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The mechano-chemistry of a viral genome packaging motor 病毒基因组包装马达的机械化学原理
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2024-11-04 DOI: 10.1016/j.sbi.2024.102945
Joshua Pajak , Nikolai S. Prokhorov , Paul J. Jardine , Marc C. Morais
{"title":"The mechano-chemistry of a viral genome packaging motor","authors":"Joshua Pajak ,&nbsp;Nikolai S. Prokhorov ,&nbsp;Paul J. Jardine ,&nbsp;Marc C. Morais","doi":"10.1016/j.sbi.2024.102945","DOIUrl":"10.1016/j.sbi.2024.102945","url":null,"abstract":"<div><div>Double-stranded DNA viruses actively package their genomes into pre-assembled protein capsids using energy derived from virus-encoded ASCE ATPase ring motors. Single molecule experiments in the aughts and early 2010s demonstrated that these motors are some of the most powerful molecular motors in nature, and that the activities of individual subunits around the ATPase ring motor are highly coordinated to ensure efficient genome encapsidation. While these studies provided a comprehensive kinetic scheme describing the events that occur during packaging, the physical basis of force generation and subunit coordination remained elusive. This article reviews recent structural and computational results that have begun to illuminate the molecular basis of force generation and DNA translocation in these powerful molecular motors.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"89 ","pages":"Article 102945"},"PeriodicalIF":6.1,"publicationDate":"2024-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142577845","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
Characterizing protein-protein interactions with thermal proteome profiling 利用热蛋白质组图谱鉴定蛋白质与蛋白质之间的相互作用
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2024-10-30 DOI: 10.1016/j.sbi.2024.102946
Brian C. Searle
{"title":"Characterizing protein-protein interactions with thermal proteome profiling","authors":"Brian C. Searle","doi":"10.1016/j.sbi.2024.102946","DOIUrl":"10.1016/j.sbi.2024.102946","url":null,"abstract":"<div><div>Thermal proteome profiling (TPP) is an innovative technique that uses the principle of protein thermal stability to identify potential protein interaction partners. Employing quantitative mass spectrometry, TPP measures protein stability across the proteome, offering a comprehensive snapshot of protein interactions in a single experiment. When studying protein-protein interactions (PPI), TPP leverages changes in apparent protein melting temperatures to identify transient and weak interactions that most traditional PPI detection methodologies struggle to measure. This review discusses current TPP methodologies, the challenges of interpreting the resulting complex datasets, and opportunities to deepen and improve PPI networks. By advancing our grasp of intricate protein interactions, TPP promises to illuminate the molecular basis of diseases and drive the discovery of novel therapeutic targets.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"89 ","pages":"Article 102946"},"PeriodicalIF":6.1,"publicationDate":"2024-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142553410","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
Retraction notice to “Liquid-EM goes viral – visualizing structure and dynamics” [Curr Opin Struct Biol 75 (August 2022) 102426] 液体电子显微镜（Liquid-EM）病毒式传播--结构与动力学可视化》撤稿通知 [Curr Opin Struct Biol 75 (August 2022) 102426]
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2024-10-28 DOI: 10.1016/j.sbi.2024.102947
Deborah F. Kelly , Liza-Anastasia DiCecco , G.M. Jonaid , William J. Dearnaley , Michael S. Spilman , Jennifer L. Gray , Madeline J. Dressel-Dukes
{"title":"Retraction notice to “Liquid-EM goes viral – visualizing structure and dynamics” [Curr Opin Struct Biol 75 (August 2022) 102426]","authors":"Deborah F. Kelly ,&nbsp;Liza-Anastasia DiCecco ,&nbsp;G.M. Jonaid ,&nbsp;William J. Dearnaley ,&nbsp;Michael S. Spilman ,&nbsp;Jennifer L. Gray ,&nbsp;Madeline J. Dressel-Dukes","doi":"10.1016/j.sbi.2024.102947","DOIUrl":"10.1016/j.sbi.2024.102947","url":null,"abstract":"","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"89 ","pages":"Article 102947"},"PeriodicalIF":6.1,"publicationDate":"2024-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142536116","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
Non-canonical amino acids for site-directed spin labeling of membrane proteins 用于膜蛋白定点自旋标记的非典型氨基酸。
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2024-10-24 DOI: 10.1016/j.sbi.2024.102936
Kaitlyn Ledwitch , Georg Künze , Elleansar Okwei , Davide Sala , Jens Meiler
{"title":"Non-canonical amino acids for site-directed spin labeling of membrane proteins","authors":"Kaitlyn Ledwitch ,&nbsp;Georg Künze ,&nbsp;Elleansar Okwei ,&nbsp;Davide Sala ,&nbsp;Jens Meiler","doi":"10.1016/j.sbi.2024.102936","DOIUrl":"10.1016/j.sbi.2024.102936","url":null,"abstract":"<div><div>Membrane proteins remain challenging targets for conventional structural biology techniques because they need to reside within complex hydrophobic lipid environments to maintain proper structure and function. Magnetic resonance combined with site-directed spin labeling is an alternative method that provides atomic-level structural and dynamical information from effects introduced by an electron- or nuclear-based spin label. With the advent of bioorthogonal click chemistries and genetically engineered non-canonical amino acids (ncAAs), options for linking spin probes to biomolecules have substantially broadened outside the conventional cysteine-based labeling scheme. Here, we highlight current strategies to spin-label membrane proteins through ncAAs for nuclear and electron paramagnetic resonance applications. Such advances are critical for developing bioorthogonal spin labeling schemes to achieve in-cell labeling and in-cell measurements of membrane protein conformational dynamics.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"89 ","pages":"Article 102936"},"PeriodicalIF":6.1,"publicationDate":"2024-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142496673","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
Empowering the molecular ruler techniques with unnatural base pair system to explore conformational dynamics of flaviviral RNAs 利用非天然碱基配对系统增强分子尺技术，探索黄病毒 RNA 的构象动力学。
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2024-10-22 DOI: 10.1016/j.sbi.2024.102944
Jie Zhang , Xianyang Fang
{"title":"Empowering the molecular ruler techniques with unnatural base pair system to explore conformational dynamics of flaviviral RNAs","authors":"Jie Zhang ,&nbsp;Xianyang Fang","doi":"10.1016/j.sbi.2024.102944","DOIUrl":"10.1016/j.sbi.2024.102944","url":null,"abstract":"<div><div>RNA's inherent flexibility and dynamics pose great challenges to characterize its structure and dynamics using conventional techniques including X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy and cryo-electron microscopy. Three complementary molecular ruler techniques, the electron paramagnetic resonance (EPR) spectroscopy, X-ray scattering interferometry (XSI) and Förster resonance energy transfer (FRET) which measure intramolecular and intermolecular pair-wise distance distributions in the nanometer range in a solution, have become increasingly popular and been widely used to explore RNA structure and dynamics. The prerequisites for successful application of such techniques are to achieve site-specific labeling of RNAs with spin labels, fluorescent tags, or gold nanoparticles, respectively, which are however, challenging, especially to large RNAs (generally &gt;200 nts). Here, we briefly review the basics of these molecular rulers, how the NaM-TPT3 unnatural base pair system empower them, and their applications to explore conformational dynamics of large RNAs, especially in the context of flavivirus RNA genome.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"89 ","pages":"Article 102944"},"PeriodicalIF":6.1,"publicationDate":"2024-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142496672","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
Editorial overview: Cryo-electron microscopy 编辑综述：冷冻电镜。
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2024-10-19 DOI: 10.1016/j.sbi.2024.102937
Pilar Cossio, Edward Egelman
{"title":"Editorial overview: Cryo-electron microscopy","authors":"Pilar Cossio,&nbsp;Edward Egelman","doi":"10.1016/j.sbi.2024.102937","DOIUrl":"10.1016/j.sbi.2024.102937","url":null,"abstract":"","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"89 ","pages":"Article 102937"},"PeriodicalIF":6.1,"publicationDate":"2024-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142460024","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
Fuzzy protein-DNA interactions and beyond: A common theme in transcription? 模糊的蛋白质-DNA相互作用及其他：转录的共同主题？
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2024-10-17 DOI: 10.1016/j.sbi.2024.102941
Elisabeth Komives , Ricardo Sanchez-Rodriguez , Hamed Taghavi , Monika Fuxreiter
{"title":"Fuzzy protein-DNA interactions and beyond: A common theme in transcription?","authors":"Elisabeth Komives ,&nbsp;Ricardo Sanchez-Rodriguez ,&nbsp;Hamed Taghavi ,&nbsp;Monika Fuxreiter","doi":"10.1016/j.sbi.2024.102941","DOIUrl":"10.1016/j.sbi.2024.102941","url":null,"abstract":"<div><div>Gene expression regulation requires both diversity and specificity. How can these two contradictory conditions be reconciled? Dynamic DNA recognition mechanisms lead to heterogeneous bound conformations, which can be shifted by the cellular cues. Here we summarise recent experimental evidence on how fuzzy interactions contribute to chromatin remodelling, regulation of DNA replication and repair and transcription factor binding. We describe how the binding mode continuum between DNA and regulatory factors lead to variable, multisite contact patterns; polyelectrolyte competitions; on-the-fly shape readouts; autoinhibition controlled by posttranslational modifications or dynamic oligomerisation mechanisms. Increasing experimental evidence supports the rugged energy landscape of the bound protein-DNA assembly, modulation of which leads to distinct functional outcomes. Recent results suggest the evolutionary conservation of these combinatorial mechanisms with moderate sequence constraints in the malleable transcriptional machinery.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"89 ","pages":"Article 102941"},"PeriodicalIF":6.1,"publicationDate":"2024-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142445949","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
Extracellular DNA-protein interactions 细胞外 DNA 蛋白相互作用
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2024-10-16 DOI: 10.1016/j.sbi.2024.102943
Steven D. Goodman
{"title":"Extracellular DNA-protein interactions","authors":"Steven D. Goodman","doi":"10.1016/j.sbi.2024.102943","DOIUrl":"10.1016/j.sbi.2024.102943","url":null,"abstract":"<div><div>Intracellular DNA primarily serves as the cellular genetic material both in eukaryotes and prokaryotes. This function is often regulated by alterations in the DNA structure to accommodate transcription, recombination, and DNA replication. Extracellularly, both eukaryotic and prokaryotic cells take advantage of DNA plenty in addition to a permissive environment and create novel structures to fulfill multiple new roles. As often occurs intracellularly, extracellular DNA requires proteins to facilitate and stabilize these important structures. Here I review, both host and eubacterial nucleoprotein structures, their composition, their functions, and how these distinct structures can interact. Even at this early stage of study, it is clear that extracellular chromatin plays important biological roles in the survival of both prokaryotic and eukaryotic organisms.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"89 ","pages":"Article 102943"},"PeriodicalIF":6.1,"publicationDate":"2024-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142441592","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
Nexus between RNA conformational dynamics and functional versatility RNA 构象动力学与功能多样性之间的联系
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2024-10-15 DOI: 10.1016/j.sbi.2024.102942
Yun-Tzai Lee
{"title":"Nexus between RNA conformational dynamics and functional versatility","authors":"Yun-Tzai Lee","doi":"10.1016/j.sbi.2024.102942","DOIUrl":"10.1016/j.sbi.2024.102942","url":null,"abstract":"<div><div>RNA conformational dynamics is pivotal for functional regulations in biology. RNA can function as versatile as protein but adopts multiple distinct structures. In this review, we provide a focused review of the recent advances in studies of RNA conformational dynamics and address some of the misconceptions about RNA structure and its conformational dynamics. We discuss why the traditional methods for structure determination come up short in describing RNA conformational space. The examples discussed provide illustrations of the structure-based mechanisms of RNAs with diverse roles, including viral, long noncoding, and catalytic RNAs, one of which focuses on the debated area of conformational heterogeneity of an RNA structural element in the HIV-1 genome.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"89 ","pages":"Article 102942"},"PeriodicalIF":6.1,"publicationDate":"2024-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142438440","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
RNA ensembles from in vitro to in vivo: Toward predictive models of RNA cellular function 从体外到体内的 RNA 组合：建立 RNA 细胞功能预测模型
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2024-10-13 DOI: 10.1016/j.sbi.2024.102915
Catherine Y. Li , Shawn Sandhu , Megan L. Ken
{"title":"RNA ensembles from in vitro to in vivo: Toward predictive models of RNA cellular function","authors":"Catherine Y. Li ,&nbsp;Shawn Sandhu ,&nbsp;Megan L. Ken","doi":"10.1016/j.sbi.2024.102915","DOIUrl":"10.1016/j.sbi.2024.102915","url":null,"abstract":"<div><div>Deepening our understanding of RNA biology and accelerating development of RNA-based therapeutics go hand-in-hand—both requiring a transition from qualitative descriptions of RNA structure to quantitative models capable of predicting RNA behaviors, and from a static to an ensemble view. Ensembles are determined from their free energy landscapes, which define the relative populations of conformational states and the energetic barriers separating them. Experimental determination of RNA ensembles over the past decade has led to powerful predictive models of RNA behavior <em>in vitro</em>. It has also been shown during this time that the cellular environment redistributes RNA ensembles, changing the abundances of functionally relevant conformers relative to <em>in vitro</em> contexts with subsequent functional RNA consequences. However, recent studies have demonstrated that testing models built from <em>in vitro</em> ensembles with highly quantitative measurements of RNA cellular function, aided by emerging computational methodologies, enables predictive modelling of cellular activity and biological discovery.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"89 ","pages":"Article 102915"},"PeriodicalIF":6.1,"publicationDate":"2024-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142433909","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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