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Current opinion in structural biology最新文献

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Editorial overview: Protein networks in health and disease.
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2024-12-05 DOI: 10.1016/j.sbi.2024.102953
Elizabeth A Komives, Gabriela Chiosis
{"title":"Editorial overview: Protein networks in health and disease.","authors":"Elizabeth A Komives, Gabriela Chiosis","doi":"10.1016/j.sbi.2024.102953","DOIUrl":"https://doi.org/10.1016/j.sbi.2024.102953","url":null,"abstract":"","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"90 ","pages":"102953"},"PeriodicalIF":6.1,"publicationDate":"2024-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142791253","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: New perspectives on the structure and dynamics of protein-nucleic acid interactions.
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2024-12-03 DOI: 10.1016/j.sbi.2024.102957
Junji Iwahara, David C Williams
{"title":"Editorial overview: New perspectives on the structure and dynamics of protein-nucleic acid interactions.","authors":"Junji Iwahara, David C Williams","doi":"10.1016/j.sbi.2024.102957","DOIUrl":"https://doi.org/10.1016/j.sbi.2024.102957","url":null,"abstract":"","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"90 ","pages":"102957"},"PeriodicalIF":6.1,"publicationDate":"2024-12-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142779643","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: 3D Genome Chromatin organization and regulation.
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2024-12-03 DOI: 10.1016/j.sbi.2024.102956
Eric Conway, Daniel R Larson
{"title":"Editorial overview: 3D Genome Chromatin organization and regulation.","authors":"Eric Conway, Daniel R Larson","doi":"10.1016/j.sbi.2024.102956","DOIUrl":"https://doi.org/10.1016/j.sbi.2024.102956","url":null,"abstract":"","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"90 ","pages":"102956"},"PeriodicalIF":6.1,"publicationDate":"2024-12-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142779641","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
Protein-nucleic acid complexes: Docking and binding affinity
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2024-11-30 DOI: 10.1016/j.sbi.2024.102955
M. Michael Gromiha, K. Harini
{"title":"Protein-nucleic acid complexes: Docking and binding affinity","authors":"M. Michael Gromiha,&nbsp;K. Harini","doi":"10.1016/j.sbi.2024.102955","DOIUrl":"10.1016/j.sbi.2024.102955","url":null,"abstract":"<div><div>Protein-nucleic interactions play essential roles in several biological processes, such as gene regulation, replication, transcription, repair and packaging. The knowledge of three-dimensional structures of protein-nucleic acid complexes and their binding affinities helps to understand these functions. In this review, we focus on two major aspects namely, (i) deciphering the three-dimensional structures of protein-nucleic acid complexes and (ii) predicting their binding affinities. The first part is devoted to the state-of-the-art methods for predicting the native structures and their performances including recent CASP targets. The second part is focused on different aspects of investigating the binding affinity of protein-nucleic acid complexes: (i) databases for thermodynamic parameters to understand the binding affinity, (ii) important features determining protein-nucleic acid binding affinity, (iii) predicting the binding affinity of protein-nucleic acid complexes using sequence and structure-based parameters and (iv) change in binding affinity upon mutation. It includes the latest developments in protein-nucleic acid docking algorithms and binding affinity predictions along with a list of computational resources for understanding protein-DNA and protein-RNA interactions.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"90 ","pages":"Article 102955"},"PeriodicalIF":6.1,"publicationDate":"2024-11-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142748010","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
Protein data bank: From two epidemics to the global pandemic to mRNA vaccines and Paxlovid 蛋白质数据库：从两次流行病到全球大流行，再到 mRNA 疫苗和 Paxlovid
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2024-11-24 DOI: 10.1016/j.sbi.2024.102954
Stephen K. Burley
{"title":"Protein data bank: From two epidemics to the global pandemic to mRNA vaccines and Paxlovid","authors":"Stephen K. Burley","doi":"10.1016/j.sbi.2024.102954","DOIUrl":"10.1016/j.sbi.2024.102954","url":null,"abstract":"<div><div>Structural biologists and the open-access Protein Data Bank (PDB) played decisive roles in combating the COVID-19 pandemic. Global biostructure data were turned into global knowledge, allowing scientists and engineers to understand the inner workings of coronaviruses and develop effective countermeasures. Two mRNA vaccines, initially designed with guidance from PDB structures of the SARS-CoV-1 and MERS-CoV spike proteins, prevented infections entirely or reduced the likelihood of morbidity and mortality for more than five billion individual recipients worldwide. Structure-guided drug discovery by Pfizer, Inc (facilitated by PDB structures), initiated in the 2000s in response to SARS-CoV-1 and resumed in 2020, yielded nirmatrelvir (the active ingredient of Paxlovid) -- a potent, orally-bioavailable inhibitor of the SARS-CoV-2 main protease. You've got to love the Protein Data Bank!</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"90 ","pages":"Article 102954"},"PeriodicalIF":6.1,"publicationDate":"2024-11-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142699731","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 heterogeneity in amyloid formation processes 淀粉样蛋白形成过程中的异质性特征。
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2024-11-19 DOI: 10.1016/j.sbi.2024.102951
Hoi Sung Chung
{"title":"Characterizing heterogeneity in amyloid formation processes","authors":"Hoi Sung Chung","doi":"10.1016/j.sbi.2024.102951","DOIUrl":"10.1016/j.sbi.2024.102951","url":null,"abstract":"<div><div>Protein aggregation is a complex process, consisting of a large number of pathways connecting monomers and mature amyloid fibrils. Recent advances in structure determination techniques, such as solid-state NMR and cryoEM, have allowed the determination of atomic resolution structures of fibril polymorphs, but most of the intermediate stages of the process including oligomer formation remain unknown. Proper characterization of the heterogeneity of the process is critical not only for physical and chemical understanding of the aggregation process but also for elucidation of the disease mechanisms and identification of therapeutic targets. This article reviews recent developments in the characterization of heterogeneity in amyloid formation processes.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"89 ","pages":"Article 102951"},"PeriodicalIF":6.1,"publicationDate":"2024-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142681273","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
Biochemistry and genetics are coming together to improve our understanding of genotype to phenotype relationships 生物化学和遗传学正在结合在一起，以提高我们对基因型与表型关系的理解。
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2024-11-12 DOI: 10.1016/j.sbi.2024.102952
Judith Notbohm , Tina Perica
{"title":"Biochemistry and genetics are coming together to improve our understanding of genotype to phenotype relationships","authors":"Judith Notbohm ,&nbsp;Tina Perica","doi":"10.1016/j.sbi.2024.102952","DOIUrl":"10.1016/j.sbi.2024.102952","url":null,"abstract":"<div><div>Since genome sequencing became accessible, determining how specific differences in genotypes lead to complex phenotypes such as disease has become one of the key goals in biomedicine. Predicting effects of sequence variants on cellular or organismal phenotype faces several challenges. First, variants simultaneously affect multiple protein properties and predicting their combined effect is complex. Second, effects of changes in a single protein propagate through the cellular network, which we only partially understand. In this review, we emphasize the importance of both biochemistry and genetics in addressing these challenges. Moreover, we highlight work that blurs the distinction between biochemistry and genetics fields to provide new insights into the genotype-to-phenotype relationships.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"89 ","pages":"Article 102952"},"PeriodicalIF":6.1,"publicationDate":"2024-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142616396","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
Deep learning for intrinsically disordered proteins: From improved predictions to deciphering conformational ensembles 内在无序蛋白质的深度学习：从改进预测到解密构象组合。
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2024-11-12 DOI: 10.1016/j.sbi.2024.102950
Gábor Erdős, Zsuzsanna Dosztányi
{"title":"Deep learning for intrinsically disordered proteins: From improved predictions to deciphering conformational ensembles","authors":"Gábor Erdős,&nbsp;Zsuzsanna Dosztányi","doi":"10.1016/j.sbi.2024.102950","DOIUrl":"10.1016/j.sbi.2024.102950","url":null,"abstract":"<div><div>Intrinsically disordered proteins (IDPs) lack a stable three-dimensional structure under physiological conditions, challenging traditional structure-based prediction methods. This review explores how modern deep learning approaches, which have revolutionized structure prediction for globular proteins, have impacted protein disorder predictions. We highlight the role of community-driven efforts in curating data and assessing state-of-the-art, which have been crucial in advancing the field. We also review state-of-the-art methods utilizing deep learning techniques, highlighting innovative approaches. We also address advancements in characterizing protein conformational ensembles directly from sequence data using novel machine learning methods.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"89 ","pages":"Article 102950"},"PeriodicalIF":6.1,"publicationDate":"2024-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142616402","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
Short circuit: Transcription factor addiction as a growing vulnerability in cancer 短路：转录因子成瘾是癌症中一个日益严重的弱点。
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2024-11-12 DOI: 10.1016/j.sbi.2024.102948
Molly Davies, Maeve Boyce, Eric Conway
{"title":"Short circuit: Transcription factor addiction as a growing vulnerability in cancer","authors":"Molly Davies,&nbsp;Maeve Boyce,&nbsp;Eric Conway","doi":"10.1016/j.sbi.2024.102948","DOIUrl":"10.1016/j.sbi.2024.102948","url":null,"abstract":"<div><div>Core regulatory circuitry refers to the network of lineage-specific transcription factors regulating expression of both their own coding genes, and that of other transcription factors. Such autoregulatory feedback loops coordinate the transcriptome and epigenome during development and cell fate decisions. This circuitry is hijacked during oncogenesis resulting in cancer cell fate being maintained by lineage-specific transcription factors. Major advances in functional genomics and chemical biology are paving the way for a new generation of cancer therapeutics aimed at disrupting this circuitry through both direct and indirect means. Here we review these critical advances in mechanistic understanding of transcription factor addiction in cancer and how the advent of proteolysis targeting chimeras and CRISPR screen assays are leading the way for a new paradigm in targeted cancer treatments.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"89 ","pages":"Article 102948"},"PeriodicalIF":6.1,"publicationDate":"2024-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142616405","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
Conformational penalties: New insights into nucleic acid recognition 构象惩罚：核酸识别的新见解。
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2024-11-09 DOI: 10.1016/j.sbi.2024.102949
Ainan Geng , Rohit Roy , Hashim M. Al-Hashimi
{"title":"Conformational penalties: New insights into nucleic acid recognition","authors":"Ainan Geng ,&nbsp;Rohit Roy ,&nbsp;Hashim M. Al-Hashimi","doi":"10.1016/j.sbi.2024.102949","DOIUrl":"10.1016/j.sbi.2024.102949","url":null,"abstract":"<div><div>The energy cost accompanying changes in the structures of nucleic acids when they bind partner molecules is a significant but underappreciated thermodynamic contribution to binding affinity and specificity. This review highlights recent advances in measuring conformational penalties and determining their contribution to the recognition, folding, and regulatory activities of nucleic acids. Notable progress includes methods for measuring and structurally characterizing lowly populated conformational states, obtaining ensemble information in high throughput, for large macromolecular assemblies, and in complex cellular environments. Additionally, quantitative and predictive thermodynamic models have been developed that relate conformational penalties to nucleic acid-protein association and cellular activity. These studies underscore the crucial role of conformational penalties in nucleic acid recognition.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"89 ","pages":"Article 102949"},"PeriodicalIF":6.1,"publicationDate":"2024-11-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142616399","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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