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Chromatin as a three-dimensional memory machine 染色质是三维记忆机器
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-10-04 DOI: 10.1016/j.sbi.2025.103160
Jeremy A. Owen , Leonid A. Mirny
{"title":"Chromatin as a three-dimensional memory machine","authors":"Jeremy A. Owen ,&nbsp;Leonid A. Mirny","doi":"10.1016/j.sbi.2025.103160","DOIUrl":"10.1016/j.sbi.2025.103160","url":null,"abstract":"<div><div>Epigenetic memory—the stable inheritance of a cellular state over cell generations—has long been associated with chromatin modifications. But individual modifications are very dynamic. How can they carry information across cell generations? Recent theoretical work suggests the answer might lie, in part, in the three-dimensional organization of the genome. Cooperation between marks brought together by genome folding can correct epigenetic errors, making stable memory units out of unstable marks. If marks direct the phase separation of chromatin, the resulting bidirectional coupling between marks and structure provides a mechanism for many of these units to operate independently along the genome. Models of bidirectional coupling have helped identify elements, such as formation of a dense compartment, 3D mark spreading, and limited enzyme, which may be key to stable epigenetic memory. An analogy between these 3D models and a classic model of associative memory hints at a way chromatin could perform sophisticated information processing.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"95 ","pages":"Article 103160"},"PeriodicalIF":6.1,"publicationDate":"2025-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145217985","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
Dictionary based approaches for studying intrinsic DNA shape in transcription factor recognition 基于字典的转录因子识别中DNA固有形状研究方法
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-10-04 DOI: 10.1016/j.sbi.2025.103166
Manisha Kalsan, Sadiya Mirza, Divyangana Bathla, Shandar Ahmad
{"title":"Dictionary based approaches for studying intrinsic DNA shape in transcription factor recognition","authors":"Manisha Kalsan,&nbsp;Sadiya Mirza,&nbsp;Divyangana Bathla,&nbsp;Shandar Ahmad","doi":"10.1016/j.sbi.2025.103166","DOIUrl":"10.1016/j.sbi.2025.103166","url":null,"abstract":"<div><div>Sequence-dependent <em>intrinsic</em> conformational dynamics confer specificity to transcriptional factor recognition of genomic DNA. Their genome-scale investigation using all-atom simulations is challenging, and alternative approaches by coarse-graining DNA into beads-and-sticks or polymer models have their own limitations. One parallel approach is what we describe here as a dictionary-based approach. This has been shown to explain several transcriptional events in biological systems but has been inadequately reviewed. These approaches represent studies based on a finite number of DNA fragments and their corresponding conformational properties, scaled up to genomes by pooling nearby fragments and machine learning models. This article aims to organize efforts made in generating these models and their recent successful applications to stimulate further development of this approach.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"95 ","pages":"Article 103166"},"PeriodicalIF":6.1,"publicationDate":"2025-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145217986","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
Recent advances in DNA-encoded libraries: From covalent targeting to protein profiling dna编码文库的最新进展：从共价靶向到蛋白质谱分析。
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-09-30 DOI: 10.1016/j.sbi.2025.103163
Rui Jin , Xiaojie Lu
{"title":"Recent advances in DNA-encoded libraries: From covalent targeting to protein profiling","authors":"Rui Jin ,&nbsp;Xiaojie Lu","doi":"10.1016/j.sbi.2025.103163","DOIUrl":"10.1016/j.sbi.2025.103163","url":null,"abstract":"<div><div>DNA-encoded library (DEL) technology has enabled efficient discovery of both non-covalent and covalent inhibitors, with covalent binders typically identified via covalent DELs (CoDELs) containing diverse electrophilic warheads. Recent developments have expanded CoDEL applications beyond cysteine to residues like lysine, tyrosine, arginine, and glutamic acid. The integration of CoDEL with activity-based protein profiling (ABPP) has further enabled the identification of potential protein targets for CoDEL screening using residue-selective warheads. Additionally, proteome profiling with fully-functionalized tags has guided target identification for focused DELs with privileged structures. This review highlights recent advances in CoDEL technologies for targeting both cysteine and non-cysteine residues, and discusses how proteomics facilitates hit discovery through CoDELs and focused DELs.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"95 ","pages":"Article 103163"},"PeriodicalIF":6.1,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145205730","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
Understanding how structure shapes the architecture of homologous recombination 了解结构如何塑造同源重组的结构。
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-09-27 DOI: 10.1016/j.sbi.2025.103164
Francesco Rinaldi , Stefania Girotto
{"title":"Understanding how structure shapes the architecture of homologous recombination","authors":"Francesco Rinaldi ,&nbsp;Stefania Girotto","doi":"10.1016/j.sbi.2025.103164","DOIUrl":"10.1016/j.sbi.2025.103164","url":null,"abstract":"<div><div>Cells have evolved multiple pathways to preserve genome integrity, with homologous recombination (HR) playing a central role in the accurate repair of DNA-double strand breaks (DSBs) by using homologous templates. Several proteins are involved in HR, and their mutations have been associated with cancer initiation and progression. In this review, we present an overview of recent structural insights into the HR pathway, highlighting the pivotal role of structural approaches in elucidating this complex and finely regulated DNA repair machinery, with the aim of advancing understanding and informing future research in the field.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"95 ","pages":"Article 103164"},"PeriodicalIF":6.1,"publicationDate":"2025-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145184958","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: Macromolecular assemblies: Technology innovations driving biological understanding 编辑概述：大分子组装：推动生物学理解的技术创新。
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-09-27 DOI: 10.1016/j.sbi.2025.103157
Christopher P. Hill, Elena V. Orlova
{"title":"Editorial overview: Macromolecular assemblies: Technology innovations driving biological understanding","authors":"Christopher P. Hill,&nbsp;Elena V. Orlova","doi":"10.1016/j.sbi.2025.103157","DOIUrl":"10.1016/j.sbi.2025.103157","url":null,"abstract":"","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"95 ","pages":"Article 103157"},"PeriodicalIF":6.1,"publicationDate":"2025-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145185018","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
Rewiring enzyme regulation: Allosteric drugs and predictive tools 重组酶调节：变构药物和预测工具
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-09-25 DOI: 10.1016/j.sbi.2025.103159
Vahap Gazi Fidan , Konuralp Ilim , Attila Gursoy , S. Banu Ozkan , Ozlem Keskin
{"title":"Rewiring enzyme regulation: Allosteric drugs and predictive tools","authors":"Vahap Gazi Fidan ,&nbsp;Konuralp Ilim ,&nbsp;Attila Gursoy ,&nbsp;S. Banu Ozkan ,&nbsp;Ozlem Keskin","doi":"10.1016/j.sbi.2025.103159","DOIUrl":"10.1016/j.sbi.2025.103159","url":null,"abstract":"<div><div>Allosteric modulation offers an increasingly attractive route for precise intervention in enzymatic pathways. This review outlines emerging strategies for the identification and exploitation of allosteric sites, emphasizing computational frameworks that integrate evolutionary, structural, and dynamic features with machine learning models. We discuss how perturbation-based simulations, network analyses, and deep mutational data are reshaping our understanding of allosteric regulation. In parallel, advances in experimental techniques have enabled validation of cryptic and functionally relevant pockets across diverse enzyme families. We further catalog FDA-approved allosteric modulators of enzymes, highlighting therapeutic designs that leverage distal regulation to enhance specificity and overcome resistance. Taken together, these developments reveal the growing utility of allostery in drug design and underscore its potential to expand the therapeutic target space beyond conventional binding sites.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"95 ","pages":"Article 103159"},"PeriodicalIF":6.1,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145155579","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
Erratum to “Structural insights into the recognition of native nucleosomes by pioneer transcription factors” [Current Opinion in structural Biology 92 (June 2025) 1–1, article number: 103,024] “通过先驱转录因子对原生核小体识别的结构见解”的勘误[结构生物学当前观点92（2025年6月）1-1，文章编号：103,024]
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-09-23 DOI: 10.1016/j.sbi.2025.103161
Bing-Rui Zhou, Benjamin Orris, Ruifang Guan, Tengfei Lian, Yawen Bai, Yawen Bai
{"title":"Erratum to “Structural insights into the recognition of native nucleosomes by pioneer transcription factors” [Current Opinion in structural Biology 92 (June 2025) 1–1, article number: 103,024]","authors":"Bing-Rui Zhou,&nbsp;Benjamin Orris,&nbsp;Ruifang Guan,&nbsp;Tengfei Lian,&nbsp;Yawen Bai,&nbsp;Yawen Bai","doi":"10.1016/j.sbi.2025.103161","DOIUrl":"10.1016/j.sbi.2025.103161","url":null,"abstract":"","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"95 ","pages":"Article 103161"},"PeriodicalIF":6.1,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145118932","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
Navigating protein–nucleic acid sequence-structure landscapes with deep learning 用深度学习导航蛋白质核酸序列结构景观
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-09-22 DOI: 10.1016/j.sbi.2025.103162
Elodie Laine , Sergei Grudinin , Roman Klypa , Isaure Chauvot de Beauchêne
{"title":"Navigating protein–nucleic acid sequence-structure landscapes with deep learning","authors":"Elodie Laine ,&nbsp;Sergei Grudinin ,&nbsp;Roman Klypa ,&nbsp;Isaure Chauvot de Beauchêne","doi":"10.1016/j.sbi.2025.103162","DOIUrl":"10.1016/j.sbi.2025.103162","url":null,"abstract":"<div><div>A few years after AlphaFold revolutionised the field of protein structure prediction, the new frontiers and limitations in structural biology have become clearer. Predicting protein–nucleic acid interactions currently stands as one of the major unresolved challenges in the field. This knowledge gap stems from the scarcity and limited diversity of experimental data, as well as the unique geometric, physicochemical, and evolutionary properties of nucleic acids. Despite these challenges, innovative ideas and promising methodological developments have emerged for both predicting protein–nucleic acid complex structures and designing nucleic acids capable of binding to specific protein conformations. This review presents these recent advances and discusses promising avenues, including the integration of high-throughput profiling data, the development of more rigourous and richer evaluation benchmarks, and the discovery of biologically meaningful regulatory and structural signals using self-supervised learning.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"95 ","pages":"Article 103162"},"PeriodicalIF":6.1,"publicationDate":"2025-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145118931","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
Chromatin higher-order folding as influenced by preferred values of linker DNA 染色质高阶折叠受连接体DNA偏好值的影响。
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-09-19 DOI: 10.1016/j.sbi.2025.103154
Zilong Li , Stephanie Portillo-Ledesma , Tamar Schlick
{"title":"Chromatin higher-order folding as influenced by preferred values of linker DNA","authors":"Zilong Li ,&nbsp;Stephanie Portillo-Ledesma ,&nbsp;Tamar Schlick","doi":"10.1016/j.sbi.2025.103154","DOIUrl":"10.1016/j.sbi.2025.103154","url":null,"abstract":"<div><div>Specific values of nucleosome spacing have long been associated with distinct chromatin organization, but recent studies reveal surprising structural and functional consequences of small changes in regular linker DNA length. This opinion article revisits experimental and modeling studies addressing the classic 10<em>n</em> versus 10<em>n</em> + 5 spacing, highlighting how this 5 bp difference can alter nucleosome orientation, fiber topology, and higher-order chromatin behavior. We underscore how differences in model parameters and system design yield different trends for the effect of linker DNA lengths on chromatin architecture. However, chromatin structure <em>in vivo</em> reflects the heterogeneous nucleosome spacing in combination with other cellular variables like salt conditions, epigenetic marks, and protein and RNA binding, which work together to shape gene folding and direct gene regulation.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"95 ","pages":"Article 103154"},"PeriodicalIF":6.1,"publicationDate":"2025-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145102550","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
Resistance mutations, drug binding and drug residence times 耐药突变、药物结合和药物停留时间。
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-09-17 DOI: 10.1016/j.sbi.2025.103158
Ran Friedman
{"title":"Resistance mutations, drug binding and drug residence times","authors":"Ran Friedman","doi":"10.1016/j.sbi.2025.103158","DOIUrl":"10.1016/j.sbi.2025.103158","url":null,"abstract":"<div><div>The rapid evolution of microorganisms and cancer cells makes it difficult to treat tumours and infectious diseases, because resistance to drugs is the rule rather than the exception. Structures or models of protein–drug complexes help to understand how mutations lead to resistance and to design better drugs. However, it is difficult to reason how small changes in the structure lead to drug resistance. Thus, protein and drug dynamics need to be considered. Strategies to increase drug residence are sought after to increase the efficacy of drugs. Computational methods to calculate the effect of mutations on drug binding and residence times are being developed and improved, but are challenging. A priori prediction of a mutation's effect on drug binding is an even greater challenge. On the other hand, knowledge about protein–drug complexes has led to the development of multiple design strategies that aim to reduce mutation-driven drug resistance.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"95 ","pages":"Article 103158"},"PeriodicalIF":6.1,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145085329","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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