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Current opinion in structural biology最新文献

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Emerging paradigms in the lateral and transverse organization in biological membrane and their functional implications: Connecting the dots with biomolecular simulations 生物膜横向和横向组织的新范式及其功能含义：用生物分子模拟连接点
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-07-31 DOI: 10.1016/j.sbi.2025.103128
Anand Srivastava
{"title":"Emerging paradigms in the lateral and transverse organization in biological membrane and their functional implications: Connecting the dots with biomolecular simulations","authors":"Anand Srivastava","doi":"10.1016/j.sbi.2025.103128","DOIUrl":"10.1016/j.sbi.2025.103128","url":null,"abstract":"<div><div>Since the publication of the first papers in the early 1990s, molecular simulation as a reliable biophysical tool in the area of membrane biophysics has come a long way. Advances in simulation algorithms, coupled with exascale computing have pushed the size and time scales of biomolecular membrane simulations to scales where connections to experiments are made with higher fidelity. When integrated with experimental data in a theoretically well-grounded manner, current biomolecular simulations are providing indispensable insights that cannot be obtained through experiments alone. Here, I summarize some recent developments where simulations have allowed a deeper understanding in membrane spatiotemporal organization. I also discuss the need for transformative method developments to meet recent breakthroughs in experimental measurements at molecular scales.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"94 ","pages":"Article 103128"},"PeriodicalIF":6.1,"publicationDate":"2025-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144739059","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 of 3D genome chromatin organization and regulation 编辑概述三维基因组染色质组织和调控
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-07-30 DOI: 10.1016/j.sbi.2025.103123
Yuan He, Yawen Bai
{"title":"Editorial overview of 3D genome chromatin organization and regulation","authors":"Yuan He,&nbsp;Yawen Bai","doi":"10.1016/j.sbi.2025.103123","DOIUrl":"10.1016/j.sbi.2025.103123","url":null,"abstract":"","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"94 ","pages":"Article 103123"},"PeriodicalIF":6.1,"publicationDate":"2025-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144724691","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
Approaches for regulating enzyme activities: Recent advances in experiment and computation 调节酶活性的方法：实验和计算的最新进展
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-07-29 DOI: 10.1016/j.sbi.2025.103124
Qiang Cui
{"title":"Approaches for regulating enzyme activities: Recent advances in experiment and computation","authors":"Qiang Cui","doi":"10.1016/j.sbi.2025.103124","DOIUrl":"10.1016/j.sbi.2025.103124","url":null,"abstract":"<div><div>Major progress has been made in recent years in terms of strategies for regulating enzyme activities. Novel high-throughput enzyme kinetic assays and efficient computational methodologies enabled a deeper understanding of molecular mechanisms that dictate the activity of enzymes, which provide guidance to rational modulation of enzyme catalysis. Continued development of efficient screening, directed evolution technologies, and machine learning–driven protein engineering tools make it possible to tune enzyme activities without having to understand the detailed mechanism of catalysis regulation. By combining these two limiting approaches, the efficiency of enzyme regulation can be substantially improved as a mechanistic understanding can help reduce the size of design space before the ‘brute-force’ engineering approach takes over. We briefly discuss relevant advances in both experiment and computation and comment on future developments that can further enhance mechanistic understanding and engineering capability for broad applications.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"94 ","pages":"Article 103124"},"PeriodicalIF":6.1,"publicationDate":"2025-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144724690","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
A to-do list for realizing the sequence-to-function paradigm of proteins 实现蛋白质从序列到功能范式的待办事项清单
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-07-17 DOI: 10.1016/j.sbi.2025.103119
Chun Kit Chan , Christine Rajarigam , Patrick Jiang , Jacob Miratsky , Mustafa Demir , Melih Sener , Abhishek Singharoy
{"title":"A to-do list for realizing the sequence-to-function paradigm of proteins","authors":"Chun Kit Chan ,&nbsp;Christine Rajarigam ,&nbsp;Patrick Jiang ,&nbsp;Jacob Miratsky ,&nbsp;Mustafa Demir ,&nbsp;Melih Sener ,&nbsp;Abhishek Singharoy","doi":"10.1016/j.sbi.2025.103119","DOIUrl":"10.1016/j.sbi.2025.103119","url":null,"abstract":"<div><div>It has been a longstanding dream of the structural biology and molecular biophysics communities to determine protein functions directly from the amino acid sequences. Most methods available today, however, are homology- or library-based and often undermine determining divergent functions from comparable sequences or vice versa. The sequence-to-function relationship is intrinsically dependent on the biophysical space of protein dynamics, which can be potentially exploited to annotate function. But, despite three decades of active research, the space of molecular dynamics data remains grossly underpopulated. By employing surveys of the existing literature, we highlight this gray area in the context of machine learning methods. Thereafter, we share examples that point toward learning biophysical representations—or signatures—and combining them with integrative models as means to robustly associate sequence with function. The aim is to avoid having to compute protein dynamics for an impossible thousand years to achieve data completeness and generalization.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"93 ","pages":"Article 103119"},"PeriodicalIF":6.1,"publicationDate":"2025-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144657182","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: Toward cellular-scale modeling: Bigger and disordered 编辑概述：向细胞尺度建模：更大和混乱
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-07-17 DOI: 10.1016/j.sbi.2025.103121
Yuji Sugita, Robert J. Woods
{"title":"Editorial overview: Toward cellular-scale modeling: Bigger and disordered","authors":"Yuji Sugita,&nbsp;Robert J. Woods","doi":"10.1016/j.sbi.2025.103121","DOIUrl":"10.1016/j.sbi.2025.103121","url":null,"abstract":"","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"93 ","pages":"Article 103121"},"PeriodicalIF":6.1,"publicationDate":"2025-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144657183","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
Multicolor single-molecule FRET studies on dynamic protein systems 动态蛋白质系统的多色单分子FRET研究
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-07-14 DOI: 10.1016/j.sbi.2025.103117
Ecenaz Bilgen, Don C. Lamb
{"title":"Multicolor single-molecule FRET studies on dynamic protein systems","authors":"Ecenaz Bilgen,&nbsp;Don C. Lamb","doi":"10.1016/j.sbi.2025.103117","DOIUrl":"10.1016/j.sbi.2025.103117","url":null,"abstract":"<div><div>Förster resonance energy transfer (FRET) is a powerful tool for studying protein conformations, interactions, and dynamics at the single-molecule level. Multicolor FRET extends conventional two-color FRET by incorporating three or more fluorophores and thereby enabling a more comprehensive view of complex biomolecular processes. This technique allows for the simultaneous tracking of multiple structural changes, detecting intermediate states, and resolving heterogeneous population distributions. In this review, we discuss the recent advancements in fluorophore labeling strategies and data analysis methods that have significantly improved the precision and applicability of multicolor FRET in protein studies. We then end this review by showcasing recent applications for investigating protein folding and processes involved in gene regulation.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"93 ","pages":"Article 103117"},"PeriodicalIF":6.1,"publicationDate":"2025-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144631193","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
Probing molecular and biophysical mechanisms of RNA and protein phase transitions with simulations and theory 用模拟和理论探索RNA和蛋白质相变的分子和生物物理机制
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-07-14 DOI: 10.1016/j.sbi.2025.103120
Pin Yu Chew , Rosana Collepardo-Guevara
{"title":"Probing molecular and biophysical mechanisms of RNA and protein phase transitions with simulations and theory","authors":"Pin Yu Chew ,&nbsp;Rosana Collepardo-Guevara","doi":"10.1016/j.sbi.2025.103120","DOIUrl":"10.1016/j.sbi.2025.103120","url":null,"abstract":"<div><div>Biomolecular condensates play crucial roles in cellular organisation, regulating diverse biological functions as well as contributing to disease pathologies when phase separation is dysregulated. Computer simulations and theoretical approaches have emerged as powerful tools to probe the molecular mechanisms governing phase transitions in these systems. This review highlights recent advancements in computational methods, focusing on coarse-grained and all-atom molecular dynamics simulations, to elucidate the driving forces underlying protein and RNA condensate formation and how their stability and material properties can be regulated and tuned. Additionally, we address new strategies for designing synthetic condensates with tunable properties and leveraging predictive models to guide experimental studies. The integration of molecular simulations, with data-driven approaches and theory, has expanded our understanding of biomolecular condensates, offering novel insights into both fundamental biology and physics, as well as potential practical applications.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"93 ","pages":"Article 103120"},"PeriodicalIF":6.1,"publicationDate":"2025-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144614740","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
Are N-linked glycans intrinsically disordered? n链聚糖本质上是无序的吗？
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-07-10 DOI: 10.1016/j.sbi.2025.103118
Eliza Gazaway , Rajan Kandel , Oliver C. Grant, Robert J. Woods
{"title":"Are N-linked glycans intrinsically disordered?","authors":"Eliza Gazaway ,&nbsp;Rajan Kandel ,&nbsp;Oliver C. Grant,&nbsp;Robert J. Woods","doi":"10.1016/j.sbi.2025.103118","DOIUrl":"10.1016/j.sbi.2025.103118","url":null,"abstract":"<div><div>The covalent attachment of oligosaccharides to asparagine side chains on protein surfaces (<em>N-</em>linked glycosylation) is a ubiquitous modification that is critical to protein stability and function. Experimental 3D structures of glycoproteins in which the <em>N-</em>linked glycans are well resolved are rare due to both the presumed flexibility of the <em>N-</em>linked glycan and to glycan microheterogeneity. To surmount these limitations, computational modeling is often applied to glycoproteins, particularly to generate an ensemble of 3D shapes for the <em>N-</em>linked glycans. While the number of glycoprotein modelling tools continues to expand, the available experimental data against which the predictions can be validated remains extremely limited. Here, we present our current understanding of the dynamic properties of <em>N-</em>linked glycans, with a particular focus on features that impact their presentation (orientation) relative to the protein surface. Additionally, we review the limits of experimental and theoretical studies of glycoproteins, and ask the question, “Are <em>N-</em>linked glycans intrinsically disordered?”.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"93 ","pages":"Article 103118"},"PeriodicalIF":6.1,"publicationDate":"2025-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144595750","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
Segmenting cryo-electron tomography data: Extracting models from cellular landscapes 分割低温电子断层扫描数据：从细胞景观中提取模型
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-07-10 DOI: 10.1016/j.sbi.2025.103114
Danielle A. Grotjahn
{"title":"Segmenting cryo-electron tomography data: Extracting models from cellular landscapes","authors":"Danielle A. Grotjahn","doi":"10.1016/j.sbi.2025.103114","DOIUrl":"10.1016/j.sbi.2025.103114","url":null,"abstract":"<div><div>Cryo-electron tomography provides an unprecedented view of cellular architecture, yet extracting meaningful biological insights remains challenging. Segmentation is a crucial step in this process through its ability to identify structural relationships between subcellular components visible in cryo-electron tomography data. While segmentation pipelines were historically low throughput, recent advancements in deep learning have significantly improved their automation, accuracy, and scalability. This review explores how these innovations redefine best practices for segmentation and accelerate biological discovery. This article highlights the critical role of segmentation in unlocking the full potential of cryo-electron tomography—not only for resolving macromolecular structures but also for quantifying their impact on subcellular organization and function.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"93 ","pages":"Article 103114"},"PeriodicalIF":6.1,"publicationDate":"2025-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144595471","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
Cryo-electron tomography: Challenges and computational strategies for particle picking 低温电子断层扫描：粒子拾取的挑战和计算策略
IF 6.1 2区 生物学
Current opinion in structural biology Pub Date : 2025-07-09 DOI: 10.1016/j.sbi.2025.103113
Thorsten Wagner, Stefan Raunser
{"title":"Cryo-electron tomography: Challenges and computational strategies for particle picking","authors":"Thorsten Wagner,&nbsp;Stefan Raunser","doi":"10.1016/j.sbi.2025.103113","DOIUrl":"10.1016/j.sbi.2025.103113","url":null,"abstract":"<div><div>Cryo-electron tomography (cryo-ET) and subtomogram averaging have emerged as powerful techniques for investigating cellular structures and their spatial organization. However, the exact localization of proteins in the crowded and noisy environment of cellular tomograms is challenging. This review provides a comprehensive overview of existing deep learning-based particle-picking procedures, which were proposed to overcome these challenges. We evaluate both annotation-based and annotation-free methods, highlighting their respective strengths, weaknesses, and ideal use cases. Furthermore, we assess these methodologies based on various criteria, such as the effort required to generate the necessary input data, inference runtime, and filament support. Additionally, we consider practical factors such as the availability of documentation and tutorials to guide researchers in selecting the most appropriate approach for their needs.</div></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"93 ","pages":"Article 103113"},"PeriodicalIF":6.1,"publicationDate":"2025-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144588940","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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