发布求助
文献互助 智能选刊 最新文献

Current opinion in structural biology最新文献

筛选
英文 中文
All-atom virus simulations to tackle airborne disease 全原子病毒模拟来对付空气传播疾病
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-05-03 DOI: 10.1016/j.sbi.2025.103048
Abigail C. Dommer , Nicholas A. Wauer , Siewert J. Marrink , Rommie E. Amaro
{"title":"All-atom virus simulations to tackle airborne disease","authors":"Abigail C. Dommer ,&nbsp;Nicholas A. Wauer ,&nbsp;Siewert J. Marrink ,&nbsp;Rommie E. Amaro","doi":"10.1016/j.sbi.2025.103048","DOIUrl":"10.1016/j.sbi.2025.103048","url":null,"abstract":"<div><div>We briefly review the latest computational studies focused on modeling viruses with classical all-atom (AA) molecular dynamics. We report on the challenges, current solutions, and ongoing developments in constructing and simulating whole viruses, and discuss unique insights derived from AA mesoscale simulations that cannot be achieved by other means. Finally, we present new opportunities in computational virology to understand viral aerostability within the context of respiratory disease transmission. Overall, we highlight the value of large-scale AA simulation and champion the need for increased interdisciplinary collaboration to generate novel insights and guide future research in respiratory disease.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"92 ","pages":"Article 103048"},"PeriodicalIF":6.1,"publicationDate":"2025-05-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143900041","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 evolving role of hydrogen/deuterium exchange mass spectrometry in early-stage drug discovery 氢/氘交换质谱法在早期药物发现中的作用
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-05-02 DOI: 10.1016/j.sbi.2025.103051
Srinath Krishnamurthy , Maria Musgaard , Benjamin Gerald Tehan, Ali Jazayeri, Idlir Liko
{"title":"The evolving role of hydrogen/deuterium exchange mass spectrometry in early-stage drug discovery","authors":"Srinath Krishnamurthy ,&nbsp;Maria Musgaard ,&nbsp;Benjamin Gerald Tehan,&nbsp;Ali Jazayeri,&nbsp;Idlir Liko","doi":"10.1016/j.sbi.2025.103051","DOIUrl":"10.1016/j.sbi.2025.103051","url":null,"abstract":"<div><div>Protein function relies on protein dynamics and therefore dynamical information can be crucial for drug discovery of challenging protein targets. Assessing protein dynamics experimentally has traditionally been nontrivial. However, amide hydrogen/deuterium exchange mass spectrometry (HDX-MS) is now an established technique that can expose details about changes in protein dynamics, binding sites and allostery at the peptide level. HDX-MS is a versatile and powerful biophysical tool to gain insights into the workings of numerous protein systems and complexes. Advances in instrumentation, automation, data analysis, and interpretation over the past two decades have led to increased uptake and democratization of HDX-MS in both academic and industry settings. Here, we outline the current uses of HDX-MS in early-stage drug discovery and illustrate the interplay with computational chemistry to maximize the value of data obtained from HDX-MS experiments. Finally, we consider approaches which may aid structural interpretation of HDX-MS data in the coming years.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"92 ","pages":"Article 103051"},"PeriodicalIF":6.1,"publicationDate":"2025-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143895638","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
Illuminating ubiquitination mechanisms: How cryo-EM has shed light on Cullin RING E3 ligase function 阐明泛素化机制：低温电镜如何揭示Cullin RING E3连接酶的功能
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-04-30 DOI: 10.1016/j.sbi.2025.103055
Zeba Rizvi, Gabriel C. Lander
{"title":"Illuminating ubiquitination mechanisms: How cryo-EM has shed light on Cullin RING E3 ligase function","authors":"Zeba Rizvi,&nbsp;Gabriel C. Lander","doi":"10.1016/j.sbi.2025.103055","DOIUrl":"10.1016/j.sbi.2025.103055","url":null,"abstract":"<div><div>The ubiquitin-proteasome system (UPS) governs protein homeostasis by orchestrating the selective degradation of regulatory and misfolded proteins through a tightly regulated series of ATP-driven ubiquitination reactions. E3 ubiquitin ligases play a central role in this process by conferring substrate specificity, yet the structural complexity and dynamic nature of these large macromolecular assemblies poses challenges for traditional structural biology techniques such as X-ray crystallography and nuclear magnetic resonance (NMR). The advent of single-particle cryo-electron microscopy (cryo-EM) has transformed our ability to study these enzymes, revealing previously inaccessible mechanistic insights into their allosteric regulation, conformational transitions, and substrate recognition. By integrating high-resolution crystallographic data with cryo-EM's ability to resolve heterogeneous and dynamic complexes, researchers have uncovered fundamental principles governing E3 ligase activity. This review explores how cryo-EM has reshaped our understanding of Ligases. We highlight key discoveries enabled by this technique, and discuss how emerging cryo-EM approaches, alongside complementary methodologies, are advancing therapeutic strategies targeting ubiquitin signaling by this family of ligases.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"92 ","pages":"Article 103055"},"PeriodicalIF":6.1,"publicationDate":"2025-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143892232","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
Structural diversity of noncanonical nucleosomes: Functions in chromatin 非典型核小体的结构多样性：在染色质中的功能
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-04-30 DOI: 10.1016/j.sbi.2025.103054
Suguru Hatazawa, Naoki Horikoshi, Hitoshi Kurumizaka
{"title":"Structural diversity of noncanonical nucleosomes: Functions in chromatin","authors":"Suguru Hatazawa,&nbsp;Naoki Horikoshi,&nbsp;Hitoshi Kurumizaka","doi":"10.1016/j.sbi.2025.103054","DOIUrl":"10.1016/j.sbi.2025.103054","url":null,"abstract":"<div><div>In eukaryotes, genomic DNA is compacted into chromatin, with nucleosomes acting as its basic structural units. In addition to canonical nucleosomes, noncanonical nucleosomes, such as hexasomes, H3–H4 octasomes, and overlapping dinucleosomes, exhibit alternative histone compositions and play key roles in chromatin remodeling, transcription, and replication. Recent cryo-electron microscopy (cryo-EM) studies have elucidated the structural details of these noncanonical nucleosomes and their interactions with histone chaperones and chromatin remodelers. This review highlights recent advances in the structural and functional understanding of noncanonical nucleosomes and their roles in maintaining chromatin integrity and facilitating transcriptional dynamics.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"92 ","pages":"Article 103054"},"PeriodicalIF":6.1,"publicationDate":"2025-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143892233","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 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
下一页 尾页
0
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整，为了账户安全，请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
现在去查看 取消
×
提示
确定
请完成安全验证×
相关产品
×
本文献相关产品
联系我们：info@booksci.cn Book学术提供免费学术资源搜索服务，方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号：481959085
Book学术官方微信