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Using residue interaction networks to understand protein function and evolution and to engineer new proteins 利用残基相互作用网络了解蛋白质功能和进化，并设计新蛋白质
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2024-09-26 DOI: 10.1016/j.sbi.2024.102922
Dariia Yehorova , Bruno Di Geronimo , Michael Robinson , Peter M. Kasson , Shina C.L. Kamerlin
{"title":"Using residue interaction networks to understand protein function and evolution and to engineer new proteins","authors":"Dariia Yehorova ,&nbsp;Bruno Di Geronimo ,&nbsp;Michael Robinson ,&nbsp;Peter M. Kasson ,&nbsp;Shina C.L. Kamerlin","doi":"10.1016/j.sbi.2024.102922","DOIUrl":"10.1016/j.sbi.2024.102922","url":null,"abstract":"<div><div>Residue interaction networks (RINs) provide graph-based representations of interaction networks within proteins, providing important insight into the factors driving protein structure, function, and stability relationships. There exists a wide range of tools with which to perform RIN analysis, taking into account different types of interactions, input (crystal structures, simulation trajectories, single proteins, or comparative analysis across proteins), as well as formats, including standalone software, web server, and a web application programming interface (API). In particular, the ability to perform comparative RIN analysis across protein families using “metaRINs” provides a valuable tool with which to dissect protein evolution. This, in turn, highlights hotspots to avoid (or target) for <em>in vitro</em> evolutionary studies, providing a powerful framework that can be exploited to engineer new proteins.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"89 ","pages":"Article 102922"},"PeriodicalIF":6.1,"publicationDate":"2024-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142324158","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
View from the PEAKs: Insights from structural studies on the PEAK family of pseudokinases 来自 PEAKs 的观点：PEAK 伪激酶家族结构研究的启示
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2024-09-24 DOI: 10.1016/j.sbi.2024.102932
Isabelle S. Lucet , Roger J. Daly
{"title":"View from the PEAKs: Insights from structural studies on the PEAK family of pseudokinases","authors":"Isabelle S. Lucet ,&nbsp;Roger J. Daly","doi":"10.1016/j.sbi.2024.102932","DOIUrl":"10.1016/j.sbi.2024.102932","url":null,"abstract":"<div><div>The PEAK family of pseudokinase scaffolds, comprising PEAK1 (originally termed SgK269), PEAK2 (SgK223, the human orthologue of rat Pragmin) and PEAK3 (C19orf35), have emerged as important regulators and integrators of cellular signaling and also play oncogenic roles in a variety of human cancers. These proteins undergo both homo- and heterotypic association that act to diversify signal output. Recently, structural and functional characterization of PEAK3 and its protein–protein interactions have shed light on PEAK signaling dynamics and the interdependency of PEAK family members, how PEAK dimerization regulates the binding of downstream effectors, and how 14-3-3 binding acts to regulate PEAK3 signal output. These important advances form the basis of this review.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"89 ","pages":"Article 102932"},"PeriodicalIF":6.1,"publicationDate":"2024-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0959440X24001593/pdfft?md5=16d184d9d4e2e0ccff5015a5e5e67ebc&pid=1-s2.0-S0959440X24001593-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142315541","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
Transcriptional machinery as an architect of genome structure 转录机制是基因组结构的设计师
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2024-09-21 DOI: 10.1016/j.sbi.2024.102920
Nadezda A. Fursova, Daniel R. Larson
{"title":"Transcriptional machinery as an architect of genome structure","authors":"Nadezda A. Fursova,&nbsp;Daniel R. Larson","doi":"10.1016/j.sbi.2024.102920","DOIUrl":"10.1016/j.sbi.2024.102920","url":null,"abstract":"<div><p>Chromatin organization, facilitated by compartmentalization and loop extrusion, is crucial for proper gene expression and cell viability. Transcription has long been considered important for shaping genome architecture due to its pervasive activity across the genome and impact on the local chromatin environment. Although earlier studies suggested a minimal contribution of transcription to shaping global genome structure, recent insights from high-resolution chromatin contact mapping, polymer simulations, and acute perturbations have revealed its critical role in dynamic chromatin organization at the level of active genes and enhancer-promoter interactions. In this review, we discuss these latest advances, highlighting the direct interplay between transcriptional machinery and loop extrusion. Finally, we explore how transcription of genes and non-coding regulatory elements may contribute to the specificity of gene regulation, focusing on enhancers as sites of targeted cohesin loading.</p></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"89 ","pages":"Article 102920"},"PeriodicalIF":6.1,"publicationDate":"2024-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142271572","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 next revolution in computational simulations: Harnessing AI and quantum computing in molecular dynamics 计算模拟的下一次革命：在分子动力学中利用人工智能和量子计算
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2024-09-21 DOI: 10.1016/j.sbi.2024.102919
Anna Lappala
{"title":"The next revolution in computational simulations: Harnessing AI and quantum computing in molecular dynamics","authors":"Anna Lappala","doi":"10.1016/j.sbi.2024.102919","DOIUrl":"10.1016/j.sbi.2024.102919","url":null,"abstract":"<div><p>The integration of artificial intelligence, machine learning and quantum computing into molecular dynamics simulations is catalyzing a revolution in computational biology, improving the accuracy and efficiency of simulations. This review describes the advancements and applications of these technologies to process vast molecular dynamics simulation datasets, adapt parameters of simulations and gain insight into complex biological processes. These advances include the use of predictive force fields, adaptive algorithms and quantum-assisted methodologies. While the integration of artificial intelligence and quantum computing with MD simulations provides insightful and stimulating improvements to our understanding of molecular mechanisms, it could introduce new issues related to data quality, interpretability of models and computational complexity. Modern multidisciplinary approaches are needed to navigate these challenges and exploit the potential of these emerging technologies for MD simulations of biomolecular systems.</p></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"89 ","pages":"Article 102919"},"PeriodicalIF":6.1,"publicationDate":"2024-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142271571","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 and dynamic studies of chromatin by solid-state NMR spectroscopy 利用固态核磁共振光谱对染色质进行结构和动态研究
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2024-09-17 DOI: 10.1016/j.sbi.2024.102921
Christopher P. Jaroniec
{"title":"Structural and dynamic studies of chromatin by solid-state NMR spectroscopy","authors":"Christopher P. Jaroniec","doi":"10.1016/j.sbi.2024.102921","DOIUrl":"10.1016/j.sbi.2024.102921","url":null,"abstract":"<div><p>Chromatin is a complex of DNA with histone proteins organized into nucleosomes that regulates genome accessibility and controls transcription, replication and repair by dynamically switching between open and compact states as a function of different parameters including histone post-translational modifications and interactions with chromatin modulators. Continuing advances in structural biology techniques including X-ray crystallography, cryo-electron microscopy and nuclear magnetic resonance (NMR) spectroscopy have facilitated studies of chromatin systems, in spite of challenges posed by their large size and dynamic nature, yielding important functional and mechanistic insights. In this review we highlight recent applications of magic angle spinning solid-state NMR – an emerging technique that is uniquely-suited toward providing atomistic information for rigid and flexible regions within biomacromolecular assemblies – to detailed characterization of structure, conformational dynamics and interactions for histone core and tail domains in condensed nucleosomes and oligonucleosome arrays mimicking chromatin at high densities characteristic of the cellular environment.</p></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"89 ","pages":"Article 102921"},"PeriodicalIF":6.1,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142242549","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 cryo-EM map and model validation: It's not crystal clear 单颗粒低温电子显微镜图和模型验证：并非清澈见底
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2024-09-17 DOI: 10.1016/j.sbi.2024.102918
Gabriel C. Lander
{"title":"Single particle cryo-EM map and model validation: It's not crystal clear","authors":"Gabriel C. Lander","doi":"10.1016/j.sbi.2024.102918","DOIUrl":"10.1016/j.sbi.2024.102918","url":null,"abstract":"<div><p>The application of single particle cryogenic electron microscopy (cryo-EM) to structure determination continues to have a transformative impact on our understanding on biological systems. While there has been a great deal of algorithmic development focused on improving attainable resolutions and streamlining atomic model building, there has not been commensurate development of validation metrics to ensure the accuracy of our cryo-EM maps and models. This review emphasizes the persistent issues that currently complicate single particle cryo-EM structure validation, and highlights the metrics that are gaining broad acceptance by the community. This article aims to underscore the need for further development of validation criteria and the potential role of machine learning methodologies in confidently assessing the quality of cryo-EM structures.</p></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"89 ","pages":"Article 102918"},"PeriodicalIF":6.1,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0959440X24001453/pdfft?md5=64a9e97a3f51624e35ee3fce42620875&pid=1-s2.0-S0959440X24001453-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142242550","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
Combining single-molecule and structural studies reveals protein and DNA conformations and assemblies that govern DNA mismatch repair 结合单分子和结构研究揭示支配 DNA 错配修复的蛋白质和 DNA 构象与组合
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2024-09-10 DOI: 10.1016/j.sbi.2024.102917
Dorothy A. Erie , Keith R. Weninger
{"title":"Combining single-molecule and structural studies reveals protein and DNA conformations and assemblies that govern DNA mismatch repair","authors":"Dorothy A. Erie ,&nbsp;Keith R. Weninger","doi":"10.1016/j.sbi.2024.102917","DOIUrl":"10.1016/j.sbi.2024.102917","url":null,"abstract":"<div><p>DNA mismatch repair (MMR) requires coordinated sequential actions of multiple proteins during a window of time after the replication apparatus makes an error and before the newly synthesized DNA undergoes chromosome compaction and/or methylation of dGATC sites in some γ-proteobacteria. In this review, we focus on the steps carried out by MutS and MutL homologs that initiate repair. We connect new structural data to early and recent single-molecule FRET and atomic force microscopy (AFM) studies to reveal insights into how signaling within the MMR cascade connects MutS homolog recognition of a mismatch to downstream repair. We present unified models of MMR initiation that account for the differences in the strand discrimination signals between methyl- and non-methyl-directed MMR.</p></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"89 ","pages":"Article 102917"},"PeriodicalIF":6.1,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142161199","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
Cryo-EM: A window into the dynamic world of RNA molecules 低温电子显微镜：了解 RNA 分子动态世界的窗口
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2024-09-03 DOI: 10.1016/j.sbi.2024.102916
Xiaojing Zhang, Shanshan Li, Kaiming Zhang
{"title":"Cryo-EM: A window into the dynamic world of RNA molecules","authors":"Xiaojing Zhang,&nbsp;Shanshan Li,&nbsp;Kaiming Zhang","doi":"10.1016/j.sbi.2024.102916","DOIUrl":"10.1016/j.sbi.2024.102916","url":null,"abstract":"<div><p>RNAs are critical for complex cellular functions, characterized by their structural versatility and ability to undergo conformational transitions in response to cellular cues. The elusive structures of RNAs are being unraveled with unprecedented clarity, thanks to the technological advancements in structural biology, including nuclear magnetic resonance (NMR), X-ray crystallography, cryo-electron microscopy (cryo-EM) etc. This review focuses on examining the revolutionary impact of cryo-EM on our comprehension of RNA structural dynamics, underscoring the technique's contributions to structural biology and envisioning the future trajectory of this rapidly evolving field.</p></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"88 ","pages":"Article 102916"},"PeriodicalIF":6.1,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142130149","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
Influence of membrane on the antigen presentation of the HIV-1 envelope membrane proximal external region (MPER) 膜对 HIV-1 包膜近端外部区域（MPER）抗原呈递的影响
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2024-08-21 DOI: 10.1016/j.sbi.2024.102897
Cesar A. López , S. Munir Alam , Cynthia A. Derdeyn , Barton F. Haynes , Sandrasegaram Gnanakaran
{"title":"Influence of membrane on the antigen presentation of the HIV-1 envelope membrane proximal external region (MPER)","authors":"Cesar A. López ,&nbsp;S. Munir Alam ,&nbsp;Cynthia A. Derdeyn ,&nbsp;Barton F. Haynes ,&nbsp;Sandrasegaram Gnanakaran","doi":"10.1016/j.sbi.2024.102897","DOIUrl":"10.1016/j.sbi.2024.102897","url":null,"abstract":"<div><p>The membrane proximal external region (MPER) of the HIV envelope glycoproteins has generated renewed interest after a recent phase I vaccine trial that presented MPER lipid-peptide epitopes demonstrated promise to elicit a broad neutralization response. The antigenicity of MPER is intimately associated with the membrane, and its presentation relies significantly on the lipid composition. This review brings together recent findings on the influence of membranes on the conformation of MPER and its recognition by broadly neutralizing antibodies. Specifically, the review highlights the importance of properly accounting for the balance between protein–protein and membrane–protein interactions in vaccine design.</p></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"88 ","pages":"Article 102897"},"PeriodicalIF":6.1,"publicationDate":"2024-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142021473","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
Untangling the pseudoknots of SARS-CoV-2: Insights into structural heterogeneity and plasticity 解开 SARS-CoV-2 的假结：洞察结构异质性和可塑性
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2024-08-21 DOI: 10.1016/j.sbi.2024.102912
Justin Aruda , Scott L. Grote , Silvi Rouskin
{"title":"Untangling the pseudoknots of SARS-CoV-2: Insights into structural heterogeneity and plasticity","authors":"Justin Aruda ,&nbsp;Scott L. Grote ,&nbsp;Silvi Rouskin","doi":"10.1016/j.sbi.2024.102912","DOIUrl":"10.1016/j.sbi.2024.102912","url":null,"abstract":"<div><p>Since the onset of the COVID-19 pandemic, one productive area of research has focused on the intricate two- and three-dimensional structures taken on by SARS-CoV-2's RNA genome. These structures control essential viral processes, making them tempting targets for therapeutic intervention. This review focuses on two such structured regions, the frameshift stimulation element (FSE), which controls the translation of viral protein, and the 3′ untranslated region (3′ UTR), which is thought to regulate genome replication. For the FSE, we discuss its canonical pseudoknot's threaded and unthreaded topologies, as well as the diversity of competing two-dimensional structures formed by local and long-distance base pairing. For the 3′ UTR, we review the evidence both for and against the formation of its replication-enabling pseudoknot.</p></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"88 ","pages":"Article 102912"},"PeriodicalIF":6.1,"publicationDate":"2024-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142011663","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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