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Recent advances in structural studies of NLRP3 and NLRP1 inflammasome regulation NLRP3和NLRP1炎性小体调控的结构研究进展
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-05-06 DOI: 10.1016/j.sbi.2025.103057
Zhikuan Zhang, Toshiyuki Shimizu
{"title":"Recent advances in structural studies of NLRP3 and NLRP1 inflammasome regulation","authors":"Zhikuan Zhang,&nbsp;Toshiyuki Shimizu","doi":"10.1016/j.sbi.2025.103057","DOIUrl":"10.1016/j.sbi.2025.103057","url":null,"abstract":"<div><div>The NOD-like receptor (NLR) family comprises inflammasome sensors that are critical intracellular pattern recognition receptors of the innate immune system. The NLR family members NLRP3 and NLRP1 can be activated by a wide range of pathogenic, chemical, self-derived and stress-related stimuli. In recent years, remarkable progress in functional and structural studies of these two receptors have shed light on their complicated and entirely different activation and regulation mechanisms. This review focuses on recent structural studies of NLRP3 and NLRP1, emphasizing the regulatory steps mediated by various activation and inhibitory factors.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"92 ","pages":"Article 103057"},"PeriodicalIF":6.1,"publicationDate":"2025-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143912331","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 biochemical studies of mobile retrotransposon proteins in action 活动的反转录转座子蛋白的结构和生化研究
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-05-06 DOI: 10.1016/j.sbi.2025.103053
Akanksha Thawani , Kathleen Collins , Eva Nogales
{"title":"Structural and biochemical studies of mobile retrotransposon proteins in action","authors":"Akanksha Thawani ,&nbsp;Kathleen Collins ,&nbsp;Eva Nogales","doi":"10.1016/j.sbi.2025.103053","DOIUrl":"10.1016/j.sbi.2025.103053","url":null,"abstract":"<div><div>Autonomous non-long-terminal repeat (non-LTR) retrotransposons, including long interspersed elements (LINEs), are mobile genetic elements abundant in eukaryotic species that shape the genomic landscape and host physiology in both health and disease. Non-LTR retrotransposons create new genomic copies through a mechanism termed target-primed reverse transcription, where the retrotransposon-encoded protein nicks target DNA to prime reverse transcription templated by bound RNA, typically its own encoding mRNA. Until recently, structural information on non-LTR retrotransposons was lacking due to challenges in purification and reconstitution of active complexes. Recent biochemical studies and cryo-electron microscopy structures of complexes from insect, bird, and turtle site-specific R2 retrotransposons and the human LINE-1 retrotransposon have provided important insights. Here we discuss these studies and their implications for retrotransposon evolution and eukaryotic genome biology.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"92 ","pages":"Article 103053"},"PeriodicalIF":6.1,"publicationDate":"2025-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143907959","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
Structures and mechanisms of AAA+ protein complexes in DNA processing DNA加工中AAA+蛋白复合物的结构和机制
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-05-06 DOI: 10.1016/j.sbi.2025.103056
Alexander Carver , Bowen Zhang , Xiaodong Zhang
{"title":"Structures and mechanisms of AAA+ protein complexes in DNA processing","authors":"Alexander Carver ,&nbsp;Bowen Zhang ,&nbsp;Xiaodong Zhang","doi":"10.1016/j.sbi.2025.103056","DOIUrl":"10.1016/j.sbi.2025.103056","url":null,"abstract":"<div><div>AAA+ proteins are a large family of ATPases involved in a myriad of cellular activities. Recent advances in AAA+ proteins, especially cryoEM structures of these proteins in complex with their substrates, have provided key insights into how they function. Here we review recent progress in structural studies and mechanistic understanding of AAA+ proteins involved in DNA processing, including gene transcription, DNA replication, repair/recombination and transposition. Using a few selected examples, we show how AAA+ proteins act on both DNA and protein peptides, which are often enclosed in the pores of AAA+ hexamers. We propose that using AAA+ proteins to translocate a peptide to partially unfold a substrate is an effective strategy in disassembling an assembled complex. Further, several studies show that although they often act as asymmetric hexamers in their active form, AAA+ proteins adopt a range of oligomers for their functions.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"92 ","pages":"Article 103056"},"PeriodicalIF":6.1,"publicationDate":"2025-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143907958","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
Primed for degradation: How weak protein interactions enable molecular glue degraders 降解：弱蛋白相互作用如何使分子胶降解
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-05-06 DOI: 10.1016/j.sbi.2025.103052
Alexander Hanzl , Clara Inghelram , Stefan Schmitt , Nicolas H. Thomä
{"title":"Primed for degradation: How weak protein interactions enable molecular glue degraders","authors":"Alexander Hanzl ,&nbsp;Clara Inghelram ,&nbsp;Stefan Schmitt ,&nbsp;Nicolas H. Thomä","doi":"10.1016/j.sbi.2025.103052","DOIUrl":"10.1016/j.sbi.2025.103052","url":null,"abstract":"<div><div>Molecular glues are small drug-like molecules that induce <em>de novo</em> protein–protein interactions or facilitate pre-existing weak interactions between proteins. In the context of a ubiquitin ligase, such binding events frequently result in ubiquitination by proximity. Rational development of these transformative modalities, however, remains a major challenge. Here we review recent insights into molecular glues and the emerging design principles. Protein surfaces can similarly be complemented by mutations or compounds inducing binding and a resulting gain of functionality. When the interaction surface between two proteins is relatively small, or when the affinity between the proteins is otherwise weak, proportionally more binding energy will have to be provided by the compound to glue the proteins together. We suggest a simple thermodynamic model to rationalize molecular glue action facilitated by compounds and mutations.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"92 ","pages":"Article 103052"},"PeriodicalIF":6.1,"publicationDate":"2025-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143907957","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
All-atom virus simulations to tackle airborne disease 全原子病毒模拟来对付空气传播疾病
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-05-03 DOI: 10.1016/j.sbi.2025.103048
Abigail C. Dommer , Nicholas A. Wauer , Siewert J. Marrink , Rommie E. Amaro
{"title":"All-atom virus simulations to tackle airborne disease","authors":"Abigail C. Dommer ,&nbsp;Nicholas A. Wauer ,&nbsp;Siewert J. Marrink ,&nbsp;Rommie E. Amaro","doi":"10.1016/j.sbi.2025.103048","DOIUrl":"10.1016/j.sbi.2025.103048","url":null,"abstract":"<div><div>We briefly review the latest computational studies focused on modeling viruses with classical all-atom (AA) molecular dynamics. We report on the challenges, current solutions, and ongoing developments in constructing and simulating whole viruses, and discuss unique insights derived from AA mesoscale simulations that cannot be achieved by other means. Finally, we present new opportunities in computational virology to understand viral aerostability within the context of respiratory disease transmission. Overall, we highlight the value of large-scale AA simulation and champion the need for increased interdisciplinary collaboration to generate novel insights and guide future research in respiratory disease.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"92 ","pages":"Article 103048"},"PeriodicalIF":6.1,"publicationDate":"2025-05-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143900041","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 evolving role of hydrogen/deuterium exchange mass spectrometry in early-stage drug discovery 氢/氘交换质谱法在早期药物发现中的作用
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-05-02 DOI: 10.1016/j.sbi.2025.103051
Srinath Krishnamurthy , Maria Musgaard , Benjamin Gerald Tehan, Ali Jazayeri, Idlir Liko
{"title":"The evolving role of hydrogen/deuterium exchange mass spectrometry in early-stage drug discovery","authors":"Srinath Krishnamurthy ,&nbsp;Maria Musgaard ,&nbsp;Benjamin Gerald Tehan,&nbsp;Ali Jazayeri,&nbsp;Idlir Liko","doi":"10.1016/j.sbi.2025.103051","DOIUrl":"10.1016/j.sbi.2025.103051","url":null,"abstract":"<div><div>Protein function relies on protein dynamics and therefore dynamical information can be crucial for drug discovery of challenging protein targets. Assessing protein dynamics experimentally has traditionally been nontrivial. However, amide hydrogen/deuterium exchange mass spectrometry (HDX-MS) is now an established technique that can expose details about changes in protein dynamics, binding sites and allostery at the peptide level. HDX-MS is a versatile and powerful biophysical tool to gain insights into the workings of numerous protein systems and complexes. Advances in instrumentation, automation, data analysis, and interpretation over the past two decades have led to increased uptake and democratization of HDX-MS in both academic and industry settings. Here, we outline the current uses of HDX-MS in early-stage drug discovery and illustrate the interplay with computational chemistry to maximize the value of data obtained from HDX-MS experiments. Finally, we consider approaches which may aid structural interpretation of HDX-MS data in the coming years.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"92 ","pages":"Article 103051"},"PeriodicalIF":6.1,"publicationDate":"2025-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143895638","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
Illuminating ubiquitination mechanisms: How cryo-EM has shed light on Cullin RING E3 ligase function 阐明泛素化机制：低温电镜如何揭示Cullin RING E3连接酶的功能
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-04-30 DOI: 10.1016/j.sbi.2025.103055
Zeba Rizvi, Gabriel C. Lander
{"title":"Illuminating ubiquitination mechanisms: How cryo-EM has shed light on Cullin RING E3 ligase function","authors":"Zeba Rizvi,&nbsp;Gabriel C. Lander","doi":"10.1016/j.sbi.2025.103055","DOIUrl":"10.1016/j.sbi.2025.103055","url":null,"abstract":"<div><div>The ubiquitin-proteasome system (UPS) governs protein homeostasis by orchestrating the selective degradation of regulatory and misfolded proteins through a tightly regulated series of ATP-driven ubiquitination reactions. E3 ubiquitin ligases play a central role in this process by conferring substrate specificity, yet the structural complexity and dynamic nature of these large macromolecular assemblies poses challenges for traditional structural biology techniques such as X-ray crystallography and nuclear magnetic resonance (NMR). The advent of single-particle cryo-electron microscopy (cryo-EM) has transformed our ability to study these enzymes, revealing previously inaccessible mechanistic insights into their allosteric regulation, conformational transitions, and substrate recognition. By integrating high-resolution crystallographic data with cryo-EM's ability to resolve heterogeneous and dynamic complexes, researchers have uncovered fundamental principles governing E3 ligase activity. This review explores how cryo-EM has reshaped our understanding of Ligases. We highlight key discoveries enabled by this technique, and discuss how emerging cryo-EM approaches, alongside complementary methodologies, are advancing therapeutic strategies targeting ubiquitin signaling by this family of ligases.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"92 ","pages":"Article 103055"},"PeriodicalIF":6.1,"publicationDate":"2025-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143892232","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 diversity of noncanonical nucleosomes: Functions in chromatin 非典型核小体的结构多样性：在染色质中的功能
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-04-30 DOI: 10.1016/j.sbi.2025.103054
Suguru Hatazawa, Naoki Horikoshi, Hitoshi Kurumizaka
{"title":"Structural diversity of noncanonical nucleosomes: Functions in chromatin","authors":"Suguru Hatazawa,&nbsp;Naoki Horikoshi,&nbsp;Hitoshi Kurumizaka","doi":"10.1016/j.sbi.2025.103054","DOIUrl":"10.1016/j.sbi.2025.103054","url":null,"abstract":"<div><div>In eukaryotes, genomic DNA is compacted into chromatin, with nucleosomes acting as its basic structural units. In addition to canonical nucleosomes, noncanonical nucleosomes, such as hexasomes, H3–H4 octasomes, and overlapping dinucleosomes, exhibit alternative histone compositions and play key roles in chromatin remodeling, transcription, and replication. Recent cryo-electron microscopy (cryo-EM) studies have elucidated the structural details of these noncanonical nucleosomes and their interactions with histone chaperones and chromatin remodelers. This review highlights recent advances in the structural and functional understanding of noncanonical nucleosomes and their roles in maintaining chromatin integrity and facilitating transcriptional dynamics.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"92 ","pages":"Article 103054"},"PeriodicalIF":6.1,"publicationDate":"2025-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143892233","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 synergy of experimental and computational approaches for visualizing glycoprotein dynamics: Exploring order within the apparent disorder of glycan conformational ensembles 可视化糖蛋白动力学的实验和计算方法的协同作用：在糖蛋白构象集合的明显无序中探索秩序
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-04-29 DOI: 10.1016/j.sbi.2025.103049
Koichi Kato , Saeko Yanaka , Takumi Yamaguchi
{"title":"The synergy of experimental and computational approaches for visualizing glycoprotein dynamics: Exploring order within the apparent disorder of glycan conformational ensembles","authors":"Koichi Kato ,&nbsp;Saeko Yanaka ,&nbsp;Takumi Yamaguchi","doi":"10.1016/j.sbi.2025.103049","DOIUrl":"10.1016/j.sbi.2025.103049","url":null,"abstract":"<div><div>Understanding the dynamic behavior of glycoproteins is crucial for deciphering their biological roles. This review explores the synergistic use of experimental and computational methods to address this complex challenge. Glycans, with their inherent flexibility and structural diversity, pose significant obstacles to traditional structural analysis. Innovative experimental techniques offer valuable snapshots of glycan conformations, but often lack the context of a physiological environment. Computational simulations provide atomic-level detail and explore the full range of dynamic motions, but require extensive resources and validation. Integrating these approaches, by using experimental data to refine and validate computational models, is essential for accurately capturing the complex interplay between glycans and proteins. This combined strategy promises to unlock a deeper understanding of glycoprotein function and inform the design of novel therapeutics.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"92 ","pages":"Article 103049"},"PeriodicalIF":6.1,"publicationDate":"2025-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143882426","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
Comparative anatomy of siphophage tails before and after interaction with their receptor 与受体相互作用前后的虹吸体尾部对比解剖
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-04-24 DOI: 10.1016/j.sbi.2025.103045
Alessio d'Acapito , Alice Decombe , Charles-Adrien Arnaud, Cécile Breyton
{"title":"Comparative anatomy of siphophage tails before and after interaction with their receptor","authors":"Alessio d'Acapito ,&nbsp;Alice Decombe ,&nbsp;Charles-Adrien Arnaud,&nbsp;Cécile Breyton","doi":"10.1016/j.sbi.2025.103045","DOIUrl":"10.1016/j.sbi.2025.103045","url":null,"abstract":"<div><div>Siphophages are tailed bacteriophages characterised by their long noncontractile tails. In this review, we compare the recent electron cryo-microscopy structures of eight siphophage tails. We confirm and extend common building block organisation within the siphophage tails, particularly within the tail tip. Moreover, the description of the structure of siphophages T5 and λ tail after receptor binding, showing conformational changes only in the tail tip, explains how the siphophage tail opens, leading to DNA ejection. Conserved structural elements point to a general mechanism of infection for Gram-negative-infecting siphophages and allow considerations regarding the classification of the receptor-binding proteins into two different categories: host recognition receptors and membrane sensing receptors that trigger DNA ejection.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"92 ","pages":"Article 103045"},"PeriodicalIF":6.1,"publicationDate":"2025-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143868046","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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