Pub Date : 2024-10-30DOI: 10.1016/j.sbi.2024.102946
Brian C. Searle
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.
热蛋白质组分析（TPP）是一项创新技术，它利用蛋白质热稳定性原理来识别潜在的蛋白质相互作用伙伴。TPP 采用定量质谱法测量整个蛋白质组的蛋白质稳定性，在一次实验中提供蛋白质相互作用的全面快照。在研究蛋白质-蛋白质相互作用（PPI）时，TPP 利用表观蛋白质熔解温度的变化来识别大多数传统 PPI 检测方法难以测量的瞬时弱相互作用。本综述讨论了当前的 TPP 方法、解读由此产生的复杂数据集所面临的挑战以及深化和改进 PPI 网络的机会。通过推进我们对错综复杂的蛋白质相互作用的掌握，TPP有望阐明疾病的分子基础并推动新型治疗靶点的发现。
{"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}
Pub Date : 2024-10-28DOI: 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 , Liza-Anastasia DiCecco , G.M. Jonaid , William J. Dearnaley , Michael S. Spilman , Jennifer L. Gray , 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}
Pub Date : 2024-10-24DOI: 10.1016/j.sbi.2024.102936
Kaitlyn Ledwitch , Georg Künze , Elleansar Okwei , Davide Sala , Jens Meiler
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.
{"title":"Non-canonical amino acids for site-directed spin labeling of membrane proteins","authors":"Kaitlyn Ledwitch , Georg Künze , Elleansar Okwei , Davide Sala , 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}
Pub Date : 2024-10-22DOI: 10.1016/j.sbi.2024.102944
Jie Zhang , Xianyang Fang
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 >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.
{"title":"Empowering the molecular ruler techniques with unnatural base pair system to explore conformational dynamics of flaviviral RNAs","authors":"Jie Zhang , 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 >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}
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.
基因表达调控既需要多样性，也需要特异性。如何协调这两个相互矛盾的条件？动态的 DNA 识别机制会导致异质的结合构象，而这些构象会因细胞线索而改变。在此，我们总结了最近的实验证据，说明模糊相互作用如何有助于染色质重塑、DNA 复制和修复调控以及转录因子结合。我们描述了 DNA 与调控因子之间的结合模式连续性如何导致可变的多位点接触模式、多电解质竞争、即时形状读数、由翻译后修饰或动态寡聚机制控制的自动抑制。越来越多的实验证据支持结合蛋白质-DNA 组装的崎岖能量景观，对其进行调节可导致不同的功能结果。最近的研究结果表明，这些组合机制在进化过程中保持了可塑性转录机制中适度的序列限制。
{"title":"Fuzzy protein-DNA interactions and beyond: A common theme in transcription?","authors":"Elisabeth Komives , Ricardo Sanchez-Rodriguez , Hamed Taghavi , 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}
Pub Date : 2024-10-16DOI: 10.1016/j.sbi.2024.102943
Steven D. Goodman
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.
细胞内 DNA 主要是真核生物和原核生物的细胞遗传物质。这一功能通常由 DNA 结构的改变来调节，以适应转录、重组和 DNA 复制。在细胞外，无论是真核细胞还是原核细胞，都会利用大量的 DNA 和有利的环境，创造新的结构来发挥多种新的作用。与细胞内的情况一样，细胞外 DNA 也需要蛋白质来促进和稳定这些重要结构。在这里，我将回顾宿主和真细菌的核蛋白结构、它们的组成、它们的功能以及这些不同的结构如何相互作用。即使是在研究的早期阶段，细胞外染色质在原核生物和真核生物的生存过程中显然都发挥着重要的生物学作用。
{"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}
Pub Date : 2024-10-15DOI: 10.1016/j.sbi.2024.102942
Yun-Tzai Lee
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.
{"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}
Pub Date : 2024-10-13DOI: 10.1016/j.sbi.2024.102915
Catherine Y. Li , Shawn Sandhu , Megan L. Ken
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 in vitro. It has also been shown during this time that the cellular environment redistributes RNA ensembles, changing the abundances of functionally relevant conformers relative to in vitro contexts with subsequent functional RNA consequences. However, recent studies have demonstrated that testing models built from in vitro ensembles with highly quantitative measurements of RNA cellular function, aided by emerging computational methodologies, enables predictive modelling of cellular activity and biological discovery.
{"title":"RNA ensembles from in vitro to in vivo: Toward predictive models of RNA cellular function","authors":"Catherine Y. Li , Shawn Sandhu , 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}
Pub Date : 2024-10-11DOI: 10.1016/j.sbi.2024.102935
David Vaisar, Natalie G. Ahn
Protein kinase inhibitors designed to compete with ATP as a primary mode of action turn out to have considerable effects that go beyond their interference of nucleotide binding. New research shows how kinase activation and sometimes noncatalytic functions of protein kinases can be controlled by allosteric properties of kinase inhibitors, communicating perturbations from the active site to distal regulatory regions.
以与 ATP 竞争为主要作用方式的蛋白激酶抑制剂，其作用远远超出了对核苷酸结合的干扰。新的研究表明，激酶抑制剂的异构特性可以控制激酶活化，有时甚至可以控制蛋白激酶的非催化功能，将扰动从活性位点传递到远端调节区域。
{"title":"Latent allosteric control of protein interactions by ATP-competitive kinase inhibitors","authors":"David Vaisar, Natalie G. Ahn","doi":"10.1016/j.sbi.2024.102935","DOIUrl":"10.1016/j.sbi.2024.102935","url":null,"abstract":"<div><div>Protein kinase inhibitors designed to compete with ATP as a primary mode of action turn out to have considerable effects that go beyond their interference of nucleotide binding. New research shows how kinase activation and sometimes noncatalytic functions of protein kinases can be controlled by allosteric properties of kinase inhibitors, communicating perturbations from the active site to distal regulatory regions.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"89 ","pages":"Article 102935"},"PeriodicalIF":6.1,"publicationDate":"2024-10-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142422870","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}
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