j.jsb.2023.108013

Oluwatoyin Campbell, Viviana Monje-Galvan

{"title":"Lipid composition modulates interactions of p7 viroporin during membrane insertion","authors":"Oluwatoyin Campbell, Viviana Monje-Galvan","doi":"10.1016/j.jsb.2023.108013","DOIUrl":"10.1016/j.jsb.2023.108013","url":null,"abstract":"<div><p>Viral proteins interact with lipid membranes during various stages in the viral life cycle to propagate infection. p7 is an ion channel forming protein of Hepatitis C virus (HCV) that participates in viral assembly. Studies show that it has close ties to lipid metabolism in the cell and anionic phosphatidylserine (PS) lipids are suggested to be key for its permeabilizing function, but the mechanism of its interaction with the lipid environment is largely unknown. To begin unraveling the molecular processes of the protein, we evaluated the impact of lipid environment on the binding and insertion mechanism of p7 prior to channel formation and viral assembly using molecular dynamics simulations. It is seen that p7 is sensitive to its lipid environment and results in different remodeling patterns in membranes. Helix 1 (H1) is especially important for peptide insertion, with deeper entry taking place when the membrane contains phosphatidylserine (PS). Helix 2 (H2) and the adjacent loop connecting to Helix 3 (H3) prompts recruitment of phosphatidylethanolamine (PE) lipids to the protein binding site in membrane models with lower surface charge. This work provides perspectives on the interplay between protein-lipid dynamics and membrane composition, and insights on membrane reorganization in mechanisms of disease.</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":"10568449","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}

引用次数: 0

Local defocus estimation in single particle analysis in cryo-electron microscopy. 低温电子显微镜中单粒子分析的局部散焦估计。

IF 3 3区生物学

Journal of structural biology Pub Date : 2023-09-01 DOI: 10.2139/ssrn.4402138

E. Fernández-Giménez, C. Sorzano, J. Carazo

引用次数: 0

PickYOLO: Fast deep learning particle detector for annotation of cryo electron tomograms PickYOLO:用于低温电子层析图注释的快速深度学习粒子检测器

IF 3 3区生物学

Journal of structural biology Pub Date : 2023-09-01 DOI: 10.1016/j.jsb.2023.107990

Erik Genthe , Sean Miletic , Indira Tekkali , Rory Hennell James , Thomas C. Marlovits , Philipp Heuser

{"title":"PickYOLO: Fast deep learning particle detector for annotation of cryo electron tomograms","authors":"Erik Genthe , Sean Miletic , Indira Tekkali , Rory Hennell James , Thomas C. Marlovits , Philipp Heuser","doi":"10.1016/j.jsb.2023.107990","DOIUrl":"10.1016/j.jsb.2023.107990","url":null,"abstract":"<div><p>Particle localization (picking) in digital tomograms is a laborious and time-intensive step in cryogenic electron tomography (cryoET) analysis often requiring considerable user involvement, thus becoming a bottleneck for automated cryoET subtomogram averaging (STA) pipelines. In this paper, we introduce a deep learning framework called PickYOLO to tackle this problem. PickYOLO is a super-fast, universal particle detector based on the deep-learning real-time object recognition system YOLO (You Only Look Once), and tested on single particles, filamentous structures, and membrane-embedded particles. After training with the centre coordinates of a few hundred representative particles, the network automatically detects additional particles with high yield and reliability at a rate of 0.24–3.75 s per tomogram. PickYOLO can automatically detect number of particles comparable to those manually selected by experienced microscopists. This makes PickYOLO a valuable tool to substantially reduce the time and manual effort needed to analyse cryoET data for STA, greatly aiding in high-resolution cryoET structure determination.</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":"10218309","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}

引用次数: 0

Three dimensional structures of the inner and outer pig petrous bone using FIB-SEM: Implications for development and ancient DNA preservation 利用FIB-SEM研究猪石质骨内外的三维结构:对发育和古代DNA保存的影响

IF 3 3区生物学

Journal of structural biology Pub Date : 2023-09-01 DOI: 10.1016/j.jsb.2023.107998

Jamal Ibrahim , Katya Rechav , Elisabetta Boaretto , Steve Weiner

{"title":"Three dimensional structures of the inner and outer pig petrous bone using FIB-SEM: Implications for development and ancient DNA preservation","authors":"Jamal Ibrahim , Katya Rechav , Elisabetta Boaretto , Steve Weiner","doi":"10.1016/j.jsb.2023.107998","DOIUrl":"10.1016/j.jsb.2023.107998","url":null,"abstract":"<div><p>We report on the 3D ultrastructure of the mineralized petrous bone of mature pig using focused ion beam – scanning electron microscopy (FIB-SEM). We divide the petrous bone into two zones based on the degree of mineralization; one zone close to the otic chamber has higher mineral density than the second zone further away from the otic chamber. The hypermineralization of the petrous bone results in the collagen D-banding being poorly revealed in the lower mineral density zone (LMD), and absent in the high mineral density zone (HMD). We therefore could not use D-banding to decipher the 3D structure of the collagen assembly. Instead we exploited the anisotropy option in the Dragonfly image processing software to visualize the less mineralized collagen fibrils and/or nanopores that surround the more mineralized zones known as tesselles. This approach therefore indirectly tracks the orientations of the collagen fibrils in the matrix itself. We show that the HMD bone has a structure similar to that of woven bone, and the LMD is composed of lamellar bone with a plywood-like structural motif. This agrees with the fact that the bone close to the otic chamber is fetal bone and is not remodeled. The lamellar structure of the bone further away from the otic chamber is consistent with modeling/remodeling. The absence of the less mineralized collagen fibrils and nanopores resulting from the confluence of the mineral tesselles may contribute to shielding DNA during diagenesis. We show that anisotropy evaluation of the less mineralized collagen fibrils could be a useful tool to analyze bone ultrastructures and in particular the directionality of collagen fibril bundles that make up the bone matrix.</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":"10218777","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}

引用次数: 2