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Role of RNA in genome folding: It's all about affinity RNA在基因组折叠中的作用：这与亲和力有关
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-08-20 DOI: 10.1016/j.sbi.2025.103136
Rafal Czapiewski, Nick Gilbert
{"title":"Role of RNA in genome folding: It's all about affinity","authors":"Rafal Czapiewski,&nbsp;Nick Gilbert","doi":"10.1016/j.sbi.2025.103136","DOIUrl":"10.1016/j.sbi.2025.103136","url":null,"abstract":"<div><div>In mammalian cells, RNA species make up ∼10% of chromatin by mass and play a structural role in the nucleus by acting as scaffolds and influencing genome organisation. Although many proteins bind nuclear RNAs, these interactions are often non-specific, making it challenging to define RNA's role in genome folding. Nonetheless, a clearer picture is emerging. Some RNAs, like NEAT1 and MALAT1, have high affinity for specific RNA-binding proteins and form the basis for nuclear bodies. In contrast, many nuclear proteins bind RNA weakly, resulting in numerous low-affinity interactions. We propose that these interactions generate a complex RNA-protein network with dynamic, gel-like properties that modulate chromatin folding and transcription factor mobility. This suggests an exciting feedback mechanism in which newly transcribed RNA contributes directly to shaping chromatin architecture.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"94 ","pages":"Article 103136"},"PeriodicalIF":6.1,"publicationDate":"2025-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144863501","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
Functional sub-states link conformational landscapes and protein evolution 功能亚态连接构象景观和蛋白质进化
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-08-16 DOI: 10.1016/j.sbi.2025.103134
Morito Sakuma , Karol Buda , H. Adrian Bunzel , Christopher Frøhlich , Nobuhiko Tokuriki
{"title":"Functional sub-states link conformational landscapes and protein evolution","authors":"Morito Sakuma ,&nbsp;Karol Buda ,&nbsp;H. Adrian Bunzel ,&nbsp;Christopher Frøhlich ,&nbsp;Nobuhiko Tokuriki","doi":"10.1016/j.sbi.2025.103134","DOIUrl":"10.1016/j.sbi.2025.103134","url":null,"abstract":"<div><div>The intrinsic conformational flexibility of proteins creates structural heterogeneity, giving rise to conformational ensembles within the energy landscape. When conformational ensembles harbor distinct functional sub-states, mutations can reshape the conformational landscape, thereby altering the distribution of functional sub-states and driving the evolution of novel functions. In this review, we provide a conceptual framework that elucidates the importance of functional sub-states and how evolution can select them. We highlight key studies that have uncovered functional sub-states and discuss recent insights into the transitions of functional sub-states during evolutionary trajectories. Finally, we outline critical techniques for studying functional sub-states, address the challenges faced in analyzing these sub-states, and explore future advancements in the field of protein evolution.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"94 ","pages":"Article 103134"},"PeriodicalIF":6.1,"publicationDate":"2025-08-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144858191","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
Modeling flexible RNA 3D structures and RNA-protein complexes 建模柔性RNA三维结构和RNA-蛋白复合物
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-08-16 DOI: 10.1016/j.sbi.2025.103137
Rui João Loureiro, Satyabrata Maiti, Kuntal Mondal, Sunandan Mukherjee, Janusz M. Bujnicki
{"title":"Modeling flexible RNA 3D structures and RNA-protein complexes","authors":"Rui João Loureiro,&nbsp;Satyabrata Maiti,&nbsp;Kuntal Mondal,&nbsp;Sunandan Mukherjee,&nbsp;Janusz M. Bujnicki","doi":"10.1016/j.sbi.2025.103137","DOIUrl":"10.1016/j.sbi.2025.103137","url":null,"abstract":"<div><div>RNA and RNA–protein (RNP) complexes are central to many cellular processes, but the determination of their structures remains challenging due to RNA flexibility and interaction diversity. This review highlights recent computational advances, particularly from the past two years, in predicting and analyzing RNA and RNP structures. We discuss template-based modeling, docking, molecular simulations, and deep learning approaches, with an emphasis on emerging hybrid methods that integrate these strategies. Special attention is given to tools for modeling conformational heterogeneity, folding pathways, and dynamic binding. We also outline machine learning and simulation techniques for ensemble prediction and explore future directions including quantum-enhanced modeling. Together, these developments are enabling more accurate and scalable modeling of both the static and dynamic aspects of RNA and RNP complexes.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"94 ","pages":"Article 103137"},"PeriodicalIF":6.1,"publicationDate":"2025-08-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144852624","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
Generative AI techniques for conformational diversity and evolutionary adaptation of proteins 蛋白质构象多样性和进化适应的生成人工智能技术
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-08-14 DOI: 10.1016/j.sbi.2025.103135
Alfie-Louise R. Brownless , Dariia Yehorova , Colin L. Welsh , Shina Caroline Lynn Kamerlin
{"title":"Generative AI techniques for conformational diversity and evolutionary adaptation of proteins","authors":"Alfie-Louise R. Brownless ,&nbsp;Dariia Yehorova ,&nbsp;Colin L. Welsh ,&nbsp;Shina Caroline Lynn Kamerlin","doi":"10.1016/j.sbi.2025.103135","DOIUrl":"10.1016/j.sbi.2025.103135","url":null,"abstract":"<div><div>The advent of AlphaFold and consumer large language models have elicited unprecedented development of artificial intelligence (AI). AI has had substantial impact in every area of research, including in molecular biology. This is principally in thanks to contributions to the Protein Data Bank and various genome sequence databases, providing an astronomical amount of data for model training. These databases contain evolutionary information explicitly and implicitly, allowing accurate predictions and deep insights into biological questions. Here, we describe recent state-of-the-art applications of AI that exploit evolutionary relationships. This includes structure prediction and design, conformational ensemble generation, and functional site identification. We present a brief snapshot of AI usage in studying protein structure and dynamics, a field that is advancing at breakneck speed.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"94 ","pages":"Article 103135"},"PeriodicalIF":6.1,"publicationDate":"2025-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144840958","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
Advances in Protein-RNA aptamer recognition and modeling: Current trends and future perspectives 蛋白质- rna适体识别和建模的进展：当前趋势和未来展望
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-08-14 DOI: 10.1016/j.sbi.2025.103133
Liming Qiu , Xiaoqin Zou
{"title":"Advances in Protein-RNA aptamer recognition and modeling: Current trends and future perspectives","authors":"Liming Qiu ,&nbsp;Xiaoqin Zou","doi":"10.1016/j.sbi.2025.103133","DOIUrl":"10.1016/j.sbi.2025.103133","url":null,"abstract":"<div><div>RNA aptamers possess a remarkable ability to selectively target a diverse spectrum of biomolecules with exceptional affinity and specificity. Their distinctive physical and chemical attributes have driven extensive research into their therapeutic, diagnostic, and analytical applications. However, experimental approaches alone are insufficient to meet the growing demand. As a result, accurate and efficient computational methods are playing an increasingly vital role in RNA aptamer sequence design and structural modeling. Recent breakthroughs in biomolecular structure prediction, particularly through deep learning, have further spurred the development of innovative algorithms. In this review, we summarize current computational models for RNA aptamer structure prediction and design, highlighting recent advances in the field.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"94 ","pages":"Article 103133"},"PeriodicalIF":6.1,"publicationDate":"2025-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144830604","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
Global dynamics behind enzyme catalysis, evolution, and design 酶催化、进化和设计背后的全球动力学
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-08-12 DOI: 10.1016/j.sbi.2025.103131
Burcu Aykac Fas , Zeynep Erge Akbas Buz , Turkan Haliloglu
{"title":"Global dynamics behind enzyme catalysis, evolution, and design","authors":"Burcu Aykac Fas ,&nbsp;Zeynep Erge Akbas Buz ,&nbsp;Turkan Haliloglu","doi":"10.1016/j.sbi.2025.103131","DOIUrl":"10.1016/j.sbi.2025.103131","url":null,"abstract":"<div><div>Enzymes are inherently dynamic entities, with their functions intricately governed by the interplay between conformational dynamics - ranging from local residue fluctuations to global motions - and biochemical activity. Deciphering how such dynamics coordinate higher-order cooperativity across multiple timescales to drive catalysis remains a fundamental challenge. This mini-review highlights the role of large-scale, collective motions involving domain-level displacements and hinge-based rearrangements, which not only facilitate substrate recognition, transformation, and release, but also emerge from and propagate through multidirectional allosteric interactions. Such dynamic mechanochemical coupling reflects evolutionary memory and provides a blueprint for enzyme design innovations.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"94 ","pages":"Article 103131"},"PeriodicalIF":6.1,"publicationDate":"2025-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144813912","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
Cool and collected: Advances in sample preparation for cryo-electron microscopy. 冷却和收集：低温电子显微镜样品制备的进展。
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-08-09 DOI: 10.1016/j.sbi.2025.103132
Shani Tcherner Elad, Noa Ben-Asher, Leeya Engel
{"title":"Cool and collected: Advances in sample preparation for cryo-electron microscopy.","authors":"Shani Tcherner Elad, Noa Ben-Asher, Leeya Engel","doi":"10.1016/j.sbi.2025.103132","DOIUrl":"https://doi.org/10.1016/j.sbi.2025.103132","url":null,"abstract":"<p><p>Cryo-electron microscopy (cryo-EM) has emerged as a transformative tool in structural biology, enabling high-resolution visualization of macromolecules in their native states. Cryo-focused ion beam milling (cryo-FIB) and other advances in sample preparation have expanded the range of biological samples that can be studied with cryo-EM to include cells and tissues. While the dream of high-resolution structural analysis of proteins within their native, cellular context is now being realized, sample preparation, especially from tissues, is still labor-intensive and technically challenging. Here we review the latest innovations in cryo-EM sample preparation, including support fabrication and functionalization, cell micropatterning, and techniques for thinning frozen biological samples. Beyond streamlining and improving the repeatability of sample preparation, these advances are expanding the impact of cryo-EM by enabling unprecedented visualization of structures within cells and tissues in healthy and diseased states, as well as structural analysis of biological processes at well-controlled time points.</p>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"94 ","pages":"103132"},"PeriodicalIF":6.1,"publicationDate":"2025-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144815961","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
Solid-state NMR of membrane proteins in situ. 原位膜蛋白的固态核磁共振。
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-08-08 DOI: 10.1016/j.sbi.2025.103129
Francesca M Marassi, Guido Pintacuda
{"title":"Solid-state NMR of membrane proteins in situ.","authors":"Francesca M Marassi, Guido Pintacuda","doi":"10.1016/j.sbi.2025.103129","DOIUrl":"10.1016/j.sbi.2025.103129","url":null,"abstract":"<p><p>Membrane proteins have evolved to function as part of specialized biological membranes, and their structures and activities are highly susceptible to their local environment. Detergents and lipid mimetics replicate certain aspects of biological membranes, and have been used to produce an exceptional body of structural data, but do not fully capture the complex, asymmetric properties of the native environment and can alter structure and function. Here, we review recent advances in nuclear magnetic resonance (NMR) that enable the examination of membrane protein structure and activity in situ, within native membranes. The development of optimized protein expression strategies, isotopic labeling schemes, powerful instrumentation and specialized pulse sequences offer new opportunities for exploring the new frontier of in situ structural biology. By outlining the framework for in situ NMR of membrane proteins from conceptualization to experiments we hope to inspire new research in this growing and important area.</p>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"94 ","pages":"103129"},"PeriodicalIF":6.1,"publicationDate":"2025-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12342655/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144811871","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
Advances in native cell membrane nanoparticles system 天然细胞膜纳米颗粒体系的研究进展
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-08-06 DOI: 10.1016/j.sbi.2025.103130
Weihua Qiu , Youzhong Guo
{"title":"Advances in native cell membrane nanoparticles system","authors":"Weihua Qiu ,&nbsp;Youzhong Guo","doi":"10.1016/j.sbi.2025.103130","DOIUrl":"10.1016/j.sbi.2025.103130","url":null,"abstract":"<div><div>The native cell membrane nanoparticles (NCMN) system utilizes membrane-active polymers specifically designed and optimized to extract and stabilize membrane proteins in the form of NCMN particlesfor biochemical and biophysical characterization. The NCMN system is a genuine and advanced detergent-free approach inspired by the membrane activity of the styrene–maleic acid copolymers (SMA), distinguishing it from the nanodisc technology, Salipro technology, and Peptidisc technology. This review introduces the current advancements in the NCMN system, including the development of NCMN polymers, the application of the NCMN system for single-particle cryo-EM analysis, and the functional characterization of membrane proteins.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"94 ","pages":"Article 103130"},"PeriodicalIF":6.1,"publicationDate":"2025-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144781331","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
HIV-1 gp160 in nanodiscs: Unravelling structures and guiding vaccine design 纳米圆盘中的HIV-1 gp160：揭示结构和指导疫苗设计
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-08-05 DOI: 10.1016/j.sbi.2025.103122
Nancy M. Elbaz, Mahmoud L. Nasr
{"title":"HIV-1 gp160 in nanodiscs: Unravelling structures and guiding vaccine design","authors":"Nancy M. Elbaz,&nbsp;Mahmoud L. Nasr","doi":"10.1016/j.sbi.2025.103122","DOIUrl":"10.1016/j.sbi.2025.103122","url":null,"abstract":"<div><div>The stabilization of HIV-1 gp160 trimers (Env) within phospholipid bilayer nanodiscs has provided critical structural insights into the membrane-proximal external region (MPER) and the broader dynamics of gp160. Cryo-EM and molecular simulations reveal that the membrane context preserves the MPER architecture and captures spontaneous trimer asymmetry, as well as ectodomain tilting. These dynamic properties expose vulnerable epitopes that are targeted by broadly neutralizing antibodies (bnAbs). Studies using nanodiscs have highlighted how interactions with the membrane affect the structure of gp160, the accessibility of epitopes, and the mechanisms of neutralization, providing important insights for immunogen design. Unlike soluble SOSIP and IDL constructs, full-length nanodisc-embedded gp160 maintains its native stability, flexibility, and the complete set of neutralization epitopes, suggesting that membrane-mimicking platforms are essential for the rational design of next-generation HIV vaccines targeting conserved regions, such as the MPER.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"94 ","pages":"Article 103122"},"PeriodicalIF":6.1,"publicationDate":"2025-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144772465","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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