Journal of structural biology最新文献_第10页

Focused ion beam-SEM 3D study of osteodentin in the teeth of the Atlantic wolfish Anarhichas lupus 聚焦离子束-扫描电子显微镜对大西洋狼鱼牙齿中骨质素的三维研究

IF 3 3区生物学

Journal of structural biology Pub Date : 2024-01-13 DOI: 10.1016/j.jsb.2024.108062

Senthil Thangadurai , Marta Majkut , Joshua Milgram , Paul Zaslansky , Ron Shahar , Emeline Raguin

{"title":"Focused ion beam-SEM 3D study of osteodentin in the teeth of the Atlantic wolfish Anarhichas lupus","authors":"Senthil Thangadurai , Marta Majkut , Joshua Milgram , Paul Zaslansky , Ron Shahar , Emeline Raguin","doi":"10.1016/j.jsb.2024.108062","DOIUrl":"10.1016/j.jsb.2024.108062","url":null,"abstract":"<div><p>The palette of mineralized tissues in fish is wide, and this is particularly apparent in fish dentin. While the teeth of all vertebrates except fish contain a single dentinal tissue type, called orthodentin, dentin in the teeth of fish can be one of several different tissue types. The most common dentin type in fish is orthodentin. Orthodentin is characterized by several key structural features that are fundamentally different from those of bone and from those of osteodentin. Osteodentin, the second-most common dentin type in fish (based on the tiny fraction of fish species out of ∼30,000 extant fish species in which tooth structure was so far studied), is found in most Selachians (sharks and rays) as well as in several teleost species, and is structurally different from orthodentin.</p><p>Here we examine the hypothesis that osteodentin is similar to anosteocytic bone tissue in terms of its micro- and nano-structure. We use Focused Ion Beam-Scanning Electron Microscopy (FIB/SEM), as well as several other high-resolution imaging techniques, to characterize the 3D architecture of the three main components of osteodentin (denteons, inter-denteonal matrix, and the transition zone between them). We show that the matrix of osteodentin, although acellular, is extremely similar to mammalian osteonal bone matrix, both in general morphology and in the three-dimensional nano-arrangement of its mineralized collagen fibrils. We also document the presence of a complex network of nano-channels, similar to such networks recently described in bone. Finally, we document the presence of strings of hyper-mineralized small ‘pearls’ which surround the denteonal canals, and characterize their structure.</p></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"216 1","pages":"Article 108062"},"PeriodicalIF":3.0,"publicationDate":"2024-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139463468","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

Structure of the prenyltransferase in bifunctional copalyl diphosphate synthase from Penicillium fellutanum reveals an open hexamer conformation 落羽青霉双功能共醛酰二磷酸合酶中的前酰基转移酶结构揭示了开放的六聚体构象

IF 3 3区生物学

Journal of structural biology Pub Date : 2024-01-05 DOI: 10.1016/j.jsb.2023.108060

Matthew N. Gaynes , Trey A. Ronnebaum , Kollin Schultz , Jacque L. Faylo , Ronen Marmorstein , David W. Christianson

{"title":"Structure of the prenyltransferase in bifunctional copalyl diphosphate synthase from Penicillium fellutanum reveals an open hexamer conformation","authors":"Matthew N. Gaynes , Trey A. Ronnebaum , Kollin Schultz , Jacque L. Faylo , Ronen Marmorstein , David W. Christianson","doi":"10.1016/j.jsb.2023.108060","DOIUrl":"10.1016/j.jsb.2023.108060","url":null,"abstract":"<div><p>Copalyl diphosphate synthase from <em>Penicillium fellutanum</em> (PfCPS) is an assembly-line terpene synthase that contains both prenyltransferase and class II cyclase activities. The prenyltransferase catalyzes processive chain elongation reactions using dimethylallyl diphosphate and three equivalents of isopentenyl diphosphate to yield geranylgeranyl diphosphate, which is then utilized as a substrate by the class II cyclase domain to generate copalyl diphosphate. Here, we report the 2.81 Å-resolution cryo-EM structure of the hexameric prenyltransferase of full-length PfCPS, which is surrounded by randomly splayed-out class II cyclase domains connected by disordered polypeptide linkers. The hexamer can be described as a trimer of dimers; surprisingly, one of the three dimer-dimer interfaces is separated to yield an open hexamer conformation, thus breaking the <em>D</em>3 symmetry typically observed in crystal structures of other prenyltransferase hexamers such as wild-type human GGPP synthase (hGGPPS). Interestingly, however, an open hexamer conformation was previously observed in the crystal structure of D188Y hGGPPS, apparently facilitated by hexamer-hexamer packing in the crystal lattice. The cryo-EM structure of the PfCPS prenyltransferase hexamer is the first to reveal that an open conformation can be achieved even in the absence of a point mutation or interaction with another hexamer. Even though PfCPS octamers are not detected, we suggest that the open hexamer conformation represents an intermediate in the hexamer-octamer equilibrium for those prenyltransferases that do exhibit oligomeric heterogeneity.</p></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"216 1","pages":"Article 108060"},"PeriodicalIF":3.0,"publicationDate":"2024-01-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139105365","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

Solid-state NMR MAS CryoProbe enables structural studies of human blood protein vitronectin bound to hydroxyapatite 固态核磁共振 MAS CryoProbe 实现了与羟基磷灰石结合的人类血液蛋白玻璃连蛋白的结构研究

IF 3 3区生物学

Journal of structural biology Pub Date : 2024-01-05 DOI: 10.1016/j.jsb.2024.108061

T. Gopinath , Kyungsoo Shin , Ye Tian , Wonpil Im , Jochem Struppe , Barbara Perrone , Alia Hassan , Francesca M. Marassi

{"title":"Solid-state NMR MAS CryoProbe enables structural studies of human blood protein vitronectin bound to hydroxyapatite","authors":"T. Gopinath , Kyungsoo Shin , Ye Tian , Wonpil Im , Jochem Struppe , Barbara Perrone , Alia Hassan , Francesca M. Marassi","doi":"10.1016/j.jsb.2024.108061","DOIUrl":"10.1016/j.jsb.2024.108061","url":null,"abstract":"<div><p>The low sensitivity of nuclear magnetic resonance (NMR) is a major bottleneck for studying biomolecular structures of complex biomolecular assemblies. Cryogenically cooled probe technology overcomes the sensitivity limitations enabling NMR applications to challenging biomolecular systems. Here we describe solid-state NMR studies of the human blood protein vitronectin (Vn) bound to hydroxyapatite (HAP), the mineralized form of calcium phosphate, using a CryoProbe designed for magic angle spinning (MAS) experiments. Vn is a major blood protein that regulates many different physiological and pathological processes. The high sensitivity of the CryoProbe enabled us to acquire three-dimensional solid-state NMR spectra for sequential assignment and characterization of site-specific water-protein interactions that provide initial insights into the organization of the Vn-HAP complex. Vn associates with HAP in various pathological settings, including macular degeneration eyes and Alzheimer's disease brains. The ability to probe these assemblies at atomic detail paves the way for understanding their formation.</p></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"216 1","pages":"Article 108061"},"PeriodicalIF":3.0,"publicationDate":"2024-01-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139105344","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

Accurate, automatic determination of astigmatism and phase with Ctfplotter in IMOD 利用 IMOD 中的 Ctfplotter 准确、自动地确定散光和相位

IF 3 3区生物学

Journal of structural biology Pub Date : 2024-01-04 DOI: 10.1016/j.jsb.2023.108057

David N. Mastronarde

{"title":"Accurate, automatic determination of astigmatism and phase with Ctfplotter in IMOD","authors":"David N. Mastronarde","doi":"10.1016/j.jsb.2023.108057","DOIUrl":"10.1016/j.jsb.2023.108057","url":null,"abstract":"<div><p>Ctfplotter in the IMOD software package is a flexible program for determination of CTF parameters in tilt series images. It uses a novel approach to find astigmatism by measuring defocus in one-dimensional power spectra rotationally averaged over a series of restricted angular ranges. Comparisons with Ctffind, Gctf, and Warp show that Ctfplotter’s estimated astigmatism is generally more reliable than that found by these programs that fit CTF parameters to two-dimensional power spectra, especially at higher tilt angles. In addition to that intrinsic advantage, Ctfplotter can reduce the variability in astigmatism estimates further by summing results over multiple tilt angles (typically 5), while still finding defocus for each individual image. Its fitting strategy also produces better phase estimates. The program now includes features for tuning the sampling of the power spectrum so that it is well-represented for analysis, and for determining an appropriate fitting range that can vary with tilt angle. It can thus be used automatically in a variety of situations, not just for fitting tilt series, and has been integrated into the SerialEM acquisition software for real-time determination of focus and astigmatism.</p></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"216 1","pages":"Article 108057"},"PeriodicalIF":3.0,"publicationDate":"2024-01-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139094457","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

DeepQs: Local quality assessment of cryo-EM density map by deep learning map-model fit score DeepQs：通过深度学习地图-模型拟合得分对低温电子显微镜密度图进行局部质量评估

IF 3 3区生物学

Journal of structural biology Pub Date : 2023-12-30 DOI: 10.1016/j.jsb.2023.108059

Ming-Feng Feng, Yu-Xuan Chen, Hong-Bin Shen

{"title":"DeepQs: Local quality assessment of cryo-EM density map by deep learning map-model fit score","authors":"Ming-Feng Feng, Yu-Xuan Chen, Hong-Bin Shen","doi":"10.1016/j.jsb.2023.108059","DOIUrl":"10.1016/j.jsb.2023.108059","url":null,"abstract":"<div><p>Cryogenic electron microscopy maps are valuable for determining macromolecule structures. A proper quality assessment method is essential for cryo-EM map selection or revision. This article presents DeepQs, a novel approach to estimate local quality for 3D cryo-EM density maps, using a deep-learning algorithm based on map-model fit score. DeepQs is a parameter-free method for users and incorporates structural information between map and its related atomic model into well-trained models by deep learning. More specifically, the DeepQs approach leverages the interplay between map and atomic model through predefined map-model fit score, Q-score. DeepQs can get close results to the ground truth map-model fit scores with only cryo-EM map as input. In experiments, DeepQs demonstrates the lowest root mean square error with standard method Fourier shell correlation metric and high correlation with map-model fit score, Q-score, when compared with other local quality estimation methods in high-resolution dataset (<=5 Å). DeepQs can also be applied to evaluate the quality of the post-processed maps. In both cases, DeepQs runs faster by using GPU acceleration. Our program is available at <span>http://www.csbio.sjtu.edu.cn/bioinf/DeepQs</span><svg><path></path></svg> for academic use.</p></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"216 1","pages":"Article 108059"},"PeriodicalIF":3.0,"publicationDate":"2023-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139069956","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

Cryo-forum: A framework for orientation recovery with uncertainty measure with the application in cryo-EM image analysis 低温论坛：在低温电子显微镜图像分析中应用带不确定性测量的定向恢复框架

IF 3 3区生物学

Journal of structural biology Pub Date : 2023-12-30 DOI: 10.1016/j.jsb.2023.108058

Szu-Chi Chung

{"title":"Cryo-forum: A framework for orientation recovery with uncertainty measure with the application in cryo-EM image analysis","authors":"Szu-Chi Chung","doi":"10.1016/j.jsb.2023.108058","DOIUrl":"10.1016/j.jsb.2023.108058","url":null,"abstract":"<div><p>In single-particle cryo-electron microscopy (cryo-EM), efficient determination of orientation parameters for particle images poses a significant challenge yet is crucial for reconstructing 3D structures. This task is complicated by the high noise levels in the datasets, which often include outliers, necessitating several time-consuming 2D clean-up processes. Recently, solutions based on deep learning have emerged, offering a more streamlined approach to the traditionally laborious task of orientation estimation. These solutions employ amortized inference, eliminating the need to estimate parameters individually for each image. However, these methods frequently overlook the presence of outliers and may not adequately concentrate on the components used within the network. This paper introduces a novel method using a 10-dimensional feature vector for orientation representation, extracting orientations as unit quaternions with an accompanying uncertainty metric. Furthermore, we propose a unique loss function that considers the pairwise distances between orientations, thereby enhancing the accuracy of our method. Finally, we also comprehensively evaluate the design choices in constructing the encoder network, a topic that has not received sufficient attention in the literature. Our numerical analysis demonstrates that our methodology effectively recovers orientations from 2D cryo-EM images in an end-to-end manner. Notably, the inclusion of uncertainty quantification allows for direct clean-up of the dataset at the 3D level. Lastly, we package our proposed methods into a user-friendly software suite named <em>cryo-forum</em>, designed for easy access by developers.</p></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"216 1","pages":"Article 108058"},"PeriodicalIF":3.0,"publicationDate":"2023-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139069109","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 deep learning approach to the automatic detection of alignment errors in cryo-electron tomographic reconstructions 自动检测低温电子断层重构中配准错误的深度学习方法

IF 3 3区生物学

Journal of structural biology Pub Date : 2023-12-14 DOI: 10.1016/j.jsb.2023.108056

F.P. de Isidro-Gómez , J.L. Vilas , P. Losana , J.M. Carazo , C.O.S. Sorzano

{"title":"A deep learning approach to the automatic detection of alignment errors in cryo-electron tomographic reconstructions","authors":"F.P. de Isidro-Gómez , J.L. Vilas , P. Losana , J.M. Carazo , C.O.S. Sorzano","doi":"10.1016/j.jsb.2023.108056","DOIUrl":"10.1016/j.jsb.2023.108056","url":null,"abstract":"<div><p>Electron tomography is an imaging technique that allows for the elucidation of three-dimensional structural information of biological specimens in a very general context, including cellular <em>in situ</em> observations. The approach starts by collecting a set of images at different projection directions by tilting the specimen stage inside the microscope. Therefore, a crucial preliminary step is to precisely define the acquisition geometry by aligning all the tilt images to a common reference. Errors introduced in this step will lead to the appearance of artifacts in the tomographic reconstruction, rendering them unsuitable for the sample study. Focusing on fiducial-based acquisition strategies, this work proposes a deep-learning algorithm to detect misalignment artifacts in tomographic reconstructions by analyzing the characteristics of these fiducial markers in the tomogram. In addition, we propose an algorithm designed to detect fiducial markers in the tomogram with which to feed the classification algorithm in case the alignment algorithm does not provide the location of the markers. This open-source software is available as part of the Xmipp software package inside of the Scipion framework, and also through the command-line in the standalone version of Xmipp.</p></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"216 1","pages":"Article 108056"},"PeriodicalIF":3.0,"publicationDate":"2023-12-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1047847723001193/pdfft?md5=2c6e8f0cde89102d24752cf1b627b980&pid=1-s2.0-S1047847723001193-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138693187","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}

引用次数: 0

Computational structural biology: Evolution of the field 计算结构生物学：领域的演变

IF 3 3区生物学

Journal of structural biology Pub Date : 2023-12-12 DOI: 10.1016/j.jsb.2023.108055

引用次数: 0

Exploring the folding landscape of leptin: Insights into threading pathways 探索瘦素的折叠景观:对线程路径的见解

IF 3 3区生物学

Journal of structural biology Pub Date : 2023-12-06 DOI: 10.1016/j.jsb.2023.108054

Fernando Bruno da Silva , Jennifer M. Simien , Rafael G. Viegas , Ellinor Haglund , Vitor Barbanti Pereira Leite

{"title":"Exploring the folding landscape of leptin: Insights into threading pathways","authors":"Fernando Bruno da Silva , Jennifer M. Simien , Rafael G. Viegas , Ellinor Haglund , Vitor Barbanti Pereira Leite","doi":"10.1016/j.jsb.2023.108054","DOIUrl":"10.1016/j.jsb.2023.108054","url":null,"abstract":"<div><p><span><span>The discovery of new protein topologies with entanglements and loop-crossings have shown the impact of local </span>amino acid arrangement and global three-dimensional structures. This phenomenon plays a crucial role in understanding how protein structure relates to folding and function, affecting the global stability, and biological activity. Protein entanglements encompassing knots and non-trivial topologies add complexity to their folding free energy landscapes. However, the initial native contacts driving the threading event for entangled proteins remains elusive. The Pierced Lasso Topology (PLT) represents an entangled topology where a covalent linker creates a loop in which the polypeptide backbone is threaded through. Compared to true knotted topologies, PLTs are simpler topologies where the covalent-loop persists in all conformations. In this work, the PLT protein leptin, is used to visualize and differentiate the preference for slipknotting over plugging transition pathways along the folding route. We utilize the Energy Landscape Visualization Method (ELViM), a multidimensional projection technique, to visualize and distinguish early threaded conformations that cannot be observed in an </span><em>in vitro</em> experiment. Critical contacts for the leptin threading mechanisms were identified where the competing pathways are determined by the formation of a hairpin loop in the unfolded basin. Thus, prohibiting the dominant slipknotting pathway. Furthermore, ELViM offers insights into distinct folding pathways associated with slipknotting and plugging providing a novel tool for <em>de novo</em> design and <em>in vitro</em> experiments with residue specific information of threading events <em>in silico</em>.</p></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"216 1","pages":"Article 108054"},"PeriodicalIF":3.0,"publicationDate":"2023-12-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138520711","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

Journal of Structural Biology – Paper of the Year 2022 结构生物学杂志-2022年度论文。

IF 3 3区生物学

Journal of structural biology Pub Date : 2023-12-01 DOI: 10.1016/j.jsb.2023.108032

Xinzheng Zhang

引用次数: 0