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Allosteric modulation of Class B1 G protein-coupled receptor activation and signaling location in the cell 细胞中B1 G类蛋白偶联受体激活和信号定位的变构调节
IF 6.1 2区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-12-01 Epub Date: 2025-10-24 DOI: 10.1016/j.sbi.2025.103170
Jean-Pierre Vilardaga , Satyaki Saha , Ji Young Lee , Lisa J. Clark , Ivet Bahar
It is now widely accepted that allosteric signaling is beyond signal transmission to, or conformational change triggered at, a distal point within a structure; it also affects different cellular pathways and functions depending on the specific allosteric modulators. A family of signaling molecules that has attracted wide attention in recent years is the Class B1 G protein-coupled receptors (GPCRs). In the classic view of GPCR signaling, cyclic adenosine monophosphate (cAMP) production is accepted to be uniquely associated with signaling events at the plasma membrane. However, a growing number of studies over the past decade, especially for the parathyroid hormone type 1 receptor (PTH1R), demonstrate that cAMP is also produced at the endosomes through a different pathway after receptor internalization. Recent advances in the structural and computational characterization of this family of allosteric receptors provide new insights into the mechanisms of their activation or inhibition, as well as determinants of differential allosteric signaling. We focus on PTH1R as a prototypical member of the family and present our current understanding of the role of selected ligands in acting as positive or negative allosteric modulators and eliciting signaling location biases in the cell.
现在被广泛接受的是,变构信号传导超出了信号传递到结构的远端点,或在结构的远端点触发构象变化;它还影响不同的细胞通路和功能取决于特定的变构调节剂。近年来引起广泛关注的一类信号分子是B1类G蛋白偶联受体(gpcr)。在GPCR信号传导的经典观点中,环磷酸腺苷(cAMP)的产生被认为是与质膜上的信号传导事件唯一相关的。然而,近十年来越来越多的研究,特别是对甲状旁腺激素1型受体(PTH1R)的研究表明,cAMP在受体内化后也通过不同的途径在核内体产生。该家族变构受体的结构和计算表征的最新进展为其激活或抑制机制以及差异变构信号传导的决定因素提供了新的见解。我们专注于PTH1R作为家族的一个原型成员,并介绍了我们目前对选择配体在细胞中作为正或负变构调节剂和引发信号定位偏差的作用的理解。
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引用次数: 0
Editorial overview: Protein-nucleic acid interactions: From origins to design 编辑概述:蛋白质-核酸相互作用:从起源到设计。
IF 6.1 2区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-12-01 Epub Date: 2025-11-03 DOI: 10.1016/j.sbi.2025.103184
Elodie Laine, Shandar Ahmad
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引用次数: 0
Rewiring enzyme regulation: Allosteric drugs and predictive tools 重组酶调节:变构药物和预测工具
IF 6.1 2区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-12-01 Epub Date: 2025-09-25 DOI: 10.1016/j.sbi.2025.103159
Vahap Gazi Fidan , Konuralp Ilim , Attila Gursoy , S. Banu Ozkan , Ozlem Keskin
Allosteric modulation offers an increasingly attractive route for precise intervention in enzymatic pathways. This review outlines emerging strategies for the identification and exploitation of allosteric sites, emphasizing computational frameworks that integrate evolutionary, structural, and dynamic features with machine learning models. We discuss how perturbation-based simulations, network analyses, and deep mutational data are reshaping our understanding of allosteric regulation. In parallel, advances in experimental techniques have enabled validation of cryptic and functionally relevant pockets across diverse enzyme families. We further catalog FDA-approved allosteric modulators of enzymes, highlighting therapeutic designs that leverage distal regulation to enhance specificity and overcome resistance. Taken together, these developments reveal the growing utility of allostery in drug design and underscore its potential to expand the therapeutic target space beyond conventional binding sites.
变构调节提供了一个越来越有吸引力的途径,以精确干预酶的途径。本文概述了识别和利用变构位点的新兴策略,强调了将进化、结构和动态特征与机器学习模型相结合的计算框架。我们讨论了基于微扰的模拟、网络分析和深层突变数据如何重塑我们对变构调节的理解。与此同时,实验技术的进步已经能够验证不同酶家族的隐性和功能相关口袋。我们进一步对fda批准的酶的变构调节剂进行分类,强调利用远端调节来增强特异性和克服耐药性的治疗设计。综上所述,这些发展揭示了变构在药物设计中的日益增长的效用,并强调了它在传统结合位点之外扩大治疗靶点空间的潜力。
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引用次数: 0
Strategies for studying discrete heterogeneity in situ using cryo-electron tomography 利用低温电子断层成像技术研究原位离散非均质性的策略。
IF 6.1 2区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-12-01 Epub Date: 2025-11-12 DOI: 10.1016/j.sbi.2025.103186
Alberto Bartesaghi
Structural variability plays a crucial role in enabling biological function, as the ability of proteins to adopt multiple conformations allows them to perform diverse cellular tasks. Cryo-electron tomography combined with subtomogram averaging and classification has emerged as a powerful technique for elucidating the conformational dynamics of proteins in their near-native environment. Increased data availability has provided a driving force for improvements in image classification algorithms which have enabled conformational heterogeneity studies of proteins in situ at higher resolutions than previously possible. In particular, the use of 2D particle projections extracted from raw tilt-series paired with constrained classification strategies of projection sets has emerged as a promising strategy for classifying particles in 3D. Despite these efforts, further method development will be needed to extend the applicability of current strategies for 3D classification to more challenging biological targets, including low-molecular weight complexes and membrane proteins.
结构变异性在实现生物功能方面起着至关重要的作用,因为蛋白质采用多种构象的能力使它们能够执行不同的细胞任务。低温电子断层扫描结合亚断层平均和分类已经成为一种强大的技术,用于阐明蛋白质在其接近天然环境中的构象动力学。数据可用性的增加为图像分类算法的改进提供了动力,这使得原位蛋白质的构象异质性研究能够以比以前更高的分辨率进行。特别是,利用从原始倾斜序列中提取的2D粒子投影与投影集的约束分类策略相结合,已经成为一种很有前途的3D粒子分类策略。尽管有这些努力,需要进一步的方法开发来扩展当前3D分类策略对更具挑战性的生物靶标的适用性,包括低分子量复合物和膜蛋白。
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引用次数: 0
Regulation of receptor tyrosine kinase hetero-interactions 受体酪氨酸激酶异质相互作用的调控。
IF 6.1 2区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-12-01 Epub Date: 2025-11-12 DOI: 10.1016/j.sbi.2025.103187
Adam W. Smith , Francisco N. Barrera
Receptor tyrosine kinases (RTKs) control myriads of cellular functions. RTKs are paradigmatic examples of receptors where activity is directly dependent on quaternary structure. In most cases, the monomeric RTK is inactive, and function arises only after a ligand binding event leads the RTK to bind to another copy of itself, activating trans-autophosphorylation of tyrosine residues. Such RTK homodimerization can be accompanied by the formation of homomers of higher stoichiometry. However, RTK monomers can also bind to a second type of RTK, forming heterodimers. RTK heteromerization is believed to result in different signaling than homomerization. Despite its importance, we have a poor understanding of the factors that define if an RTK will form homomers or heteromers. This short review covers recent discoveries on the heteromerization of RTK, in what is called the RTK interactome. We discuss its translational potential, and how ligands and membrane lipids affect heteromer formation.
受体酪氨酸激酶(rtk)控制着无数的细胞功能。rtk是活性直接依赖于四级结构的受体的典型例子。在大多数情况下,单体RTK是无活性的,只有在配体结合事件导致RTK与自身的另一个拷贝结合,激活酪氨酸残基的反式自磷酸化后,才会产生功能。这种RTK同二聚化可以伴随着更高化学计量的同聚体的形成。然而,RTK单体也可以与第二种类型的RTK结合,形成异源二聚体。RTK异质化被认为与同源化产生不同的信号。尽管它很重要,但我们对定义RTK是否会形成同质体或异质体的因素了解甚少。这篇简短的综述涵盖了RTK异聚的最新发现,即所谓的RTK相互作用组。我们讨论了它的翻译潜力,以及配体和膜脂如何影响异构体的形成。
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引用次数: 0
Old and new tactics of CRISPR-centric competition between bacteria and bacteriophages 细菌和噬菌体之间以crispr为中心的竞争的新旧策略。
IF 6.1 2区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-12-01 Epub Date: 2025-10-15 DOI: 10.1016/j.sbi.2025.103168
Iktae Kim , Jeong-Yong Suh
The CRISPR-Cas system provides adaptive immunity for prokaryotes against mobile genetic elements (MGEs) such as bacteriophages and plasmids. As a countermeasure, MGEs have evolved various anti-CRISPR (Acr) mechanisms that neutralize the CRISPR-mediated immunity. Canonical Acr proteins block target binding of Cas proteins in a stoichiometric or enzymatic manner. New findings reveal that Acr also disintegrates functional Cas complexes, induces promiscuous target binding, and mimics Cas proteins and crRNA with defective mutations. Here, we summarize a broad repertoire of structural and functional mechanisms underlying CRISPR-centric competition, highlighting recent discoveries of molecular machinery that modulates CRISPR function.
CRISPR-Cas系统为原核生物提供了针对移动遗传元件(MGEs)(如噬菌体和质粒)的适应性免疫。作为对策,MGEs进化出各种抗crispr (Acr)机制来中和crispr介导的免疫。典型Acr蛋白以化学计量学或酶促的方式阻断Cas蛋白的靶结合。新的研究结果表明,Acr还能分解功能性Cas复合物,诱导混杂靶标结合,并模拟Cas蛋白和crRNA的缺陷突变。在这里,我们总结了以CRISPR为中心的竞争背后的广泛的结构和功能机制,重点介绍了最近发现的调节CRISPR功能的分子机制。
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引用次数: 0
The influence of lipids and biological membranes on the conformational equilibria of GPCRs: Insights from NMR spectroscopy 脂质和生物膜对gpcr构象平衡的影响:来自核磁共振光谱的见解
IF 6.1 2区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-10-01 Epub Date: 2025-06-27 DOI: 10.1016/j.sbi.2025.103103
Greeshma Jain, Matthew T. Eddy
G protein-coupled receptors (GPCRs) function within cellular membranes, complex and dynamic environments. Rather than serving as a passive background, lipid membranes actively influence GPCR drug responses and signaling. Studies utilizing nuclear magnetic resonance (NMR) spectroscopy have revealed key insights into receptor–lipid interactions, enabled by the compatibility of NMR experiments with many different membrane systems and physiological temperature, conditions more closely reflecting the native cellular environment. NMR data have revealed new mechanistic insights that explain how specific lipids regulate GPCR activation, how bulk membrane properties influence receptor dynamics, and how different membrane mimetics affect GPCR behavior. These findings establish a framework for bridging in vitro structural studies with in vivo biological and pharmacological data.
G蛋白偶联受体(gpcr)在细胞膜、复杂和动态环境中起作用。而不是作为一个被动的背景,脂质膜积极影响GPCR药物反应和信号。利用核磁共振(NMR)光谱学的研究揭示了受体-脂质相互作用的关键见解,通过核磁共振实验与许多不同的膜系统和生理温度的兼容性,更紧密地反映了天然细胞环境。核磁共振数据揭示了新的机制见解,解释了特定脂质如何调节GPCR激活,大块膜特性如何影响受体动力学,以及不同的膜模拟物如何影响GPCR行为。这些发现为连接体外结构研究与体内生物学和药理学数据建立了框架。
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引用次数: 0
Editorial overview: Protein folding and binding — With a little help from AI 编辑概述:蛋白质折叠和结合-与人工智能的一点帮助
IF 6.1 2区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-10-01 Epub Date: 2025-06-23 DOI: 10.1016/j.sbi.2025.103068
Yana Bromberg, Benjamin Schuler
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引用次数: 0
Recent advances in quantifying protein conformational ensembles with dipolar EPR spectroscopy 偶极EPR光谱定量蛋白质构象群的最新进展
IF 6.1 2区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-10-01 Epub Date: 2025-08-23 DOI: 10.1016/j.sbi.2025.103139
Reza Dastvan , Stefan Stoll
This perspective highlights recent applications and technological progress in dipolar electron paramagnetic resonance (EPR) spectroscopy, including double electron–electron resonance (DEER) spectroscopy. These methods provide nanoscale distance distributions between site-specific spin labels in biomacromolecules. The resulting data are particularly well suited for quantifying the structure and energetics of conformational ensembles of multi-state and flexible proteins. Recent applications span a wide range of systems and are accompanied by innovations in spin labeling, deuteration, in-cell measurements, integrative multi-technique approaches, and novel computational modeling methods combined with structure prediction tools.
本文重点介绍了偶极电子顺磁共振(EPR)光谱学,包括双电子-电子共振(DEER)光谱学的最新应用和技术进展。这些方法提供了生物大分子中位点特异性自旋标记之间的纳米级距离分布。所得数据特别适合于量化多态和柔性蛋白质的构象集合体的结构和能量学。最近的应用跨越了广泛的系统,并伴随着自旋标记、氘化、细胞内测量、综合多技术方法和结合结构预测工具的新型计算建模方法的创新。
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引用次数: 0
Cryo-focused ion beam milling for cryo-electron tomography: Shaping the future of in situ structural biology 低温聚焦离子束铣削用于低温电子断层扫描:塑造原位结构生物学的未来
IF 6.1 2区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-10-01 Epub Date: 2025-08-22 DOI: 10.1016/j.sbi.2025.103138
Sven Klumpe , Jürgen M. Plitzko
Cryo-focused ion beam instruments to produce cellular thin sections for subsequent imaging by cryo-electron tomography have become an integral part of the methodologies for in situ structural biology, enabling high-resolution imaging of biological structures in their native environment. The application of these instruments has opened windows into cells that allowed unprecedented insights into the ultrastructure of cells and more recently, small multicellular organisms and tissues. While great strides have been made in the characterization of cryo-FIB milling and the streamlining of workflows with these tools, many limitations and technical challenges remain to be resolved. Here, we discuss the technical and technological challenges ahead to continue the steep rise of biological discoveries by in-cell cryo-electron tomography to enable cellular structural biology in the multicellular context.
低温聚焦离子束仪器为随后的低温电子断层成像生产细胞薄切片,已经成为原位结构生物学方法的一个组成部分,使生物结构在其原生环境中的高分辨率成像成为可能。这些仪器的应用为研究细胞打开了一扇窗,使我们能够前所未有地深入了解细胞的超微结构,以及最近的小型多细胞生物和组织。虽然在低温fib铣削表征和使用这些工具简化工作流程方面取得了很大进展,但仍有许多限制和技术挑战有待解决。在这里,我们讨论了未来的技术和技术挑战,以继续通过细胞内低温电子断层扫描来实现多细胞环境下的细胞结构生物学的生物学发现。
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引用次数: 0
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Current opinion in structural biology
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