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Are N-linked glycans intrinsically disordered? n链聚糖本质上是无序的吗？
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-07-10 DOI: 10.1016/j.sbi.2025.103118
Eliza Gazaway , Rajan Kandel , Oliver C. Grant, Robert J. Woods
{"title":"Are N-linked glycans intrinsically disordered?","authors":"Eliza Gazaway ,&nbsp;Rajan Kandel ,&nbsp;Oliver C. Grant,&nbsp;Robert J. Woods","doi":"10.1016/j.sbi.2025.103118","DOIUrl":"10.1016/j.sbi.2025.103118","url":null,"abstract":"<div><div>The covalent attachment of oligosaccharides to asparagine side chains on protein surfaces (<em>N-</em>linked glycosylation) is a ubiquitous modification that is critical to protein stability and function. Experimental 3D structures of glycoproteins in which the <em>N-</em>linked glycans are well resolved are rare due to both the presumed flexibility of the <em>N-</em>linked glycan and to glycan microheterogeneity. To surmount these limitations, computational modeling is often applied to glycoproteins, particularly to generate an ensemble of 3D shapes for the <em>N-</em>linked glycans. While the number of glycoprotein modelling tools continues to expand, the available experimental data against which the predictions can be validated remains extremely limited. Here, we present our current understanding of the dynamic properties of <em>N-</em>linked glycans, with a particular focus on features that impact their presentation (orientation) relative to the protein surface. Additionally, we review the limits of experimental and theoretical studies of glycoproteins, and ask the question, “Are <em>N-</em>linked glycans intrinsically disordered?”.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"93 ","pages":"Article 103118"},"PeriodicalIF":6.1,"publicationDate":"2025-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144595750","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
Segmenting cryo-electron tomography data: Extracting models from cellular landscapes 分割低温电子断层扫描数据：从细胞景观中提取模型
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-07-10 DOI: 10.1016/j.sbi.2025.103114
Danielle A. Grotjahn
{"title":"Segmenting cryo-electron tomography data: Extracting models from cellular landscapes","authors":"Danielle A. Grotjahn","doi":"10.1016/j.sbi.2025.103114","DOIUrl":"10.1016/j.sbi.2025.103114","url":null,"abstract":"<div><div>Cryo-electron tomography provides an unprecedented view of cellular architecture, yet extracting meaningful biological insights remains challenging. Segmentation is a crucial step in this process through its ability to identify structural relationships between subcellular components visible in cryo-electron tomography data. While segmentation pipelines were historically low throughput, recent advancements in deep learning have significantly improved their automation, accuracy, and scalability. This review explores how these innovations redefine best practices for segmentation and accelerate biological discovery. This article highlights the critical role of segmentation in unlocking the full potential of cryo-electron tomography—not only for resolving macromolecular structures but also for quantifying their impact on subcellular organization and function.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"93 ","pages":"Article 103114"},"PeriodicalIF":6.1,"publicationDate":"2025-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144595471","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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-electron tomography: Challenges and computational strategies for particle picking 低温电子断层扫描：粒子拾取的挑战和计算策略
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-07-09 DOI: 10.1016/j.sbi.2025.103113
Thorsten Wagner, Stefan Raunser
{"title":"Cryo-electron tomography: Challenges and computational strategies for particle picking","authors":"Thorsten Wagner,&nbsp;Stefan Raunser","doi":"10.1016/j.sbi.2025.103113","DOIUrl":"10.1016/j.sbi.2025.103113","url":null,"abstract":"<div><div>Cryo-electron tomography (cryo-ET) and subtomogram averaging have emerged as powerful techniques for investigating cellular structures and their spatial organization. However, the exact localization of proteins in the crowded and noisy environment of cellular tomograms is challenging. This review provides a comprehensive overview of existing deep learning-based particle-picking procedures, which were proposed to overcome these challenges. We evaluate both annotation-based and annotation-free methods, highlighting their respective strengths, weaknesses, and ideal use cases. Furthermore, we assess these methodologies based on various criteria, such as the effort required to generate the necessary input data, inference runtime, and filament support. Additionally, we consider practical factors such as the availability of documentation and tutorials to guide researchers in selecting the most appropriate approach for their needs.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"93 ","pages":"Article 103113"},"PeriodicalIF":6.1,"publicationDate":"2025-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144588940","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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 practical look at cryo-electron tomography image processing: Key considerations for new biological discoveries 冷冻电子断层成像图像处理的实际观察：新生物学发现的关键考虑因素
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-07-08 DOI: 10.1016/j.sbi.2025.103116
William Wan
{"title":"A practical look at cryo-electron tomography image processing: Key considerations for new biological discoveries","authors":"William Wan","doi":"10.1016/j.sbi.2025.103116","DOIUrl":"10.1016/j.sbi.2025.103116","url":null,"abstract":"<div><div>Cryo-electron tomography (cryo-ET) enables 3D visualization of complex biological environments without the need for purification, thereby preserving the native biological context of the specimen. For determining macromolecular structures, repeating molecules can be localized in tomograms and subjected to subtomogram averaging, the 3D analog to single particle analysis. In addition to molecular structure, tomograms have a wealth of other information that can be accessed through image processing, including the analysis of membrane surfaces, cytoskeletal filaments, and the relationships between molecules of interest. Here, we provide an overview of recent developments in cryo-ET image processing with the goal of clarifying key considerations to help new users obtain novel biological findings.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"93 ","pages":"Article 103116"},"PeriodicalIF":6.1,"publicationDate":"2025-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144572536","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
Generation of protein dynamics by machine learning 通过机器学习生成蛋白质动力学
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-07-08 DOI: 10.1016/j.sbi.2025.103115
Giacomo Janson, Michael Feig
{"title":"Generation of protein dynamics by machine learning","authors":"Giacomo Janson,&nbsp;Michael Feig","doi":"10.1016/j.sbi.2025.103115","DOIUrl":"10.1016/j.sbi.2025.103115","url":null,"abstract":"<div><div>Machine learning has advanced protein structure prediction to deliver accurate but mostly static models. Capturing protein dynamics as conformational ensembles remains a significant challenge. Recent developments, especially generative models, are enabling the prediction of structural ensembles beyond traditional simulations. This review examines emerging machine learning approaches for modeling protein dynamics, in terms of generating PDB-like ensembles, accelerating molecular simulations, modeling non-globular protein ensembles, and integrating experimental data. General-purpose and system-specific models are discussed, particularly in terms of conformational coverage, transferability, and responsiveness to environmental conditions. Hybrid models, which combine experimental and simulation data, represent a promising direction. Nonetheless, key challenges remain, including generating states with correct probabilities, modeling unseen conformations, and integrating experimental constraints rigorously.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"93 ","pages":"Article 103115"},"PeriodicalIF":6.1,"publicationDate":"2025-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144572535","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
Innovations in cryo-electron tomography for tissues: Challenges and future prospects 组织低温电子断层扫描的创新：挑战和未来展望
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-07-07 DOI: 10.1016/j.sbi.2025.103112
Zhe Chen , Qiang Guo
{"title":"Innovations in cryo-electron tomography for tissues: Challenges and future prospects","authors":"Zhe Chen ,&nbsp;Qiang Guo","doi":"10.1016/j.sbi.2025.103112","DOIUrl":"10.1016/j.sbi.2025.103112","url":null,"abstract":"<div><div>Cryo-electron tomography (cryo-ET) is revolutionizing <em>in situ</em> structural analysis of single-cell specimens, yet its application to tissues has been hindered, primarily due to challenges posed by tissue thickness. Advances in sample vitrification, cryo-focused ion beam (cryo-FIB) milling, and lift-out techniques have substantially improved tissue preparation, enabling thin, electron microscopy-compatible samples. Furthermore, the integration of automation, complementary imaging modalities, and AI has streamlined imaging workflows and data analysis. This review highlights these technological developments, their implications for tissue analysis, and the future potential of cryo-ET in advancing structural biology and biomedical research.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"93 ","pages":"Article 103112"},"PeriodicalIF":6.1,"publicationDate":"2025-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144570448","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
Evolution of protein-RNA interactions 蛋白质- rna相互作用的进化
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-07-07 DOI: 10.1016/j.sbi.2025.103109
Michal H. Kolář , Klára Hlouchová
{"title":"Evolution of protein-RNA interactions","authors":"Michal H. Kolář ,&nbsp;Klára Hlouchová","doi":"10.1016/j.sbi.2025.103109","DOIUrl":"10.1016/j.sbi.2025.103109","url":null,"abstract":"<div><div>Since the Hadean–Eoarchaean era of Earth’s history, peptides/proteins and RNA have undergone a complex evolutionary trajectory. Originating from simple monomeric units, these molecules evolved abiotically under various biochemical and biophysical constraints into functional biomolecules that contributed to the emergence of the first living cells. Within these cells, their interactions could then evolve through Darwinian selection. In this review, we examine current understanding of how protein–RNA interactions emerged under prebiotic conditions and developed into today’s iconic biomolecular machines such as the ribosome. Particular emphasis is placed on the types of physicochemical interactions accessible to early protein–RNA complexes. Special attention is given to how the limited prebiotic amino acid repertoire influenced these interactions and their roles in driving spatial organization and compartmentalization in protocellular environments.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"94 ","pages":"Article 103109"},"PeriodicalIF":6.1,"publicationDate":"2025-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144569923","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
Probing structural dynamics and interactions in macromolecular complexes with single-molecule force spectroscopy 用单分子力谱法探测大分子配合物的结构动力学和相互作用
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-07-07 DOI: 10.1016/j.sbi.2025.103110
Abhishek Narayan , Michael T. Woodside
{"title":"Probing structural dynamics and interactions in macromolecular complexes with single-molecule force spectroscopy","authors":"Abhishek Narayan ,&nbsp;Michael T. Woodside","doi":"10.1016/j.sbi.2025.103110","DOIUrl":"10.1016/j.sbi.2025.103110","url":null,"abstract":"<div><div>Many cellular processes involve assemblies of diverse biological molecules acting in concert. Single-molecule force spectroscopy offers a powerful approach for deciphering how the components of such complexes interact dynamically. By applying mechanical forces to individual molecules within the complex, multiple features can be explored, including the conformation of these molecules, the strength of their interactions with other members of the complex, and association/dissociation rates. We discuss recent advances from force spectroscopy studies of complexes involving protein–nucleic acid, protein–protein, and protein-lipid interactions, which provide insight into processes relevant for both biological function and disease.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"93 ","pages":"Article 103110"},"PeriodicalIF":6.1,"publicationDate":"2025-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144569931","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
The evolution and mechanism of bacterial and archaeal ESCRT-III-like systems 细菌和古细菌escrt - iii样系统的进化和机制
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-07-06 DOI: 10.1016/j.sbi.2025.103111
Tom A. Williams , Harry H. Low
{"title":"The evolution and mechanism of bacterial and archaeal ESCRT-III-like systems","authors":"Tom A. Williams ,&nbsp;Harry H. Low","doi":"10.1016/j.sbi.2025.103111","DOIUrl":"10.1016/j.sbi.2025.103111","url":null,"abstract":"<div><div>The endosomal sorting complex required for transport-III (ESCRT-III) system is an ancient protein family involved in membrane remodelling. Recent phylogenetic and structural analyses reveal its conservation across the tree of life, including bacteria and archaea, suggesting an evolutionary origin predating the last universal common ancestor. These findings underscore the importance of the ESCRT-III superfamily to our origins, particularly with the recognition of their contribution to eukaryogenesis through the Asgard archaea lineage. Bacterial systems, often with a single ESCRT-III–like protein, offer a simple model for understanding how ESCRT-III can function as both membrane sensor and sculptor. This review explores the structural dynamics, evolutionary trajectories, and biological significance of ESCRT-III in bacteria and archaea. We describe how ESCRT-III polymerises and assembles conserved filaments with the coating of flat or positively curved membranes prevalent, at least <em>in vitro</em>. Finally, we highlight common mechanistic principles and unique adaptations that enable ESCRT-III systems to support diverse cellular processes across evolutionary domains.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"93 ","pages":"Article 103111"},"PeriodicalIF":6.1,"publicationDate":"2025-07-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144570449","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
Minimal models for RNA simulations RNA模拟的最小模型
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-07-05 DOI: 10.1016/j.sbi.2025.103107
D. Thirumalai , Naoto Hori , Hung T. Nguyen
{"title":"Minimal models for RNA simulations","authors":"D. Thirumalai ,&nbsp;Naoto Hori ,&nbsp;Hung T. Nguyen","doi":"10.1016/j.sbi.2025.103107","DOIUrl":"10.1016/j.sbi.2025.103107","url":null,"abstract":"<div><div>The increasing importance of RNA as a prime player in biology can hardly be overstated. Problems in RNA, such as folding and RNA–RNA interactions that drive phase separation, require cations. Because experiments alone cannot reveal the dynamics of cation-RNA interactions, well calibrated theory and computations are needed to predict how ions control the behavior of RNA. The perspective describes the development and use of coarse-grained models at different resolutions. We focus on single- and three-interaction site models, in which electrostatic interactions are treated using a combination of explicit and implicit representations. Applications to the folding of ribozymes and riboswitches are discussed, with emphasis on the role of monovalent and divalent cations. We also discuss phase separation in low-complexity sequences. Challenges in the simulation of complex problems such as ribosome assembly and RNA chaperones, requiring developments of models for RNA-protein interactions, are pointed out.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"93 ","pages":"Article 103107"},"PeriodicalIF":6.1,"publicationDate":"2025-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144563738","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
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