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Current opinion in structural biology最新文献

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TF paralogs—Natural experiments in DNA binding DNA结合的自然实验。
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-12-01 Epub Date: 2025-10-22 DOI: 10.1016/j.sbi.2025.103171
Shubham Khetan , Martha L. Bulyk
{"title":"TF paralogs—Natural experiments in DNA binding","authors":"Shubham Khetan ,&nbsp;Martha L. Bulyk","doi":"10.1016/j.sbi.2025.103171","DOIUrl":"10.1016/j.sbi.2025.103171","url":null,"abstract":"<div><div>Transcription factor (TF) paralogs provide unique insights into how DNA-binding specificity evolves and diversifies. While paralogous TFs share conserved, highly similar DNA-binding domains, they achieve distinct regulatory functions through mechanisms that are now being elucidated. This review examines how sequence variations between paralogs translate into functional diversity, including how mutations distant from the DNA interface can allosterically modulate binding specificity. We focus on competitive binding dynamics when paralogs are co-expressed and discuss emerging evidence that TFs recognize extensive repertoires of lower-affinity binding sites. Differential preferences for lower-affinity binding sites create paralog-specific binding patterns that determine TF genomic occupancy. These insights have important implications for interpreting the impact of coding and noncoding variation on TF–DNA interactions and human disease.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"95 ","pages":"Article 103171"},"PeriodicalIF":6.1,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145354001","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: Artificial intelligence methodologies in structural biology 编辑概述：结构生物学中的人工智能方法
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-12-01 Epub Date: 2025-09-13 DOI: 10.1016/j.sbi.2025.103156
Chaok Seok, Pratyush Tiwary
{"title":"Editorial overview: Artificial intelligence methodologies in structural biology","authors":"Chaok Seok,&nbsp;Pratyush Tiwary","doi":"10.1016/j.sbi.2025.103156","DOIUrl":"10.1016/j.sbi.2025.103156","url":null,"abstract":"","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"95 ","pages":"Article 103156"},"PeriodicalIF":6.1,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145047694","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
Allosteric binding cooperativity in kinases signaling, signalopathies, and drug development 激酶信号、信号病变和药物开发中的变构结合协同性。
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-12-01 Epub Date: 2025-10-16 DOI: 10.1016/j.sbi.2025.103169
Cristina Olivieri , Jian Wu , Susan S. Taylor , Gianluigi Veglia
{"title":"Allosteric binding cooperativity in kinases signaling, signalopathies, and drug development","authors":"Cristina Olivieri ,&nbsp;Jian Wu ,&nbsp;Susan S. Taylor ,&nbsp;Gianluigi Veglia","doi":"10.1016/j.sbi.2025.103169","DOIUrl":"10.1016/j.sbi.2025.103169","url":null,"abstract":"<div><div>Protein kinases catalyze the transfer of phosphate groups from ATP to specific substrates, initiating, modulating, or terminating signaling cascades. Generally, the response of these enzymes to stimuli is characterized by ultrasensitive rather than graded responses and mediated by cooperative binding interactions. Here, we provide examples of positive and negative cooperativity processes regulating several protein kinases. We first examine the binding cooperativity between nucleotide and substrate in protein kinase A, showing how dysfunctional cooperativity may be linked to signalopathies. We then illustrate how certain drugs exploit cooperativity to inhibit kinase homo- and hetero-dimerization or select for active and inactive conformational states. A molecular understanding of binding cooperativity could lead to the development of new kinase-specific inhibitors, opening up novel therapeutic possibilities.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"95 ","pages":"Article 103169"},"PeriodicalIF":6.1,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145312582","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
Labeling systems for cryo-electron tomography 低温电子断层扫描标记系统
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-12-01 Epub Date: 2025-11-25 DOI: 10.1016/j.sbi.2025.103189
Richard G. Held
{"title":"Labeling systems for cryo-electron tomography","authors":"Richard G. Held","doi":"10.1016/j.sbi.2025.103189","DOIUrl":"10.1016/j.sbi.2025.103189","url":null,"abstract":"<div><div>The unrealized goal of cryo-electron tomography (cryo-ET) is to visualize every protein within its cellular context. Such capability would enable molecular resolution mapping of three-dimensional protein topography and structure determination within a native context. Current technology limits the proteins identifiable within an individual tomogram to high-molecular-weight complexes. Localization of smaller target proteins requires the use of labeling systems that act as fiducial markers of target protein localization. Several labeling systems have been developed and recently employed, all of which involve trade-offs. The choice of which system to use depends on the biological question of interest. This review outlines considerations for the design and choice of labeling systems for cryo-ET, highlights recent applications, and outlines areas for future development.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"95 ","pages":"Article 103189"},"PeriodicalIF":6.1,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145620070","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 : 2025-12-01 Epub 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":"2025-12-01","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
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 : 2025-12-01 Epub 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":"2025-12-01","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 : 2025-12-01 Epub 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":"2025-12-01","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
Toward understanding whole enzymatic reaction cycles using multi-scale molecular simulations 利用多尺度分子模拟来理解整个酶促反应循环
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-12-01 Epub Date: 2025-09-11 DOI: 10.1016/j.sbi.2025.103153
Shingo Ito , Chigusa Kobayashi , Kiyoshi Yagi , Yuji Sugita
{"title":"Toward understanding whole enzymatic reaction cycles using multi-scale molecular simulations","authors":"Shingo Ito ,&nbsp;Chigusa Kobayashi ,&nbsp;Kiyoshi Yagi ,&nbsp;Yuji Sugita","doi":"10.1016/j.sbi.2025.103153","DOIUrl":"10.1016/j.sbi.2025.103153","url":null,"abstract":"<div><div>Enzymes effectively catalyze chemical reactions at their active sites. The reactions involve three microscopic events at the active sites: substrate binding, multi-step chemical reactions, and product release. These events are often coupled with enzyme conformational changes, making theoretical and computational analyses more challenging. Advanced molecular simulations, involving molecular dynamics (MD) and hybrid quantum mechanics/molecular mechanics (QM/MM), are now utilized to investigate the functions of enzymes such as tryptophan synthase and P-type ATPases. Here, we summarize recent multiscale molecular simulations that incorporate multiple microscopic events in enzyme functions. The coupling of enzyme conformational changes and chemical reactions can predict a proper direction in enzymatic reaction cycles, which requires accurate predictions of the free energy changes between different physiological states. Using machine learning (ML) methods, all the microscopic events in enzyme catalysis could be described with the same accuracy as quantum chemistry. We also discuss recent developments in ML/MM simulations for enzyme catalysis.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"95 ","pages":"Article 103153"},"PeriodicalIF":6.1,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145047693","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 : 2025-12-01 Epub 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":"2025-12-01","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
Editorial overview 社论的概述。
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-12-01 Epub Date: 2025-11-06 DOI: 10.1016/j.sbi.2025.103185
Hoi Sung Chung, Francesca M. Marassi
{"title":"Editorial overview","authors":"Hoi Sung Chung,&nbsp;Francesca M. Marassi","doi":"10.1016/j.sbi.2025.103185","DOIUrl":"10.1016/j.sbi.2025.103185","url":null,"abstract":"","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"95 ","pages":"Article 103185"},"PeriodicalIF":6.1,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145470846","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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