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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
Photo-crosslinkers boost structural information from crosslinking mass spectrometry 光交联剂提高结构信息从交联质谱
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-07-04 DOI: 10.1016/j.sbi.2025.103102
Anthony Ciancone, Francis J. O'Reilly
{"title":"Photo-crosslinkers boost structural information from crosslinking mass spectrometry","authors":"Anthony Ciancone,&nbsp;Francis J. O'Reilly","doi":"10.1016/j.sbi.2025.103102","DOIUrl":"10.1016/j.sbi.2025.103102","url":null,"abstract":"<div><div>Crosslinking mass spectrometry has emerged as a powerful tool in structural biology. This technology utilizes chemical crosslinkers to capture spatial proximities between protein residues to probe the organization, stoichiometry, and flexibility of protein assemblies under near-native conditions. Photo-crosslinking reagents have become increasingly used in crosslinking MS, with chemical properties that offer significant advantages when studying dynamic protein structures. This review explores the fundamentals, applications, and future potential of photo-crosslinkers in crosslinking mass spectrometry.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"93 ","pages":"Article 103102"},"PeriodicalIF":6.1,"publicationDate":"2025-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144563737","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
Review: Membrane protein nanodiscs for antibody discovery 综述：用于抗体发现的膜蛋白纳米片
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-07-03 DOI: 10.1016/j.sbi.2025.103104
Xiaojie Yao , Christy A. Thomson
{"title":"Review: Membrane protein nanodiscs for antibody discovery","authors":"Xiaojie Yao ,&nbsp;Christy A. Thomson","doi":"10.1016/j.sbi.2025.103104","DOIUrl":"10.1016/j.sbi.2025.103104","url":null,"abstract":"<div><div>Membrane proteins play pivotal roles in cellular signaling, transport, and immune responses. Dysregulation of these proteins frequently underlies diverse disease states, making them appealing targets for drug development, including therapeutic antibodies. Traditionally, the extraction and stabilization of membrane proteins involve detergents, which may compromise the protein's native conformation, thus impeding antibody discovery. The shift toward detergent-free formulations using membrane protein nanodiscs formed by membrane scaffold proteins (MSPs), copolymers, saposins, or peptides has opened new avenues in membrane protein research and antibody discovery. They allow for the stabilization of membrane proteins in a more native-like environment, preserving structural integrity and function. This review discusses various membrane protein nanodiscs, and their applications in antibody discovery, alongside current advancements and challenges.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"94 ","pages":"Article 103104"},"PeriodicalIF":6.1,"publicationDate":"2025-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144535514","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
All-atom simulations of biomolecular condensates 生物分子凝聚物的全原子模拟
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-07-03 DOI: 10.1016/j.sbi.2025.103101
Miloš T. Ivanović , Robert B. Best
{"title":"All-atom simulations of biomolecular condensates","authors":"Miloš T. Ivanović ,&nbsp;Robert B. Best","doi":"10.1016/j.sbi.2025.103101","DOIUrl":"10.1016/j.sbi.2025.103101","url":null,"abstract":"<div><div>Biomolecular condensates shape a wide spectrum of physiological and pathological processes, yet the molecular mechanisms underlying their formation and activity are still to be fully understood. Molecular simulations can provide valuable insights into the structure and dynamics of such condensates, and coarse-grained simulations have been widely used to characterize phenomena related to their phase equilibrium. All-atom simulations provide a complementary picture–while too expensive to readily study equilibrium between dense and dilute phases, they offer molecular detail on the dense phase that is missing from coarse-grained models, as well as accurate dynamical information. We provide an overview of this nascent application of atomistic simulations to condensates and the insights they have yielded on their structure and dynamics.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"93 ","pages":"Article 103101"},"PeriodicalIF":6.1,"publicationDate":"2025-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144536129","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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