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Quantitative analysis methods for free diffusion single-molecule FRET experiments 自由扩散单分子FRET实验的定量分析方法
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-06-09 DOI: 10.1016/j.sbi.2025.103075
Irina V. Gopich, Hoi Sung Chung
{"title":"Quantitative analysis methods for free diffusion single-molecule FRET experiments","authors":"Irina V. Gopich,&nbsp;Hoi Sung Chung","doi":"10.1016/j.sbi.2025.103075","DOIUrl":"10.1016/j.sbi.2025.103075","url":null,"abstract":"<div><div>Single-molecule Förster Resonance Energy Transfer (smFRET) is a powerful technique for investigating the structure and dynamics of biomolecules. This review focuses on recent advances in quantitative methods to analyze freely diffusing molecules in smFRET. The methods include traditional approaches of analyzing FRET efficiency and advanced photon-by-photon techniques based on maximum likelihood estimation without binning photon sequences. More recently, methods explicitly accounting for molecular diffusion have been developed, addressing biases arising from variations in brightness and diffusivity among molecular states and species. Applications of these tools include studies of protein folding, DNA dynamics, and oligomerization processes of neurodegenerative proteins. These advancements expand the ability of free diffusion-based smFRET to elucidate the dynamic behavior of biomolecules on the timescales relevant to their biological processes.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"93 ","pages":"Article 103075"},"PeriodicalIF":6.1,"publicationDate":"2025-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144241908","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
HDX-MS in micelles and membranes for small molecule and biopharmaceutical development 用于小分子和生物制药开发的胶束和膜中的HDX-MS
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-06-06 DOI: 10.1016/j.sbi.2025.103077
Charlotte Guffick , Argyris Politis
{"title":"HDX-MS in micelles and membranes for small molecule and biopharmaceutical development","authors":"Charlotte Guffick ,&nbsp;Argyris Politis","doi":"10.1016/j.sbi.2025.103077","DOIUrl":"10.1016/j.sbi.2025.103077","url":null,"abstract":"<div><div>While protein characterisation is critical for continuing drug discovery and development, many techniques fall short of capturing the range of conformational dynamics that underpin the targeted protein activity. Hydrogen–deuterium exchange mass spectrometry (HDX-MS) is a powerful tool for investigation of protein structural dynamics, particularly for membrane proteins in different mimetic environments. This measurement of intrinsic protein behaviour is invaluable in outlining pathogenic protein dynamics, protein–ligand profiles, and druggable protein centres that are often inaccessible in other structural techniques. This minireview will cover how recent advances have been applied to HDX-MS of membrane proteins and peptides widening the use of HDX for drug discovery.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"94 ","pages":"Article 103077"},"PeriodicalIF":6.1,"publicationDate":"2025-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144230903","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
In situ cryo-electron microscopy and tomography of cellular and organismal samples 细胞和有机体样品的原位冷冻电子显微镜和断层扫描
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-06-04 DOI: 10.1016/j.sbi.2025.103076
Parijat Majumder , Peijun Zhang
{"title":"In situ cryo-electron microscopy and tomography of cellular and organismal samples","authors":"Parijat Majumder ,&nbsp;Peijun Zhang","doi":"10.1016/j.sbi.2025.103076","DOIUrl":"10.1016/j.sbi.2025.103076","url":null,"abstract":"<div><div>As cryo-electron microscopy (cryo-EM) and cryo-electron tomography (cryo-ET) continue to advance, the ability to visualize cellular and organismal structures with unprecedented clarity is redefining the landscape of structural biology. Breakthroughs in imaging technology, sample preparation and image processing now enable the detailed elucidation of cellular architecture, macromolecular organization, and dynamic biological processes at sub-nanometer resolution. Recent methodological advances have propelled the field to new frontiers, facilitating the investigation of complex biological questions across scales—from macromolecular complexes to organism-wide structural insights. This review explores rapidly emerging trends, highlights key innovations that are pushing the boundaries of in situ structural biology, and addresses persistent challenges in expanding the applicability of cryo-EM and cryo-ET across diverse biological systems.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"93 ","pages":"Article 103076"},"PeriodicalIF":6.1,"publicationDate":"2025-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144204870","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
Unsymmetric or hybrid detergents for membrane protein structural study 用于膜蛋白结构研究的非对称或杂化洗涤剂
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-06-02 DOI: 10.1016/j.sbi.2025.103074
Youngsun Moon , Yewon Lee , Ho Jin Lee , Bernadette Byrne , Pil Seok Chae
{"title":"Unsymmetric or hybrid detergents for membrane protein structural study","authors":"Youngsun Moon ,&nbsp;Yewon Lee ,&nbsp;Ho Jin Lee ,&nbsp;Bernadette Byrne ,&nbsp;Pil Seok Chae","doi":"10.1016/j.sbi.2025.103074","DOIUrl":"10.1016/j.sbi.2025.103074","url":null,"abstract":"<div><div>Detergent micelles are widely used as a membrane-mimetic system for membrane protein extraction, isolation and structural study. Many recently developed detergents feature multiple tail and head groups, with architectures that are symmetric (i.e. the same alkyl chain) and non-hybrid (single head group type). Further diversification has involved incorporating structural differences in the tail groups (unsymmetric), head groups (hybrid), or both head and tail groups (unsymmetric hybrid). In this mini-review, we introduce these novel detergents, focusing on the relationships between their structural features, physical properties and performance in membrane protein applications. The detergent design strategy utilizing unsymmetric/hybrid structures expands the detergent repertoire and the detergent structure–property-efficacy relationships presented offer valuable design guidelines, collectively advancing membrane protein research.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"93 ","pages":"Article 103074"},"PeriodicalIF":6.1,"publicationDate":"2025-06-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144189277","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
Extending the reach of single-particle cryoEM 扩大单粒子低温电镜的应用范围。
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-06-01 DOI: 10.1016/j.sbi.2025.103005
Ardan Patwardhan , Richard Henderson , Christopher J. Russo
{"title":"Extending the reach of single-particle cryoEM","authors":"Ardan Patwardhan ,&nbsp;Richard Henderson ,&nbsp;Christopher J. Russo","doi":"10.1016/j.sbi.2025.103005","DOIUrl":"10.1016/j.sbi.2025.103005","url":null,"abstract":"<div><div>Molecular structure determination using electron cryomicroscopy (cryoEM) is poised in early 2025 to surpass X-ray crystallography as the most used method for experimentally determining new structures. But the technique has not reached the physical limits set by radiation damage and the signal-to-noise ratio in individual images of molecules. By examining these limits and comparing the number and resolution of structures determined versus molecular weight, we identify opportunities for extending the application of single-particle cryoEM. This will help guide technology development to continue the exponential growth of structural biology.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"92 ","pages":"Article 103005"},"PeriodicalIF":6.1,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143556200","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
Publisher’s Note: Thank you to Marius Clore and Welcome to Annalisa Pastore! 出版商注：感谢Marius Clore，欢迎来到Annalisa Pastore！
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-06-01 DOI: 10.1016/j.sbi.2025.103098
{"title":"Publisher’s Note: Thank you to Marius Clore and Welcome to Annalisa Pastore!","authors":"","doi":"10.1016/j.sbi.2025.103098","DOIUrl":"10.1016/j.sbi.2025.103098","url":null,"abstract":"","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"92 ","pages":"Article 103098"},"PeriodicalIF":6.1,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144221810","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
Nanodisc-reconstitution for single particle cryo-EM structure determination of membrane proteins 膜蛋白单颗粒低温电镜结构测定的纳米圆盘重构
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-05-28 DOI: 10.1016/j.sbi.2025.103072
Arshay J. Grant , Ingeborg Schmidt-Krey
{"title":"Nanodisc-reconstitution for single particle cryo-EM structure determination of membrane proteins","authors":"Arshay J. Grant ,&nbsp;Ingeborg Schmidt-Krey","doi":"10.1016/j.sbi.2025.103072","DOIUrl":"10.1016/j.sbi.2025.103072","url":null,"abstract":"<div><div>Reconstitution of membrane proteins in nanodiscs has proven to be a highly effective approach to study membrane protein structures in a lipid bilayer, resulting in many recent single particle cryo-EM structures. While most of these studies employed membrane scaffold protein (MSP) nanodiscs, additional types of nanodiscs were developed based on MSPs and provide alternative approaches. Nanodiscs have been particularly effective in solving structures of different protein conformations and of bound lipids, demonstrating key roles of specific lipids in structural integrity and protein function. At the same time, discrepancies of lipid behavior in nanodiscs compared to native membranes and liposomes necessitate careful scrutiny of reconstitution parameters and further evaluation. This brief review covers an overview of types of nanodiscs currently in use for cryo-EM structural studies, their advantages and limitations, as well as examples of the dramatically increased understanding they can reveal.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"93 ","pages":"Article 103072"},"PeriodicalIF":6.1,"publicationDate":"2025-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144169514","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
Molecular dynamics simulations of biological membranes and membrane-associated phenomena across scales 跨尺度生物膜和膜相关现象的分子动力学模拟
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-05-26 DOI: 10.1016/j.sbi.2025.103071
Noah Trebesch, Hale S. Hasdemir, Tianle Chen, Po-Chao Wen, Emad Tajkhorshid
{"title":"Molecular dynamics simulations of biological membranes and membrane-associated phenomena across scales","authors":"Noah Trebesch,&nbsp;Hale S. Hasdemir,&nbsp;Tianle Chen,&nbsp;Po-Chao Wen,&nbsp;Emad Tajkhorshid","doi":"10.1016/j.sbi.2025.103071","DOIUrl":"10.1016/j.sbi.2025.103071","url":null,"abstract":"<div><div>Membranes are fundamental components of cells that are involved in a wide variety of cellular functions. They are inherently complex, being composed of hugely diverse collections of lipids and proteins, and their various functions arise directly from the intricate interplay between their components. To investigate the interactions between these components in detail, molecular dynamics (MD) simulations have proven to be an invaluable tool. In this mini-review, we highlight several recent studies that illustrate the current state of the art in using MD to study membrane systems. In particular, we first examine how MD is being used to characterize membrane binding of peripheral membrane proteins, we next describe how interactions between lipids and integral membrane proteins are being probed with MD, and we conclude by discussing new tools that have recently been developed to address the significant challenge of building simulateable models of large-scale membranes with complex curvature.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"93 ","pages":"Article 103071"},"PeriodicalIF":6.1,"publicationDate":"2025-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144139242","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
Nanodiscs and solution nuclear magnetic resonance 纳米片和溶液核磁共振
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-05-26 DOI: 10.1016/j.sbi.2025.103067
Olga Vinogradova
{"title":"Nanodiscs and solution nuclear magnetic resonance","authors":"Olga Vinogradova","doi":"10.1016/j.sbi.2025.103067","DOIUrl":"10.1016/j.sbi.2025.103067","url":null,"abstract":"<div><div>Although membrane proteins constitute a significant portion of the genomes of all species and represent well-validated targets for numerous therapeutic interventions, high-resolution structural knowledge of this class of proteins still falls behind that of their soluble counterparts. Despite serious technological developments in the methods presently available for structural characterizations, as well as decades spent on such investigations, membrane proteins remain notoriously difficult to study. This is particularly true for environments which mimic native membranes well enough to maintain their proper functional states. This mini review covers the most recent advances in the structural and dynamic characterization of membrane proteins through the utilization of solution nuclear magnetic resonance methods applied to lipid nanodiscs.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"93 ","pages":"Article 103067"},"PeriodicalIF":6.1,"publicationDate":"2025-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144139241","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
Recent advances and future trends for protein–small molecule interaction predictions with protein language models 用蛋白质语言模型预测蛋白质-小分子相互作用的最新进展和未来趋势
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-05-24 DOI: 10.1016/j.sbi.2025.103070
Alexander Kroll, Yvan Rousset
{"title":"Recent advances and future trends for protein–small molecule interaction predictions with protein language models","authors":"Alexander Kroll,&nbsp;Yvan Rousset","doi":"10.1016/j.sbi.2025.103070","DOIUrl":"10.1016/j.sbi.2025.103070","url":null,"abstract":"<div><div>In recent years, the application of natural language models to protein amino acid sequences, referred to as protein language models (PLMs), has demonstrated a significant potential for uncovering hidden patterns related to protein structure, function, and stability. The critical functions of proteins in biological processes often arise through interactions with small molecules; central examples are enzymes, receptors, and transporters. Understanding these interactions is particularly important for drug design, for bioengineering, and for understanding cellular metabolism. In this review, we present state-of-the-art PLMs and explore how they can be integrated with small molecule information to predict protein-small molecule interactions. We present several such prediction tasks and discuss current limitations and potential areas for improvement.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"93 ","pages":"Article 103070"},"PeriodicalIF":6.1,"publicationDate":"2025-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144125023","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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