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Evolution of protein-RNA interactions 蛋白质- rna相互作用的进化
IF 6.1 2区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY
Current opinion in structural biology
Pub Date : 2025-10-01 Epub Date: 2025-07-07 DOI: 10.1016/j.sbi.2025.103109
Michal H. Kolář , Klára Hlouchová
Since the Hadean–Eoarchaean era of Earth’s history, peptides/proteins and RNA have undergone a complex evolutionary trajectory. Originating from simple monomeric units, these molecules evolved abiotically under various biochemical and biophysical constraints into functional biomolecules that contributed to the emergence of the first living cells. Within these cells, their interactions could then evolve through Darwinian selection. In this review, we examine current understanding of how protein–RNA interactions emerged under prebiotic conditions and developed into today’s iconic biomolecular machines such as the ribosome. Particular emphasis is placed on the types of physicochemical interactions accessible to early protein–RNA complexes. Special attention is given to how the limited prebiotic amino acid repertoire influenced these interactions and their roles in driving spatial organization and compartmentalization in protocellular environments.
自地球历史的冥古宙-太古代以来，肽/蛋白质和RNA经历了一个复杂的进化轨迹。这些分子起源于简单的单体单位，在各种生物化学和生物物理限制下非生物地进化成具有功能的生物分子，促成了第一批活细胞的出现。在这些细胞内，它们之间的相互作用可以通过达尔文选择进化。在这篇综述中，我们研究了目前对蛋白质- rna相互作用如何在益生元条件下出现并发展成今天标志性的生物分子机器（如核糖体）的理解。特别强调的是早期蛋白质- rna复合物的物理化学相互作用的类型。特别关注有限的益生元氨基酸库如何影响这些相互作用及其在驱动原细胞环境中的空间组织和区隔化中的作用。
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引用次数: 0
Frustration, dynamics, and catalysis 挫折，动力和催化
IF 6.1 2区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY
Current opinion in structural biology
Pub Date : 2025-10-01 Epub Date: 2025-08-05 DOI: 10.1016/j.sbi.2025.103127
R. Gonzalo Parra , Diego U. Ferreiro
The controlled dissipation of chemical potentials is the fundamental way cells make a living. Enzyme-mediated catalysis allows the various transformations to proceed at biologically relevant rates with remarkable precision and efficiency. Theory, experiments, and computational studies coincide to show that local frustration is a useful concept to relate protein dynamics with catalytic power. Local frustration gives rise to the asperities of the energy landscapes that can harness the thermal fluctuations to guide the functional protein motions. We review here recent advances into these relationships from various fields of protein science. The biologically relevant dynamics is tuned by the evolution of protein sequences that modulate local frustration patterns to near-optimal values.
控制化学势的耗散是细胞生存的基本方式。酶介导的催化使各种转化以生物学相关的速度进行，具有显著的精度和效率。理论、实验和计算研究一致表明，局部挫折是一个有用的概念，将蛋白质动力学与催化力联系起来。局部挫折导致能量景观的凹凸不平，可以利用热波动来指导功能性蛋白质的运动。在此，我们回顾了蛋白质科学各个领域对这些关系的最新进展。生物相关的动态是通过蛋白质序列的进化来调节局部挫折模式到接近最佳值。
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引用次数: 0
Optogenetic enzymes: A deep dive into design and impact 光遗传酶：深入研究设计和影响
IF 6.1 2区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY
Current opinion in structural biology
Pub Date : 2025-10-01 Epub Date: 2025-08-05 DOI: 10.1016/j.sbi.2025.103126
Tanaya Basu Roy , Mana Heidari , Nikolay V. Dokholyan
Optogenetically regulated enzymes offer unprecedented spatiotemporal control over protein activity, intermolecular interactions, and intracellular signaling. Many design strategies have been developed for their fabrication based on the principles of intrinsic allostery, oligomerization or ‘split’ status, intracellular compartmentalization, and steric hindrance. In addition to employing photosensory domains as part of the traditional optogenetic toolset, the specificity of effector domains has also been leveraged for endogenous applications. Here, we discuss the dynamics of light activation while providing a bird's eye view of the crafting approaches, targets, and impact of optogenetic enzymes in orchestrating cellular functions, as well as the bottlenecks and an outlook into the future.
光遗传学调节酶提供了前所未有的时空控制蛋白质活性，分子间相互作用和细胞内信号。基于内在变构、寡聚或“分裂”状态、细胞内区隔化和空间位阻的原理，已经开发了许多设计策略。除了利用光敏结构域作为传统光遗传学工具集的一部分外，效应结构域的特异性也被用于内源性应用。在这里，我们讨论了光激活的动力学，同时提供了制作方法，目标和光遗传酶在协调细胞功能中的影响的鸟瞰图，以及瓶颈和对未来的展望。
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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 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY
Current opinion in structural biology
Pub Date : 2025-10-01 Epub Date: 2025-08-06 DOI: 10.1016/j.sbi.2025.103130
Weihua Qiu , Youzhong Guo
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.
天然细胞膜纳米颗粒（NCMN）系统利用专门设计和优化的膜活性聚合物，以NCMN颗粒的形式提取和稳定膜蛋白，用于生化和生物物理表征。NCMN系统是一种真正先进的无洗涤剂方法，其灵感来自于苯乙烯-马来酸共聚物（SMA）的膜活性，将其与纳米盘技术、Salipro技术和肽盘技术区分开来。本文介绍了NCMN系统的最新进展，包括NCMN聚合物的发展，NCMN系统在单颗粒低温电镜分析中的应用，以及膜蛋白的功能表征。
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引用次数: 0
HDX-MS in micelles and membranes for small molecule and biopharmaceutical development 用于小分子和生物制药开发的胶束和膜中的HDX-MS
IF 6.1 2区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY
Current opinion in structural biology
Pub Date : 2025-10-01 Epub Date: 2025-06-06 DOI: 10.1016/j.sbi.2025.103077
Charlotte Guffick , Argyris Politis
While protein characterisation is critical for continuing drug discovery and development, many techniques fall short of capturing the range of conformational dynamics that underpin the targeted protein activity. Hydrogen–deuterium exchange mass spectrometry (HDX-MS) is a powerful tool for investigation of protein structural dynamics, particularly for membrane proteins in different mimetic environments. This measurement of intrinsic protein behaviour is invaluable in outlining pathogenic protein dynamics, protein–ligand profiles, and druggable protein centres that are often inaccessible in other structural techniques. This minireview will cover how recent advances have been applied to HDX-MS of membrane proteins and peptides widening the use of HDX for drug discovery.
虽然蛋白质表征对于持续的药物发现和开发至关重要，但许多技术无法捕获支撑靶向蛋白质活性的构象动力学范围。氢-氘交换质谱（HDX-MS）是研究蛋白质结构动力学，特别是膜蛋白在不同模拟环境中的强大工具。这种内在蛋白质行为的测量在概述致病性蛋白质动力学、蛋白质配体谱和其他结构技术通常无法获得的可药物蛋白质中心方面是无价的。这篇小型综述将涵盖最近的进展如何应用于膜蛋白和肽的HDX- ms，扩大HDX在药物发现中的应用。
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引用次数: 0
Fuzziness in enzymatic catalysis 酶催化的模糊性
IF 6.1 2区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY
Current opinion in structural biology
Pub Date : 2025-08-01 Epub Date: 2025-06-27 DOI: 10.1016/j.sbi.2025.103106
Sachin S. Katti , Tvesha Parikh , Rachel J. Godek , Rebecca Page , Wolfgang Peti
Intrinsically disordered proteins/regions (IDPs/IDRs) frequently engage in dynamic charge:charge interactions, commonly referred to as ‘fuzzy’ interactions. These fuzzy interactions play critical roles in enzymatic regulation and substrate recruitment, especially for protein kinases and protein phosphatases. Here, we review recent advances that demonstrate how inter- and intramolecular fuzzy interactions among kinases and phosphatases and their cognate regulators and substrates allow for enzyme assembly, activation and substrate recruitment. We also highlight a unique mechanism of protein inhibition, where a protein phosphatase is inhibited by dynamic fuzzy interactions with its active site metals.
内在无序蛋白质/区域（IDPs/IDRs）经常参与动态电荷相互作用，通常被称为“模糊”相互作用。这些模糊的相互作用在酶调节和底物招募中起着关键作用，特别是对于蛋白激酶和蛋白磷酸酶。在这里，我们回顾了最近的进展，证明了激酶和磷酸酶及其同源调节剂和底物之间的分子间和分子内模糊相互作用如何允许酶组装，激活和底物募集。我们还强调了蛋白质抑制的独特机制，其中蛋白质磷酸酶通过与其活性位点金属的动态模糊相互作用被抑制。
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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 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY
Current opinion in structural biology
Pub Date : 2025-08-01 Epub Date: 2025-07-14 DOI: 10.1016/j.sbi.2025.103117
Ecenaz Bilgen, Don C. Lamb
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.
Förster共振能量转移（FRET）是在单分子水平上研究蛋白质构象，相互作用和动力学的强大工具。多色FRET扩展传统的双色FRET纳入三个或更多的荧光团，从而使复杂的生物分子过程的更全面的看法。该技术允许同时跟踪多个结构变化，检测中间状态，并解决异质种群分布。在这篇综述中，我们讨论了荧光团标记策略和数据分析方法的最新进展，这些方法显著提高了多色FRET在蛋白质研究中的精度和适用性。然后，我们通过展示研究蛋白质折叠和基因调控过程的最新应用来结束这一综述。
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引用次数: 0
In situ cryo-electron microscopy and tomography of cellular and organismal samples 细胞和有机体样品的原位冷冻电子显微镜和断层扫描
IF 6.1 2区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY
Current opinion in structural biology
Pub Date : 2025-08-01 Epub Date: 2025-06-04 DOI: 10.1016/j.sbi.2025.103076
Parijat Majumder , Peijun Zhang
As cryo-electron microscopy (cryo-EM) and cryo-electron tomography (cryo-ET) continue to advance, the ability to visualize cellular and organismal structures with unprecedented clarity is redefining the landscape of structural biology. Breakthroughs in imaging technology, sample preparation and image processing now enable the detailed elucidation of cellular architecture, macromolecular organization, and dynamic biological processes at sub-nanometer resolution. Recent methodological advances have propelled the field to new frontiers, facilitating the investigation of complex biological questions across scales—from macromolecular complexes to organism-wide structural insights. This review explores rapidly emerging trends, highlights key innovations that are pushing the boundaries of in situ structural biology, and addresses persistent challenges in expanding the applicability of cryo-EM and cryo-ET across diverse biological systems.
随着低温电子显微镜（cryo-EM）和低温电子断层扫描（cryo-ET）的不断进步，以前所未有的清晰度可视化细胞和生物体结构的能力正在重新定义结构生物学的景观。在成像技术、样品制备和图像处理方面的突破，现在可以在亚纳米分辨率下详细阐明细胞结构、大分子组织和动态生物过程。最近的方法进步将该领域推向了新的前沿，促进了跨尺度复杂生物学问题的研究——从大分子复合物到整个生物体的结构见解。这篇综述探讨了快速出现的趋势，强调了推动原位结构生物学边界的关键创新，并解决了在扩大低温电镜和低温电镜在不同生物系统中的适用性方面的持续挑战。
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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 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY
Current opinion in structural biology
Pub Date : 2025-08-01 Epub Date: 2025-07-09 DOI: 10.1016/j.sbi.2025.103113
Thorsten Wagner, Stefan Raunser
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.
低温电子断层扫描（cryo-ET）和亚层析成像平均已经成为研究细胞结构及其空间组织的有力技术。然而，在拥挤和嘈杂的细胞断层摄影环境中精确定位蛋白质是具有挑战性的。这篇综述全面概述了现有的基于深度学习的粒子拾取程序，这些程序是为了克服这些挑战而提出的。我们评估了基于注释和无注释的方法，突出了它们各自的优点、缺点和理想用例。此外，我们根据各种标准评估这些方法，例如生成必要的输入数据、推理运行时和灯丝支持所需的工作量。此外，我们考虑实际因素，如文件和教程的可用性，以指导研究人员选择最适合他们需要的方法。
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引用次数: 0
Photo-crosslinkers boost structural information from crosslinking mass spectrometry 光交联剂提高结构信息从交联质谱
IF 6.1 2区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY
Current opinion in structural biology
Pub Date : 2025-08-01 Epub Date: 2025-07-04 DOI: 10.1016/j.sbi.2025.103102
Anthony Ciancone, Francis J. O'Reilly
Crosslinking mass spectrometry has emerged as a powerful tool in structural biology. This technology utilizes chemical crosslinkers to capture spatial proximities between protein residues to probe the organization, stoichiometry, and flexibility of protein assemblies under near-native conditions. Photo-crosslinking reagents have become increasingly used in crosslinking MS, with chemical properties that offer significant advantages when studying dynamic protein structures. This review explores the fundamentals, applications, and future potential of photo-crosslinkers in crosslinking mass spectrometry.
交联质谱法已成为结构生物学研究的有力工具。该技术利用化学交联剂捕获蛋白质残基之间的空间接近度，以探测在接近天然条件下蛋白质组装的组织、化学计量和灵活性。光交联试剂在交联质谱中的应用越来越广泛，其化学性质为研究动态蛋白质结构提供了显著的优势。本文综述了光交联剂在交联质谱分析中的基本原理、应用及发展前景。
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引用次数: 0
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