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Nickel-NTA lipid-monolayer affinity grids allow for high-resolution structure determination by cryo-EM 镍- nta脂质单层亲和栅格允许通过低温电镜高分辨率结构测定。
IF 2.7 3区 生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-10-11 DOI: 10.1016/j.jsb.2025.108253
Aleksandra Skrajna , Clara Lenger , Emily Robinson , Kevin Cannon , Reta Sarsam , Richard G. Ouellette , Alberta M. Abotsi , Patrick Brennwald , Robert K. McGinty , Joshua D. Strauss , Richard W. Baker
Grid preparation is a rate-limiting step in determining high-resolution structures by single particle cryo-EM. Particle interaction with the air–water interface often leads to denaturation, aggregation, or a preferred orientation within the ice. Some samples yield insufficient quantities of particles when using traditional grid making techniques and require the use of solid supports that concentrate samples onto the grid. Recent advances in grid-preparation show that affinity grids are promising tools to selectively concentrate proteins while simultaneously protecting samples from the air–water interface. One such technique utilizes lipid monolayers containing a lipid species with an affinity handle. Some of the first affinity grids used a holey carbon layer coated with nickel nitrilotriacetic acid (Ni-NTA) lipid, which allowed for the binding of proteins bearing the commonly used poly-histidine affinity tag. These studies however used complicated protocols and were conducted before the “resolution revolution” of cryo-EM. Here, we provide a straightforward preparation method and systematic analysis of Ni-NTA lipid monolayers as a tool for high-resolution single particle cryo-EM. We found the lipid affinity grids concentrate particles away from the AWI in thin ice (∼30 nm). We determined three structures ranging from 2.4 to 3.0 Å resolution, showing this method is amenable to high-resolution. Furthermore, we determined a 3.1 Å structure of a sub-100 kDa protein without symmetry, demonstrating the utility for a range of biological macromolecules. Lipid monolayers are therefore an easily extendable tool for most systems and help alleviate common problems such as low yield, disruption by the air–water interface, and thicker ice.
栅格制备是用单粒子低温电镜测定高分辨率结构的一个限制速率的步骤。粒子与空气-水界面的相互作用经常导致冰内的变性、聚集或首选取向。当使用传统的网格制作技术时,一些样品产生的颗粒数量不足,需要使用固体支撑将样品集中到网格上。网格制备的最新进展表明,亲和网格是一种有前途的工具,可以选择性地浓缩蛋白质,同时保护样品免受空气-水界面的影响。一种这样的技术利用含有具有亲和柄的脂质种类的脂质单分子层。一些最初的亲和栅格使用了一层有孔的碳层,涂有镍硝基三乙酸(Ni-NTA)脂质,允许携带常用的多组氨酸亲和标签的蛋白质结合。然而,这些研究使用了复杂的方案,并且是在冷冻电镜“分辨率革命”之前进行的。在这里,我们提供了一种简单的制备方法和系统分析的Ni-NTA脂质单层,作为高分辨率单颗粒冷冻电镜的工具。我们发现脂质亲和网格将颗粒集中在离AWI很远的薄冰中(~ 30 nm)。我们确定了从2.4到3.0 Å分辨率的三种结构,表明该方法适用于高分辨率。此外,我们确定了一个低于100 kDa蛋白的3.1 Å结构,而不对称,证明了它在一系列生物大分子中的实用性。因此,脂质单分子层是一种易于扩展的工具,适用于大多数系统,并有助于缓解常见问题,如产量低,空气-水界面破坏和较厚的冰。
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引用次数: 0
Prediction of a structural change in the orientation of the cytoplasmic signaling unit of human Toll-like receptor 9 upon binding of agonistic and antagonistic DNA molecules 预测人类toll样受体9在结合激动和拮抗DNA分子时细胞质信号单元方向的结构变化。
IF 2.7 3区 生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-10-10 DOI: 10.1016/j.jsb.2025.108252
Kazuaki Hoshi
Toll-like receptor 9 (TLR9) recognizes pathogenic DNA molecules containing unmethylated cytosine-phosphate-guanine motifs (CpG DNA) and initiates signaling cascades essential for enhancing immune responses. TLR9 is a type I transmembrane receptor comprising an N-terminal leucine-rich repeat (LRR) domain, a transmembrane domain, and a C-terminal Toll/interleukin-1 receptor (TIR) domain. Most studies have focused on the interaction between the LRR domain and its DNA ligands. However, the TIR domain is crucial for interacting with adapter proteins such as myeloid differentiation factor 88 (MyD88). The aim of this study was to predict changes in the orientation of the TIR domain in human TLR9 (hTLR9) and its complexes with agonistic or antagonistic DNA molecules using the AlphaFold server. AlphaFold predicted the overall structure of hTLR9 with high confidence scores, including part of the TIR domain. Interestingly, binding of agonistic and antagonistic DNA molecules to the N-terminal LRR domain induced a structural change in the orientation of the TIR domain compared to the unbound TLR9 structure. The TIR domain in the predicted hTLR9 model displayed a secondary structure similar to that of the previously reported human TLR1 crystal structure. The predicted model suggests that ligand binding to the N-terminal LRR domain causes a change in the orientation of the TIR domain of hTLR9, likely due to bending of the transmembrane region.
toll样受体9 (TLR9)识别含有未甲基化胞嘧啶-磷酸-鸟嘌呤基序(CpG DNA)的致病性DNA分子,并启动增强免疫应答所必需的信号级联反应。TLR9是一种I型跨膜受体,包括n端富含亮氨酸重复序列(LRR)结构域、跨膜结构域和c端Toll/白细胞介素-1受体(TIR)结构域。大多数研究都集中在LRR结构域与其DNA配体的相互作用上。然而,TIR结构域对于与适配蛋白(如髓样分化因子88 (MyD88))相互作用至关重要。本研究的目的是利用AlphaFold服务器预测人类TLR9 (hTLR9)及其与激动或拮抗DNA分子复合物中TIR结构域方向的变化。AlphaFold以较高的置信度预测hTLR9的整体结构,包括部分TIR结构域。有趣的是,与未结合的TLR9结构相比,与n端LRR结构域结合的激动性和拮抗性DNA分子诱导了TIR结构域方向的结构变化。hTLR9模型中的TIR结构域显示出与先前报道的人类TLR1晶体结构相似的二级结构。预测模型表明,与n端LRR结构域结合的配体导致hTLR9的TIR结构域的取向发生变化,可能是由于跨膜区域的弯曲。
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引用次数: 0
Hurdles and advancements in experimental membrane protein structural biology 实验膜蛋白结构生物学的障碍与进展。
IF 2.7 3区 生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-09-28 DOI: 10.1016/j.jsb.2025.108251
Ruchika Bajaj
This short review article traces the evolution of membrane protein structural biology over time and describes various challenges faced and overcome by researchers in the field, highlighting some of the major breakthroughs and advancements in the field. It presents a thematic exploration of membrane protein structural biology emphasizing on persistent technical and conceptual challenges from protein expression to structural techniques shaping the field with landmark innovations advancing our ability to determine membrane protein structures. The review specifically focus on a few key areas: sourcing and expressing membrane proteins, developing purification strategies and membrane mimetics, and the emergence of powerful structural tools such as X-ray crystallography, cryo-electron microscopy (cryo-EM) and micro-electron diffraction (MicroED). Each section discusses major advancements addressing long standing bottlenecks and opening avenues to understand structure–function relationships in membrane proteins. Furthermore, it also briefly discusses the impact of important discoveries and future perspectives for the field. The review concludes by discussing current emerging frontiers in the field including in-situ structural methods, AI driven structure prediction and future directions for integrative and dynamic membrane protein research.
这篇简短的综述文章追溯了膜蛋白结构生物学的发展历程,描述了该领域研究人员面临和克服的各种挑战,重点介绍了该领域的一些重大突破和进展。它提出了膜蛋白结构生物学的主题探索,强调从蛋白质表达到结构技术的持续技术和概念挑战,塑造了具有里程碑意义的创新,提高了我们确定膜蛋白结构的能力。该综述特别关注几个关键领域:膜蛋白的来源和表达,开发纯化策略和膜模拟物,以及强大的结构工具如x射线晶体学,冷冻电子显微镜(cryo-EM)和微电子衍射(MicroED)的出现。每个部分都讨论了解决长期存在的瓶颈和打开理解膜蛋白结构功能关系的途径的主要进展。此外,它还简要讨论了重要发现的影响和该领域的未来前景。综述最后讨论了当前该领域的新兴前沿,包括原位结构方法,人工智能驱动的结构预测以及综合和动态膜蛋白研究的未来方向。
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引用次数: 0
Mind the corner: Fillets in cryo-FIB lamella preparation to minimise sample loss caused by stress concentration and lamella breakage 注意角落:在冷冻fib薄片制备过程中,将薄片因应力集中和薄片破裂造成的样品损失降到最低
IF 2.7 3区 生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-09-20 DOI: 10.1016/j.jsb.2025.108249
Sergey Gorelick , Sailakshmi Velamoor , Patrick Cleeve , Sylvain Trépout , Le Ying , Vivek Naranbhai , Georg Ramm
Cryo-FIB milling of biological specimens is a critical and limiting step in the cryo-electron tomography workflow. Preparing electron-transparent cryo-lamellae is a serial, low-throughput process. Even with automation, a skilled operator can typically only produce 15–25 lamellae in a single cryo-FIB session. During sample handling, milling and transfer, the cryo-fixed cells as well as the supporting film layer face various mechanical forces and thermal stresses due to temperature fluctuations. Moreover, after cells are cryo-FIB milled, the resulting thin lamellae continue to endure external forces from mechanical handling and thermal stress. We propose a simple, yet highly effective modification to the standard rectangular milling pattern by implementing “fillets” or corner smoothing providing better mechanical stability. This adjustment helps to avoid sharp corners at the lamella edges, thereby reducing stress concentration. As a result, this modification decreases the likelihood of lamella breakage and improves the overall yield of ready-for-TEM lamellae by over 40 % as verified experimentally.
生物标本的冷冻fib铣削是冷冻电子断层成像工作流程中的关键和限制步骤。制备电子透明冷晶片是一个连续的、低通量的过程。即使采用自动化,熟练的操作人员通常也只能在单次冷冻fib会话中生产15-25片薄片。在样品处理、铣削和转移过程中,由于温度波动,冷冻固定细胞以及支撑膜层面临各种机械力和热应力。此外,细胞经过低温fib铣削后,产生的薄片继续承受机械处理和热应力的外力。我们提出了一个简单的,但非常有效的修改标准的矩形铣削模式通过实施“圆角”或角平滑提供更好的机械稳定性。这种调整有助于避免在薄片边缘的尖角,从而减少应力集中。结果,实验证实,这种改性降低了片层断裂的可能性,并将准备透射电镜的片层的总收率提高了40%以上。
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引用次数: 0
A Multi-Technique Investigation to Explore the Structural Integrity and Chemical Complexity of the Brachiopod Lingula anatina (Lamarck, 1801) Shells 利用多种技术研究腕足动物Lingula anatina (Lamarck, 1801)壳的结构完整性和化学复杂性。
IF 2.7 3区 生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-09-13 DOI: 10.1016/j.jsb.2025.108248
Prabad Pratim Pal, Sourav Bar, Santosh Kumar Bera, Debkumar Sahoo, Sudipta Kumar Ghorai
The shell of Lingula anatina, a living representative of early brachiopods, exemplifies a unique organophosphatic biomineralization strategy that integrates mineral phases with organic components for structural enhancement. This study employs scanning electron microscopy (SEM), energy-dispersive X-ray spectroscopy (EDS), inductively coupled plasma optical emission spectrometry (ICP-OES), X-ray diffraction (XRD), and Raman spectroscopy to comprehensively analyse the microstructure, composition, and mineralogy of the shell. SEM imaging reveals distinct regional microarchitectures, from compact fibrous laminae to porous, reticulate layers, indicating functional specialization in structural reinforcement and flexibility. Elemental analyses confirm a calcium-phosphate matrix dominated by fluorapatite and enriched with trace elements like Mg, Mn, and Fe. XRD and Raman data validate the coexistence of crystalline fluorapatite and calcite with significant amorphous phases. These findings highlight Lingula’s evolutionary retention of a hierarchical, organic–inorganic composite shell adapted for environmental interaction, structural resilience, and biomineral control.
Lingula anatina是早期腕足动物的活代表,它的壳体现了一种独特的有机磷生物矿化策略,将矿物相与有机成分相结合,以增强结构。本研究采用扫描电镜(SEM)、能量色散x射线能谱(EDS)、电感耦合等离子体发射光谱(ICP-OES)、x射线衍射(XRD)、拉曼光谱等方法对壳的微观结构、组成、矿物学等进行了综合分析。扫描电镜成像显示了不同区域的微结构,从致密的纤维层到多孔的网状层,表明结构增强和灵活性的功能专业化。元素分析证实了以氟磷灰石为主的磷酸钙基质,并富含微量元素,如Mg、Mn和Fe。XRD和Raman数据验证了氟磷灰石和方解石晶体共存,并具有明显的非晶相。这些发现强调了Lingula进化保留了一种适应环境相互作用、结构弹性和生物矿物控制的分层有机-无机复合外壳。
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引用次数: 0
Structural insights into IMP2 dimerization and RNA binding IMP2二聚化和RNA结合的结构见解
IF 2.7 3区 生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-09-12 DOI: 10.1016/j.jsb.2025.108247
Stephen A. Zorc , Paola Munoz-Tello , Timothy O’Leary , Xiaoyu Yu , Mithun Nag Karadi Giridhar , Alexander D. Hondros , Althea Hansel-Harris , Stefano Forli , Patrick R. Griffin , Douglas J. Kojetin , Raktim N. Roy , Michalina Janiszewska
IGF2BP2 (IMP2) is an RNA-binding protein that contributes to tumorigenesis and metabolic disorders. Structural studies focused on individual IMP2 domains have provided important mechanistic insights into IMP2 function; however, structural information on full-length IMP2 is lacking but necessary to understand how to target IMP2 activity in drug discovery. In this study, we investigated the behavior of full-length IMP2 and the influence of RNA binding using biophysical and structural methods including mass photometry, hydrogen–deuterium exchange coupled to mass spectrometry (HDX-MS), and small angle x-ray scattering (SAXS). We found that full-length IMP2 forms multiple oligomeric states but predominantly adopts a dimeric conformation. Molecular models derived from SAXS data suggest the dimer is formed in a head-to-tail orientation by the KH34 and RRM1 domains. Upon RNA binding, IMP2 forms a pseudo-symmetric dimer different from its apo/RNA-free state. We also found that the formation of IMP2 oligomeric species, which includes dimers and higher-order oligomers, is sensitive to ionic strength and RNA binding. Our findings provide the first insight into the structural properties of full-length IMP2, which may lead to novel opportunities for disrupting its function.
IGF2BP2 (IMP2)是一种与肿瘤发生和代谢紊乱有关的rna结合蛋白。针对单个IMP2结构域的结构研究为IMP2功能提供了重要的机制见解;然而,缺乏全长IMP2的结构信息,但这对于了解如何靶向药物发现中的IMP2活性是必要的。在这项研究中,我们利用生物物理和结构方法,包括质谱法、氢-氘交换耦合质谱法(HDX-MS)和小角度x射线散射法(SAXS),研究了全长IMP2的行为和RNA结合的影响。我们发现全长IMP2形成多种低聚态,但主要采用二聚体构象。从SAXS数据得出的分子模型表明,二聚体是由KH34和RRM1结构域以头到尾的方向形成的。在RNA结合后,IMP2形成与无载脂蛋白/RNA状态不同的伪对称二聚体。我们还发现,IMP2低聚物的形成,包括二聚体和高阶低聚物,对离子强度和RNA结合敏感。我们的发现首次深入了解了全长IMP2的结构特性,这可能为破坏其功能提供新的机会。
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引用次数: 0
CRISP: A modular platform for cryo-EM image segmentation and processing with Conditional Random Field CRISP:一个具有条件随机场的低温电镜图像分割和处理的模块化平台
IF 2.7 3区 生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-09-09 DOI: 10.1016/j.jsb.2025.108239
Szu-Chi Chung, Po-Cheng Chou
Distinguishing signal from background in cryogenic electron microscopy (cryo-EM) micrographs is a critical processing step but remains challenging owing to the inherently low signal-to-noise ratio (SNR), contaminants, variable ice thickness, and densely packed particles of heterogeneous sizes. Recent image-segmentation methods provide pixel-level precision and thus offer several advantages over traditional object-detection approaches: segmented-blob mass can be computed to suppress false-positive particles, particle centering can be improved by leveraging the full brightness profile, and irregularly shaped particles can be identified more reliably. However, low SNR makes it difficult to obtain accurate pixel-level annotations for training segmentation models, and, in the absence of systematic evaluation platforms, most segmentation pipelines still rely on ad-hoc design choices.
Here, we introduce a modular platform that automatically generates high-quality segmentation maps to serve as reference labels. The platform supports flexible combinations of segmentation architectures, feature extractors, and loss functions, and it integrates novel Conditional Random Fields (CRFs) with class-discriminative features to refine coarse predictions into fine-grained segmentations. On synthetic data, models trained with our reference labels achieve pixel-level accuracy, recall, precision, Intersection-over-Union (IoU), and F1 scores all exceeding 90%. We further show that the resulting segmentations can be used directly for particle picking, yielding higher-resolution 3D density maps from real experimental datasets; these reconstructions match those curated by human experts and surpass the results of existing particle-picking tools. To facilitate further research, we release our methods as the open-source package CRISP, available at https://github.com/phonchi/CryoParticleSegment.
在低温电子显微镜(cryo-EM)显微照片中,从背景中区分信号是一个关键的处理步骤,但由于固有的低信噪比(SNR)、污染物、可变冰厚和密集排列的大小不一的颗粒,仍然具有挑战性。最近的图像分割方法提供了像素级的精度,因此与传统的目标检测方法相比有几个优势:可以计算分割的斑点质量来抑制假阳性颗粒,可以利用全亮度剖面来改善颗粒的定心,并且可以更可靠地识别不规则形状的颗粒。然而,低信噪比使得训练分割模型难以获得准确的像素级注释,并且在缺乏系统评估平台的情况下,大多数分割管道仍然依赖于自定义设计选择。在这里,我们介绍了一个模块化的平台,可以自动生成高质量的分割图作为参考标签。该平台支持分割架构、特征提取器和损失函数的灵活组合,并集成了具有类别区分特征的新型条件随机场(CRFs),将粗预测细化为细粒度分割。在合成数据上,使用我们的参考标签训练的模型实现了像素级的准确率、召回率、精度、交叉超过联合(IoU)和F1分数都超过了90%。我们进一步表明,所得到的分割可以直接用于粒子拾取,从真实的实验数据集产生更高分辨率的3D密度图;这些重建结果与人类专家的结果相匹配,超过了现有的颗粒拾取工具的结果。为了便于进一步的研究,我们将我们的方法作为开源包CRISP发布,可在https://github.com/phonchi/CryoParticleSegment上获得。
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引用次数: 0
Characterization of NMDA receptor Allostery modulation NMDA受体变构调节的表征
IF 2.7 3区 生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-08-15 DOI: 10.1016/j.jsb.2025.108238
Yunsheng Liu , Wangsheng Song , Rongde Zhong , Jinfang Zhang , Xianlin Wu , Yanyan Jia , Zengwei Kou
NMDA receptors are subject to numerous endogenous and exogenous allosteric regulations, which are essential for their complex pathophysiological functions in the brain, and serve as a basis for therapeutic targeting. However, the structural basis of many of these allosteric mechanisms remains unclear. In this study, we first utilized AlphaFold to predict the structural conformations of different NMDA receptor subtypes. Subsequent comparative analyses with experimentally resolved protein structures, coupled with validation using disulfide bond formation, revealed the high precision of these computational predictions. Based on these structures, we systematically investigated the allosteric regulation of NMDA receptors using RoseTTAFold-All-Atom. Our findings elucidated the binding sites of several allosteric modulators across different NMDA receptor subtypes and identified the key amino acids required for binding. These results reveal the structural basis of NMDA receptor allosteric regulation, providing new insights into its physiological and pathological roles, and offering potential avenues for drug development.
NMDA受体受多种内源性和外源性变构调节,这是其在大脑中复杂病理生理功能所必需的,也是治疗靶向的基础。然而,许多这些变构机制的结构基础仍不清楚。在本研究中,我们首先利用AlphaFold预测不同NMDA受体亚型的结构构象。随后与实验解决的蛋白质结构的比较分析,加上使用二硫键形成的验证,揭示了这些计算预测的高精度。基于这些结构,我们使用RoseTTAFold-All-Atom系统地研究了NMDA受体的变构调节。我们的研究结果阐明了几种不同NMDA受体亚型的变构调节剂的结合位点,并确定了结合所需的关键氨基酸。这些结果揭示了NMDA受体变构调节的结构基础,为其生理和病理作用提供了新的见解,并为药物开发提供了潜在的途径。
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引用次数: 0
Sequence/structural/functional relationships between Ganoderma fungal immunomodulatory proteins (gFIPs) and proteins involved in the modulation of immune response 灵芝真菌免疫调节蛋白(gFIPs)与免疫应答调节蛋白之间的序列/结构/功能关系
IF 2.7 3区 生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-08-13 DOI: 10.1016/j.jsb.2025.108237
Nikola Schlosserová , Giulia Chiara Maria Perrone , Jakub Treml , Maria Noemi Sgobba , Lorenzo Guerra , Ciro Leonardo Pierri
Fungal Immunomodulatory Proteins from Ganoderma species (gFIPs) have garnered significant interest due to their potential therapeutic applications in modulating immune responses. This study investigates the sequence, structural, and functional relationships of gFIPs with other proteins involved in immune modulation. Utilizing molecular modelling, multiple sequence alignments, and structural superimposition, we analysed two FIP crystallized structures (PDB IDs: 3F3H and 3KCW) alongside homologous sequences from various taxonomic groups. Our results reveal conserved motifs across fungal, bacterial, and human sequences, indicating potential functional similarities. Comparative structural analysis highlights significant conservation in FIP architecture, with variations primarily in the N-terminal regions. Notably, structural alignment with bacterial toxins, such as ADP-ribosylating binary toxin from Clostridium difficile or protective antigen of Anthrax toxin from Bacillus anthracis suggests mechanistic insights into FIP’s immunomodulatory actions. Structural similarities between gFIPs and immune-related proteins, such as bacterial toxin-binding domains, antibody fragments, T-cell receptor components, and immune checkpoint regulators (PD-1) suggest their potential involvement in immune response/inflammation signalling pathways. This comprehensive analysis elucidates the structural basis for the diverse biological activities of gFIPs and underscores their potential as therapeutic agents in immune-related diseases.
来自灵芝物种的真菌免疫调节蛋白(gFIPs)由于其在调节免疫反应方面的潜在治疗应用而引起了极大的兴趣。本研究探讨了gFIPs与其他参与免疫调节的蛋白的序列、结构和功能关系。利用分子模型、多序列比对和结构叠加,我们分析了两个FIP晶体结构(PDB id: 3F3H和3KCW)以及来自不同分类类群的同源序列。我们的研究结果揭示了真菌、细菌和人类序列中的保守基序,表明潜在的功能相似性。比较结构分析强调了FIP结构的显著保存,其变化主要在n端区域。值得注意的是,与细菌毒素的结构一致性,如艰难梭菌的adp核糖基化二元毒素或炭疽芽孢杆菌的炭疽毒素保护性抗原,表明FIP免疫调节作用的机制。gFIPs与免疫相关蛋白(如细菌毒素结合结构域、抗体片段、t细胞受体成分和免疫检查点调节因子(PD-1))之间的结构相似性表明它们可能参与TCR信号通路。这项综合分析阐明了gFIPs多种生物活性的结构基础,并强调了它们作为免疫相关疾病治疗剂的潜力。
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引用次数: 0
1-Deoxy-D-xylulose 5-phosphate synthase: structural perspectives on an essential enzyme in isoprenoid biosynthesis 1-脱氧- d -木糖5-磷酸合成酶:一类类异戊二烯生物合成必需酶的结构研究。
IF 2.7 3区 生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-08-08 DOI: 10.1016/j.jsb.2025.108236
Victor O. Gawriljuk , Rick Oerlemans , Eswar R. Reddem , Robin M. Gierse , Anna K.H. Hirsch , Matthew R. Groves
Isoprenoids represent one of the largest and functionally diverse class of natural products, playing essential roles in cellular processes across all domains of life. Unlike humans, many pathogenic organisms such as bacteria and protozoa produce their isoprenoid precursors through the 2-C-methylerythritol phosphate (MEP) pathway. 1-deoxy-D-xylulose 5-phosphate synthase (DXPS) is the first and rate-limiting enzyme of this pathway. Despite its biological importance and potential as a drug target, structural studies on DXPS were limited due to its intrinsic flexibility and difficulties in crystallisation. Recent advances, including the development of more crystallisation-friendly constructs and the application of single-particle cryo-electron microscopy (cryo-EM), have significantly expanded our structural understanding of DXPS. This review provides a comprehensive overview of the structural insights gained over the past decades, focusing on the overall architecture of DXPS, its catalytic mechanism, and emerging relevance in structure-based drug discovery.
类异戊二烯是最大的、功能多样的天然产物之一,在生命所有领域的细胞过程中发挥着重要作用。与人类不同,许多致病生物如细菌和原生动物通过2- c -甲基赤藓糖醇磷酸(MEP)途径产生类异戊二烯前体。1-脱氧-d -木糖5-磷酸合酶(DXPS)是该途径的第一酶和限速酶。尽管DXPS具有重要的生物学意义和作为药物靶点的潜力,但由于其固有的灵活性和结晶困难,对DXPS的结构研究受到限制。最近的进展,包括更多结晶友好结构的发展和单粒子冷冻电子显微镜(cryo-EM)的应用,极大地扩展了我们对DXPS的结构理解。这篇综述提供了一个全面的概述,在过去的几十年里获得的结构见解,重点是DXPS的整体结构,它的催化机制,并在基于结构的药物发现新兴的相关性。
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引用次数: 0
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