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The synergy of experimental and computational approaches for visualizing glycoprotein dynamics: Exploring order within the apparent disorder of glycan conformational ensembles 可视化糖蛋白动力学的实验和计算方法的协同作用：在糖蛋白构象集合的明显无序中探索秩序
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-04-29 DOI: 10.1016/j.sbi.2025.103049
Koichi Kato , Saeko Yanaka , Takumi Yamaguchi
{"title":"The synergy of experimental and computational approaches for visualizing glycoprotein dynamics: Exploring order within the apparent disorder of glycan conformational ensembles","authors":"Koichi Kato ,&nbsp;Saeko Yanaka ,&nbsp;Takumi Yamaguchi","doi":"10.1016/j.sbi.2025.103049","DOIUrl":"10.1016/j.sbi.2025.103049","url":null,"abstract":"<div><div>Understanding the dynamic behavior of glycoproteins is crucial for deciphering their biological roles. This review explores the synergistic use of experimental and computational methods to address this complex challenge. Glycans, with their inherent flexibility and structural diversity, pose significant obstacles to traditional structural analysis. Innovative experimental techniques offer valuable snapshots of glycan conformations, but often lack the context of a physiological environment. Computational simulations provide atomic-level detail and explore the full range of dynamic motions, but require extensive resources and validation. Integrating these approaches, by using experimental data to refine and validate computational models, is essential for accurately capturing the complex interplay between glycans and proteins. This combined strategy promises to unlock a deeper understanding of glycoprotein function and inform the design of novel therapeutics.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"92 ","pages":"Article 103049"},"PeriodicalIF":6.1,"publicationDate":"2025-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143882426","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
Comparative anatomy of siphophage tails before and after interaction with their receptor 与受体相互作用前后的虹吸体尾部对比解剖
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-04-24 DOI: 10.1016/j.sbi.2025.103045
Alessio d'Acapito , Alice Decombe , Charles-Adrien Arnaud, Cécile Breyton
{"title":"Comparative anatomy of siphophage tails before and after interaction with their receptor","authors":"Alessio d'Acapito ,&nbsp;Alice Decombe ,&nbsp;Charles-Adrien Arnaud,&nbsp;Cécile Breyton","doi":"10.1016/j.sbi.2025.103045","DOIUrl":"10.1016/j.sbi.2025.103045","url":null,"abstract":"<div><div>Siphophages are tailed bacteriophages characterised by their long noncontractile tails. In this review, we compare the recent electron cryo-microscopy structures of eight siphophage tails. We confirm and extend common building block organisation within the siphophage tails, particularly within the tail tip. Moreover, the description of the structure of siphophages T5 and λ tail after receptor binding, showing conformational changes only in the tail tip, explains how the siphophage tail opens, leading to DNA ejection. Conserved structural elements point to a general mechanism of infection for Gram-negative-infecting siphophages and allow considerations regarding the classification of the receptor-binding proteins into two different categories: host recognition receptors and membrane sensing receptors that trigger DNA ejection.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"92 ","pages":"Article 103045"},"PeriodicalIF":6.1,"publicationDate":"2025-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143868046","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
Single-particle cryogenic electron microscopy structure determination for membrane proteins 膜蛋白单粒子低温电镜结构测定
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-04-13 DOI: 10.1016/j.sbi.2025.103047
Chih-Ta Chien , Merritt Maduke , Wah Chiu
{"title":"Single-particle cryogenic electron microscopy structure determination for membrane proteins","authors":"Chih-Ta Chien ,&nbsp;Merritt Maduke ,&nbsp;Wah Chiu","doi":"10.1016/j.sbi.2025.103047","DOIUrl":"10.1016/j.sbi.2025.103047","url":null,"abstract":"<div><div>Membrane proteins are crucial to many cellular functions but are notoriously difficult for structural studies due to their instability outside their natural environment and their amphipathic nature with dual hydrophobic and hydrophilic regions. Single-particle cryogenic electron microscopy (cryo-EM) has emerged as a transformative approach, providing near–atomic-resolution structures without the need for crystallization. This review discusses advancements in cryo-EM, emphasizing membrane sample preparation and data processing techniques. It explores innovations in capturing membrane protein structures within native environments, analyzing their dynamics, binding partner interactions, lipid associations, and responses to electrochemical gradients. These developments continue to enhance our understanding of these vital biomolecules, advancing the contributions of structural biology for basic and translational biomedicine.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"92 ","pages":"Article 103047"},"PeriodicalIF":6.1,"publicationDate":"2025-04-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143825583","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
Characterization of conformationally heterogeneous proteins by electron paramagnetic resonance spectroscopy 电子顺磁共振波谱法表征异质蛋白质构象
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-04-11 DOI: 10.1016/j.sbi.2025.103046
Gunnar Jeschke
{"title":"Characterization of conformationally heterogeneous proteins by electron paramagnetic resonance spectroscopy","authors":"Gunnar Jeschke","doi":"10.1016/j.sbi.2025.103046","DOIUrl":"10.1016/j.sbi.2025.103046","url":null,"abstract":"<div><div>The Anfinsen paradigm of representing a protein by a single conformer is challenged by the uncertainty predictions that come with AlphaFold models, which suggest a greater extent of disorder. Characterization of such conformation heterogeneity requires experimental approaches that do not depend on long-range order. Site-directed spin labeling (SDSL) coupled with electron paramagnetic resonance (EPR) spectroscopy is such an approach. The double electron–electron resonance (DEER) technique can access site-pair distance distributions in the 15–100 Å range, directly informing on ensemble width. SDSL-EPR can be applied in cellular environments, and recent work indicates that protein disorder is even more pervasive than predicted by AlphaFold. This suggests that the Anfinsen paradigm should be replaced by an ensemble paradigm.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"92 ","pages":"Article 103046"},"PeriodicalIF":6.1,"publicationDate":"2025-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143820312","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
Simulating biomolecules for physiological timescales 模拟生理时间尺度的生物分子
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-04-10 DOI: 10.1016/j.sbi.2025.103039
Paul C. Whitford , José N. Onuchic
{"title":"Simulating biomolecules for physiological timescales","authors":"Paul C. Whitford ,&nbsp;José N. Onuchic","doi":"10.1016/j.sbi.2025.103039","DOIUrl":"10.1016/j.sbi.2025.103039","url":null,"abstract":"<div><div>Advances in structural biology are providing many opportunities to simulate complex conformational motions in large-scale assemblies. While some models are limited by computational resources, all-atom and coarse-grained structure-based models have been particularly effective at elucidating mechanistic, energetic, and kinetic properties of collective rearrangements. Here, we highlight recent examples where structure-based models (e.g. \"SMOG\" models) have provided insights into long-timescale dynamics of large-scale processes. These models are sufficient to predict all structural characteristics of the energy landscape, where the use of explicit-solvent simulations has allowed for precise calibration of energetics and kinetics. Together, long-timescale simulations of complex assemblies, such as viral fusion proteins or the ribosome, are revealing how a balance of energetics and structural disorder drives biological and disease processes.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"92 ","pages":"Article 103039"},"PeriodicalIF":6.1,"publicationDate":"2025-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143816837","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 remain indispensable for Cryo-EM studies of membrane proteins 纳米光盘仍是膜蛋白冷冻电镜研究不可或缺的工具
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-04-08 DOI: 10.1016/j.sbi.2025.103042
Giorgos Hiotis , Ryan Q. Notti , Huan Bao , Thomas Walz
{"title":"Nanodiscs remain indispensable for Cryo-EM studies of membrane proteins","authors":"Giorgos Hiotis ,&nbsp;Ryan Q. Notti ,&nbsp;Huan Bao ,&nbsp;Thomas Walz","doi":"10.1016/j.sbi.2025.103042","DOIUrl":"10.1016/j.sbi.2025.103042","url":null,"abstract":"<div><div>Nanodiscs, small discoidal membrane patches stabilized by membrane-scaffold proteins (MSPs), are popular tools to stabilize integral membrane proteins (IMPs) for structural studies by cryogenic electron microscopy (cryo-EM). While nanodiscs provide a near-native membrane environment for the incorporated IMPs, they do not reproduce all characteristics of a native membrane. Also, IMPs must first be purified in detergent before they can be reconstituted into MSP-based nanodiscs, a problem that has been overcome by newer approaches, such as copolymer-based native nanodiscs and cell-derived vesicles. In this review, we argue that despite these advances, MSP-based nanodiscs remain a unique tool for the structural interrogation of IMPs.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"92 ","pages":"Article 103042"},"PeriodicalIF":6.1,"publicationDate":"2025-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143790941","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
Virtual reality in drug design: Benefits, applications and industrial perspectives 虚拟现实在药物设计中的应用和工业前景
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-04-07 DOI: 10.1016/j.sbi.2025.103044
Marc Baaden , David R. Glowacki
{"title":"Virtual reality in drug design: Benefits, applications and industrial perspectives","authors":"Marc Baaden ,&nbsp;David R. Glowacki","doi":"10.1016/j.sbi.2025.103044","DOIUrl":"10.1016/j.sbi.2025.103044","url":null,"abstract":"<div><div>Virtual reality (VR) is a tool which has transformative potential in domains which involve the visualization of complex 3D data such as structure-based drug design (SBDD), where it offers new ways to visualize and manipulate complex molecular structures in three dimensions, and enable intuitive exploration of protein-ligand complexes. In this article, we outline three levels of interaction which are available in immersive VR environments for drug discovery, and provide illustrative case studies with applications in COVID-19 research and protein-ligand docking. We discuss VR's role in drug discovery based on conversations with experts from the pharmaceutical industry. While industry experts are mostly optimistic about the potential of VR, they point to the challenges related to integration with existing workflows and the need for improved hardware ergonomics, as well as ensuring a synergistic relationship between VR and an expanding suite of artificial intelligence (AI) tools.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"92 ","pages":"Article 103044"},"PeriodicalIF":6.1,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143785386","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
The evolving role of solid state nuclear magnetic resonance methods in studies of amyloid fibrils 固态核磁共振方法在淀粉样蛋白原纤维研究中的发展作用
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-04-07 DOI: 10.1016/j.sbi.2025.103043
Robert Tycko
{"title":"The evolving role of solid state nuclear magnetic resonance methods in studies of amyloid fibrils","authors":"Robert Tycko","doi":"10.1016/j.sbi.2025.103043","DOIUrl":"10.1016/j.sbi.2025.103043","url":null,"abstract":"<div><div>Beginning in the 1990s, solid state nuclear magnetic resonance (ssNMR) methods played a major role in elucidating the molecular structures and properties of amyloid fibrils. General principles that explain these structures and properties were uncovered and experimentally-based structural models were first developed from ssNMR data. Since 2017, cryogenic electron microscopy (cryo-EM) techniques have become capable of solving amyloid structures at near-atomic resolution. Although cryo-EM measurements are now the main approach for structural studies of amyloid fibrils, ssNMR measurements remain essential for studies of certain structures and structural features, as well as studies of dynamical and mechanistic aspects. Recent publications from various research groups illustrate the continuing importance of ssNMR and the unique information available from ssNMR measurements in amyloid research.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"92 ","pages":"Article 103043"},"PeriodicalIF":6.1,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143785387","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
Raman spectroscopy and imaging of protein droplet formation and aggregation 蛋白质液滴形成和聚集的拉曼光谱和成像
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-04-01 DOI: 10.1016/j.sbi.2025.103041
Matthew D. Watson, Jennifer C. Lee
{"title":"Raman spectroscopy and imaging of protein droplet formation and aggregation","authors":"Matthew D. Watson,&nbsp;Jennifer C. Lee","doi":"10.1016/j.sbi.2025.103041","DOIUrl":"10.1016/j.sbi.2025.103041","url":null,"abstract":"<div><div>Raman microscopy offers a unique combination of chemical and spatial resolution with structural sensitivity. This makes it an ideal tool for studies of protein structural changes in heterogenous samples such as protein liquid–liquid phase separation (LLPS) and amyloid formation. These processes are characterized by the spontaneous assembly of proteins to form either microscopic liquid droplets or insoluble filaments stabilized by β-sheets. LLPS and amyloid formation are closely related, with many proteins that undergo LLPS also forming amyloids. This has led to the proposal that development of β-sheets in droplets is an initiating event in toxic amyloid formation. This review surveys recent applications of Raman microscopic methods to studies of LLPS and amyloid formation both <em>in vitro</em> and <em>in cellulo</em>.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"92 ","pages":"Article 103041"},"PeriodicalIF":6.1,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143739213","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 structural perspective on enzymes and their catalytic mechanisms 酶的结构研究及其催化机理
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-03-29 DOI: 10.1016/j.sbi.2025.103040
Neera Borkakoti , António J.M. Ribeiro , Janet M. Thornton
{"title":"A structural perspective on enzymes and their catalytic mechanisms","authors":"Neera Borkakoti ,&nbsp;António J.M. Ribeiro ,&nbsp;Janet M. Thornton","doi":"10.1016/j.sbi.2025.103040","DOIUrl":"10.1016/j.sbi.2025.103040","url":null,"abstract":"<div><div>In this perspective, we analyse the progress made in our knowledge of enzyme sequences, structures and functions in the last 2 years. We review how much new enzyme data have been garnered and annotated, derived from the study of proteins using structural and computational approaches. Recent advances towards capturing ‘Catalysis <em>in silico</em>’ are described, including knowledge and predictions of enzyme structures, their interactions and mechanisms. We highlight the flood of enzyme data, driven by metagenomic sequencing, the improved enzyme data resources, the high coverage in Protein Data Bank of E.C. classes and the AI-driven structure prediction techniques that facilitate the accurate prediction of protein structures. We note the focus on disordered regions in the context of enzyme regulation and specificity and comment on emerging bioinformatic approaches that capture reaction mechanisms computationally for comparing and predicting enzyme mechanisms. We also consider the drivers of progress in this field in the next five years.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"92 ","pages":"Article 103040"},"PeriodicalIF":6.1,"publicationDate":"2025-03-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143725468","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
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