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The power of computational proteomics platforms to decipher protein-protein interactions 计算蛋白质组学平台破解蛋白质-蛋白质相互作用的威力
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2024-07-13 DOI: 10.1016/j.sbi.2024.102882
Mariela González-Avendaño , Joaquín López , Ariela Vergara-Jaque , Oscar Cerda
{"title":"The power of computational proteomics platforms to decipher protein-protein interactions","authors":"Mariela González-Avendaño ,&nbsp;Joaquín López ,&nbsp;Ariela Vergara-Jaque ,&nbsp;Oscar Cerda","doi":"10.1016/j.sbi.2024.102882","DOIUrl":"https://doi.org/10.1016/j.sbi.2024.102882","url":null,"abstract":"<div><p>Adopting computational tools for analyzing extensive biological datasets has profoundly transformed our understanding and interpretation of biological phenomena. Innovative platforms have emerged, providing automated analysis to unravel essential insights about proteins and the complexities of their interactions. These computational advancements align with traditional studies, which employ experimental techniques to discern and quantify physical and functional protein-protein interactions (PPIs). Among these techniques, tandem mass spectrometry is notably recognized for its precision and sensitivity in identifying PPIs. These approaches might serve as important information enabling the identification of PPIs with potential pharmacological significance. This review aims to convey our experience using computational tools for detecting PPI networks and offer an analysis of platforms that facilitate predictions derived from experimental data.</p></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"88 ","pages":"Article 102882"},"PeriodicalIF":6.1,"publicationDate":"2024-07-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141606931","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
Expanding insights from in situ cryo-EM 扩展原位低温电子显微镜的洞察力
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2024-07-11 DOI: 10.1016/j.sbi.2024.102885
Joshua Hutchings , Elizabeth Villa
{"title":"Expanding insights from in situ cryo-EM","authors":"Joshua Hutchings ,&nbsp;Elizabeth Villa","doi":"10.1016/j.sbi.2024.102885","DOIUrl":"https://doi.org/10.1016/j.sbi.2024.102885","url":null,"abstract":"<div><p>The combination of cryo-electron tomography and subtomogram analysis affords 3D high-resolution views of biological macromolecules in their native cellular environment, or <em>in situ</em>. Streamlined methods for acquiring and processing these data are advancing attainable resolutions into the realm of drug discovery. Yet regardless of resolution, structure prediction driven by artificial intelligence (AI) combined with subtomogram analysis is becoming powerful in understanding macromolecular assemblies. Automated and AI-assisted data mining is increasingly necessary to cope with the growing wealth of tomography data and to maximize the information obtained from them. Leveraging developments from AI and single-particle analysis could be essential in fulfilling the potential of <em>in situ</em> cryo-EM. Here, we highlight new developments for <em>in situ</em> cryo-EM and the emerging potential for AI in this process.</p></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"88 ","pages":"Article 102885"},"PeriodicalIF":6.1,"publicationDate":"2024-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141594538","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
Trends in co-fractionation mass spectrometry: A new gold-standard in global protein interaction network discovery 共分馏质谱的发展趋势：发现全球蛋白质相互作用网络的新黄金标准
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2024-07-11 DOI: 10.1016/j.sbi.2024.102880
Raghuveera Kumar Goel , Nazmin Bithi , Andrew Emili
{"title":"Trends in co-fractionation mass spectrometry: A new gold-standard in global protein interaction network discovery","authors":"Raghuveera Kumar Goel ,&nbsp;Nazmin Bithi ,&nbsp;Andrew Emili","doi":"10.1016/j.sbi.2024.102880","DOIUrl":"https://doi.org/10.1016/j.sbi.2024.102880","url":null,"abstract":"<div><p>Co-fractionation mass spectrometry (CF-MS) uses biochemical fractionation to isolate and characterize macromolecular complexes from cellular lysates without the need for affinity tagging or capture. In recent years, this has emerged as a powerful technique for elucidating global protein-protein interaction networks in a wide variety of biospecimens. This review highlights the latest advancements in CF-MS experimental workflows including machine learning-guided analyses, for uncovering dynamic and high-resolution protein interaction landscapes with enhanced sensitivity, accuracy and throughput, enabling better biophysical characterization of endogenous protein complexes. By addressing challenges and emergent opportunities in the field, this review underscores the transformative potential of CF-MS in advancing our understanding of functional protein interaction networks in health and disease.</p></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"88 ","pages":"Article 102880"},"PeriodicalIF":6.1,"publicationDate":"2024-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0959440X24001076/pdfft?md5=b3acfd623677af78f58e661c180906b7&pid=1-s2.0-S0959440X24001076-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141594537","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
Pioneer factors: Emerging rules of engagement for transcription factors on chromatinized DNA 先锋因子：染色质 DNA 上转录因子的新规则。
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2024-07-10 DOI: 10.1016/j.sbi.2024.102875
Manuel Carminati , Luca Vecchia , Lisa Stoos , Nicolas H. Thomä
{"title":"Pioneer factors: Emerging rules of engagement for transcription factors on chromatinized DNA","authors":"Manuel Carminati ,&nbsp;Luca Vecchia ,&nbsp;Lisa Stoos ,&nbsp;Nicolas H. Thomä","doi":"10.1016/j.sbi.2024.102875","DOIUrl":"10.1016/j.sbi.2024.102875","url":null,"abstract":"<div><p>Pioneering transcription factors (TFs) can drive cell fate changes by binding their DNA motifs in a repressive chromatin environment. Recent structures illustrate emerging rules for nucleosome engagement: TFs distort the nucleosomal DNA to gain access or employ alternative DNA-binding modes with smaller footprints, they preferentially access solvent-exposed motifs near the entry/exit sites, and frequently interact with histones. The extent of TF–histone interactions, in turn, depends on the motif location on the nucleosome, the type of DNA-binding fold, and adjacent domains present. TF–histone interactions can phase TF motifs relative to nucleosomes, and we discuss how these complex and surprisingly diverse interactions between nucleosomes and TFs contribute to function.</p></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"88 ","pages":"Article 102875"},"PeriodicalIF":6.1,"publicationDate":"2024-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0959440X24001027/pdfft?md5=d4afa1b763b97504bc80bc151367e940&pid=1-s2.0-S0959440X24001027-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141589854","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
Connecting the dots: Computational network analysis for disease insight and drug repurposing 连接点：通过计算网络分析深入了解疾病和药物再利用。
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2024-07-10 DOI: 10.1016/j.sbi.2024.102881
Nicoleta Siminea , Eugen Czeizler , Victor-Bogdan Popescu , Ion Petre , Andrei Păun
{"title":"Connecting the dots: Computational network analysis for disease insight and drug repurposing","authors":"Nicoleta Siminea ,&nbsp;Eugen Czeizler ,&nbsp;Victor-Bogdan Popescu ,&nbsp;Ion Petre ,&nbsp;Andrei Păun","doi":"10.1016/j.sbi.2024.102881","DOIUrl":"10.1016/j.sbi.2024.102881","url":null,"abstract":"<div><p>Network biology is a powerful framework for studying the structure, function, and dynamics of biological systems, offering insights into the balance between health and disease states. The field is seeing rapid progress in all of its aspects: data availability, network synthesis, network analytics, and impactful applications in medicine and drug development. We review the most recent and significant results in network biomedicine, with a focus on the latest data, analytics, software resources, and applications in medicine. We also discuss what in our view are the likely directions of impactful development over the next few years.</p></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"88 ","pages":"Article 102881"},"PeriodicalIF":6.1,"publicationDate":"2024-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0959440X24001088/pdfft?md5=594d269cfca7f6de847e09948b124963&pid=1-s2.0-S0959440X24001088-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141589853","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
Assembly and activation of replicative helicases at origin DNA for replication initiation 在原点 DNA 上组装和激活复制螺旋酶，以启动复制。
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2024-07-09 DOI: 10.1016/j.sbi.2024.102876
Qiongdan Zhang, Wai Hei Lam, Yuanliang Zhai
{"title":"Assembly and activation of replicative helicases at origin DNA for replication initiation","authors":"Qiongdan Zhang,&nbsp;Wai Hei Lam,&nbsp;Yuanliang Zhai","doi":"10.1016/j.sbi.2024.102876","DOIUrl":"10.1016/j.sbi.2024.102876","url":null,"abstract":"<div><p>To initiate DNA replication, it is essential to properly assemble a pair of replicative helicases at each replication origin. While the general principle of this process applies universally from prokaryotes to eukaryotes, the specific mechanisms governing origin selection, helicase loading, and subsequent helicase activation vary significantly across different species. Recent advancements in cryo-electron microscopy (cryo-EM) have revolutionized our ability to visualize large protein or protein-DNA complexes involved in the initiation of DNA replication. Complemented by real-time single-molecule analysis, the available high-resolution cryo-EM structures have greatly enhanced our understanding of the dynamic regulation of this process at origin DNA. This review primarily focuses on the latest structural discoveries that shed light on the key molecular machineries responsible for driving replication initiation, with a particular emphasis on the assembly of pre-replication complex (pre-RC) in eukaryotes.</p></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"88 ","pages":"Article 102876"},"PeriodicalIF":6.1,"publicationDate":"2024-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141579226","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
Computational tools to predict context-specific protein complexes 预测特异性蛋白质复合体的计算工具。
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2024-07-09 DOI: 10.1016/j.sbi.2024.102883
Attila Csikász-Nagy , Erzsébet Fichó , Santiago Noto , István Reguly
{"title":"Computational tools to predict context-specific protein complexes","authors":"Attila Csikász-Nagy ,&nbsp;Erzsébet Fichó ,&nbsp;Santiago Noto ,&nbsp;István Reguly","doi":"10.1016/j.sbi.2024.102883","DOIUrl":"10.1016/j.sbi.2024.102883","url":null,"abstract":"<div><p>Interactions between thousands of proteins define cells' protein–protein interaction (PPI) network. Some of these interactions lead to the formation of protein complexes. It is challenging to identify a protein complex in a haystack of protein–protein interactions, and it is even more difficult to predict all protein complexes of the complexome. Simulations and machine learning approaches try to crack these problems by looking at the PPI network or predicted protein structures. Clustering of PPI networks led to the first protein complex predictions, while most recently, atomistic models of protein complexes and deep-learning-based structure prediction methods have also emerged. The simulation of PPI level interactions even enables the quantitative prediction of protein complexes. These methods, the required data sources, and their potential future developments are discussed in this review.</p></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"88 ","pages":"Article 102883"},"PeriodicalIF":6.1,"publicationDate":"2024-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0959440X24001106/pdfft?md5=da1bf2571918bf0c9b8dbc244aeafb83&pid=1-s2.0-S0959440X24001106-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141579227","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
Ensembles of interconverting protein complexes with multiple interaction domains 具有多个相互作用结构域的相互转换蛋白质复合物组合。
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2024-07-08 DOI: 10.1016/j.sbi.2024.102874
Sanjay Ramprasad, Afua Nyarko
{"title":"Ensembles of interconverting protein complexes with multiple interaction domains","authors":"Sanjay Ramprasad,&nbsp;Afua Nyarko","doi":"10.1016/j.sbi.2024.102874","DOIUrl":"10.1016/j.sbi.2024.102874","url":null,"abstract":"<div><p>Many critical biological processes depend on protein complexes that exist as ensembles of subcomplexes rather than a discrete complex. The subcomplexes dynamically interconvert with one another, and the ability to accurately resolve the composition of the diverse molecular species in the ensemble is crucial for understanding the contribution of each subcomplex to the overall function of the protein complex. Advances in computational programs have made it possible to predict the various molecular species in these ensembles, but experimental approaches to identify the pool of subcomplexes and associated stoichiometries are often challenging. This review highlights some experimental approaches that can be used to resolve the diverse molecular species in protein complexes that exist as ensembles of sub complexes.</p></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"88 ","pages":"Article 102874"},"PeriodicalIF":6.1,"publicationDate":"2024-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141562898","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 method in the madness: Transcriptional control from stochastic action at the single-molecule scale 疯狂中的方法：单分子尺度随机作用的转录控制
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2024-07-01 DOI: 10.1016/j.sbi.2024.102873
Peter H. Whitney , Timothée Lionnet
{"title":"The method in the madness: Transcriptional control from stochastic action at the single-molecule scale","authors":"Peter H. Whitney ,&nbsp;Timothée Lionnet","doi":"10.1016/j.sbi.2024.102873","DOIUrl":"https://doi.org/10.1016/j.sbi.2024.102873","url":null,"abstract":"<div><p>Cell states result from the ordered activation of gene expression by transcription factors. Transcription factors face opposing design constraints: they need to be dynamic to trigger rapid cell state transitions, but also stable enough to maintain terminal cell identities indefinitely. Recent progress in live-cell single-molecule microscopy has helped define the biophysical principles underlying this paradox. Beyond transcription factor activity, single-molecule experiments have revealed that at nearly every level of transcription regulation, control emerges from multiple short-lived stochastic interactions, rather than deterministic, stable interactions typical of other biochemical pathways. This architecture generates consistent outcomes that can be rapidly choreographed. Here, we highlight recent results that demonstrate how order in transcription regulation emerges from the apparent molecular-scale chaos and discuss remaining conceptual challenges.</p></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"87 ","pages":"Article 102873"},"PeriodicalIF":6.1,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0959440X24001003/pdfft?md5=d913b86c0066c43f43f1df248951093a&pid=1-s2.0-S0959440X24001003-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141482581","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
From disorder comes function: Regulation of small GTPase function by intrinsically disordered lipidated membrane anchor 无序产生功能：内在无序脂质化膜锚对小 GTPase 功能的调控。
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2024-06-28 DOI: 10.1016/j.sbi.2024.102869
Chase M. Hutchins , Alemayehu A. Gorfe
{"title":"From disorder comes function: Regulation of small GTPase function by intrinsically disordered lipidated membrane anchor","authors":"Chase M. Hutchins ,&nbsp;Alemayehu A. Gorfe","doi":"10.1016/j.sbi.2024.102869","DOIUrl":"10.1016/j.sbi.2024.102869","url":null,"abstract":"<div><p>The intrinsically disordered, lipid-modified membrane anchor of small GTPases is emerging as a critical modulator of function through its ability to sort lipids in a conformation-dependent manner. We reviewed recent computational and experimental studies that have begun to shed light on the sequence-ensemble-function relationship in this unique class of lipidated intrinsically disordered regions (LIDRs).</p></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"87 ","pages":"Article 102869"},"PeriodicalIF":6.1,"publicationDate":"2024-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141466794","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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