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Recent advances and future trends for protein–small molecule interaction predictions with protein language models 用蛋白质语言模型预测蛋白质-小分子相互作用的最新进展和未来趋势
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-05-24 DOI: 10.1016/j.sbi.2025.103070
Alexander Kroll, Yvan Rousset
{"title":"Recent advances and future trends for protein–small molecule interaction predictions with protein language models","authors":"Alexander Kroll,&nbsp;Yvan Rousset","doi":"10.1016/j.sbi.2025.103070","DOIUrl":"10.1016/j.sbi.2025.103070","url":null,"abstract":"<div><div>In recent years, the application of natural language models to protein amino acid sequences, referred to as protein language models (PLMs), has demonstrated a significant potential for uncovering hidden patterns related to protein structure, function, and stability. The critical functions of proteins in biological processes often arise through interactions with small molecules; central examples are enzymes, receptors, and transporters. Understanding these interactions is particularly important for drug design, for bioengineering, and for understanding cellular metabolism. In this review, we present state-of-the-art PLMs and explore how they can be integrated with small molecule information to predict protein-small molecule interactions. We present several such prediction tasks and discuss current limitations and potential areas for improvement.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"93 ","pages":"Article 103070"},"PeriodicalIF":6.1,"publicationDate":"2025-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144125023","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
High-throughput cryo-electron tomography enables multiscale visualization of the inner life of microbes 高通量低温电子断层扫描使微生物的内部生活的多尺度可视化
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-05-16 DOI: 10.1016/j.sbi.2025.103065
Samira Heydari , Jun Liu
{"title":"High-throughput cryo-electron tomography enables multiscale visualization of the inner life of microbes","authors":"Samira Heydari ,&nbsp;Jun Liu","doi":"10.1016/j.sbi.2025.103065","DOIUrl":"10.1016/j.sbi.2025.103065","url":null,"abstract":"<div><div>Cryo-electron tomography (cryo-ET) is an advanced and rapidly evolving imaging technique that enables three-dimensional visualization of biological structures in their native state. Although cryo-ET has historically faced significant challenges, including limited applications, tedious data acquisition, labor-intensive image processing, and lower resolution when compared with single particle cryo-electron microscopy (cryo-EM), recent breakthroughs in hardware and software development have significantly improved the entire cryo-ET workflow to enable higher throughput and resolution. These advances have accelerated discoveries in structural and cellular biology, particularly in microbiology, where cryo-ET has unveiled unprecedented insights into the inner life of microbes. This review presents pivotal advances propelling high-throughput cryo-ET and the visualization of microbial architecture. As innovations in imaging technologies, workflow automation, and computational methods continue progressing rapidly, cryo-ET is expected to be increasingly utilized across various fields of life sciences, shaping the future of biological research and biomedical discoveries.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"93 ","pages":"Article 103065"},"PeriodicalIF":6.1,"publicationDate":"2025-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144069605","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
Profiling regulatory elements in vivo by genome-wide methods 通过全基因组方法分析体内调控元件
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-05-15 DOI: 10.1016/j.sbi.2025.103064
Kami Ahmad , Steven Henikoff
{"title":"Profiling regulatory elements in vivo by genome-wide methods","authors":"Kami Ahmad ,&nbsp;Steven Henikoff","doi":"10.1016/j.sbi.2025.103064","DOIUrl":"10.1016/j.sbi.2025.103064","url":null,"abstract":"<div><div>The biology of gene regulation in eukaryotic genomes is a mature field. The biochemical principles of factor binding to DNA are well-known from <em>in vitro</em> studies, as are the structural interactions in which specific domains of these proteins interface across a short stretch of DNA to confer sequence-specific recognition. Whereas the basic principles of binding and dissociation defined <em>in vitro</em> apply <em>in vivo</em>, the living nucleus is a dynamic compartment crowded with molecules, including motors that drive chromatin movements critical for the regulation of gene expression. Understanding these dynamics <em>in vivo</em> has spurred the development of cutting-edge technologies to observe factor–DNA interactions. The biological significance of chromatin dynamics is now revealed by a wide variety of high-resolution chromatin profiling methods.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"92 ","pages":"Article 103064"},"PeriodicalIF":6.1,"publicationDate":"2025-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143947519","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
Template matching and machine learning for cryo-electron tomography 低温电子断层扫描的模板匹配与机器学习
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-05-14 DOI: 10.1016/j.sbi.2025.103058
Antonio Martinez-Sanchez
{"title":"Template matching and machine learning for cryo-electron tomography","authors":"Antonio Martinez-Sanchez","doi":"10.1016/j.sbi.2025.103058","DOIUrl":"10.1016/j.sbi.2025.103058","url":null,"abstract":"<div><div>Cryo-electron tomography is the best-suited imaging technique for visual proteomics. Recent advances have increased the number, quality, and resolution of tomograms. However, object detection is the bottleneck task of the analysis workflow because, so far, only a few molecules can be detected by computer methods for pattern recognition. This article introduces the major challenges in detecting molecular complexes for cryo-electron tomography. This paper also identifies the limitations of the current methods. Finally, it describes the approaches proposed to overcome these limitations.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"93 ","pages":"Article 103058"},"PeriodicalIF":6.1,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143943078","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
Biological insights from integrative modeling of intrinsically disordered protein systems 从内在无序的蛋白质系统的综合建模生物学见解
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-05-10 DOI: 10.1016/j.sbi.2025.103063
Zi Hao Liu , Maria Tsanai , Oufan Zhang , Teresa Head-Gordon , Julie D. Forman-Kay
{"title":"Biological insights from integrative modeling of intrinsically disordered protein systems","authors":"Zi Hao Liu ,&nbsp;Maria Tsanai ,&nbsp;Oufan Zhang ,&nbsp;Teresa Head-Gordon ,&nbsp;Julie D. Forman-Kay","doi":"10.1016/j.sbi.2025.103063","DOIUrl":"10.1016/j.sbi.2025.103063","url":null,"abstract":"<div><div>Intrinsically disordered proteins and regions are increasingly appreciated for their abundance in the proteome and the many functional roles they play in the cell. In this short review, we describe a variety of approaches used to obtain biological insight from the structural ensembles of disordered proteins, regions, and complexes and the integrative biology challenges that arise from combining diverse experiments and computational models. Importantly, we highlight findings regarding structural and dynamic characterization of disordered regions involved in binding and phase separation, as well as drug targeting of disordered regions, using a broad framework of integrative modeling approaches.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"93 ","pages":"Article 103063"},"PeriodicalIF":6.1,"publicationDate":"2025-05-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143932250","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
In-cell chromatin structure by Cryo-FIB and Cryo-ET 通过Cryo-FIB和Cryo-ET分析细胞内染色质结构
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-05-10 DOI: 10.1016/j.sbi.2025.103060
Zhen Hou , Peijun Zhang
{"title":"In-cell chromatin structure by Cryo-FIB and Cryo-ET","authors":"Zhen Hou ,&nbsp;Peijun Zhang","doi":"10.1016/j.sbi.2025.103060","DOIUrl":"10.1016/j.sbi.2025.103060","url":null,"abstract":"<div><div>Chromatin, the complex of DNA and proteins that organises genetic material in eukaryotic cells, has been a focal point of biological research for over a century. Its structure determines critical functions such as gene regulation, DNA replication and chromosome segregation. Early models of chromatin were limited by technological constraints, but advancements in imaging, particularly X-ray and electron microscopy (EM), gradually unveiled its hierarchical organisation. The recent emergence of cryo-electron tomography (cryo-ET) coupled with cryo-focused ion beam (cryo-FIB) milling has revolutionised our understanding of chromatin organisation by providing native, three-dimensional (3D) views of various macromolecules and architectures of chromatin at unprecedented resolution. This review traces the historical progression of chromatin structural studies, from early EM and fluorescence microscopy to the transformative insights offered by cryo-ET, culminating in a synthesis of current knowledge and future directions.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"92 ","pages":"Article 103060"},"PeriodicalIF":6.1,"publicationDate":"2025-05-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143929195","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
Salipro technology in membrane protein research Salipro技术在膜蛋白研究中的应用
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-05-10 DOI: 10.1016/j.sbi.2025.103050
Siavash Mostafavi , Tânia F. Custódio , Katharina E.J. Jungnickel , Christian Löw
{"title":"Salipro technology in membrane protein research","authors":"Siavash Mostafavi ,&nbsp;Tânia F. Custódio ,&nbsp;Katharina E.J. Jungnickel ,&nbsp;Christian Löw","doi":"10.1016/j.sbi.2025.103050","DOIUrl":"10.1016/j.sbi.2025.103050","url":null,"abstract":"<div><div>Reconstitution and direct extraction of membrane proteins using saposins is an emerging technique for solubilizing and stabilizing membrane proteins. The Salipro technology offers several advantages over traditional detergent solubilization, including a more native lipid environment, increased protein stability, and maintenance of functionality. This review covers recent studies that have used Salipros to characterize membrane proteins, as well as advances in direct extraction methods that have enabled the structural and functional characterization of a variety of targets.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"93 ","pages":"Article 103050"},"PeriodicalIF":6.1,"publicationDate":"2025-05-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143927756","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 decoding the mechanisms that shape sub-megabase-scale genome organization 解码形成亚兆级基因组组织的机制
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-05-08 DOI: 10.1016/j.sbi.2025.103062
Joseph M. Paggi, Bin Zhang
{"title":"Toward decoding the mechanisms that shape sub-megabase-scale genome organization","authors":"Joseph M. Paggi,&nbsp;Bin Zhang","doi":"10.1016/j.sbi.2025.103062","DOIUrl":"10.1016/j.sbi.2025.103062","url":null,"abstract":"<div><div>Understanding genome organization at the kilobase to megabase scale is critical, as it encompasses genes and regulatory elements. Improvements in the resolution of experimental techniques have revealed novel structural motifs at this scale, including micro-compartments, nucleosome clutches, microdomains, and packing domains. Here we review recent progress on developing theories to explain these observations. Key advances include elucidating the role of nucleosome positioning and epigenetic modifications, the role and mechanisms of compartmentalization in local structure, and the interplay between loop extrusion and phase separation. This work has revealed probable mechanisms by which the observed structures emerge, but it remains unclear how these factors act together in the cell. To this end, recent studies have used chromatin conformation capture data in concert with diverse genomics datasets to create native-like models of chromatin at nucleosome resolution and below. While several roadblocks remain, this strategy promises to decode how molecular forces sum to shape chromatin structure and ultimately regulate transcription.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"92 ","pages":"Article 103062"},"PeriodicalIF":6.1,"publicationDate":"2025-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143916251","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
Structure and function of histone chaperones in replication-coupled chromatin assembly 组蛋白伴侣在复制偶联染色质组装中的结构和功能
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-05-07 DOI: 10.1016/j.sbi.2025.103059
Chao-Pei Liu , Rui-Ming Xu
{"title":"Structure and function of histone chaperones in replication-coupled chromatin assembly","authors":"Chao-Pei Liu ,&nbsp;Rui-Ming Xu","doi":"10.1016/j.sbi.2025.103059","DOIUrl":"10.1016/j.sbi.2025.103059","url":null,"abstract":"<div><div>Eukaryotic cell divisions pass on genetic and epigenetic information from parental to daughter cells through replication of the chromatin, which needs to be reestablished following DNA replication, as its building block, the nucleosome, is disrupted by the passage of the DNA replication fork. This replication-coupled (RC) nucleosome assembly process takes place in distinct pathways depending on whether newly synthesized or parental histones are used. This review highlights recent progress in structural and biochemical studies of RC nucleosome assembly, focusing on the roles of histone chaperones in both <em>de novo</em> assembly of nucleosomes from newly synthesized histones and the recycling of parental histones. We also discuss the interactions between histone chaperones and replisome components that govern the coupling of nucleosome assembly to chromatin replication. Finally, we offer our perspective on future efforts in advancing this important research direction.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"92 ","pages":"Article 103059"},"PeriodicalIF":6.1,"publicationDate":"2025-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143912329","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
Deciphering the language of mingling lipids and proteins 破译混合脂质和蛋白质的语言
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-05-07 DOI: 10.1016/j.sbi.2025.103061
Michael Overduin , Rakesh Bhat , Thibaud Dieudonné , Peijun Zhang , Troy A. Kervin
{"title":"Deciphering the language of mingling lipids and proteins","authors":"Michael Overduin ,&nbsp;Rakesh Bhat ,&nbsp;Thibaud Dieudonné ,&nbsp;Peijun Zhang ,&nbsp;Troy A. Kervin","doi":"10.1016/j.sbi.2025.103061","DOIUrl":"10.1016/j.sbi.2025.103061","url":null,"abstract":"<div><div>Each cell possesses a genetic and a proteolipid code that together convey molecular information in a perpetual cycle. One element of this cycle is the recognition of lipids that work together to specify subcellular locations for biochemical activity. These “lipidons” are now being resolved in protein structures from eukaryotic plasma membranes, endosomes, mitochondria, prokaryotes, and viruses with technologies like <em>in situ</em> cryo-electron imaging and membrane-active polymers. This adds to an expanding catalogue of codified protein-lipid interactions that are recontextualizing cell biology and drug discovery.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"92 ","pages":"Article 103061"},"PeriodicalIF":6.1,"publicationDate":"2025-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143912330","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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