Journal of structural biology最新文献_第7页

Insights into the pathogenic mechanisms associated with the SARS-CoV-2 spike protein 深入了解与SARS-CoV-2刺突蛋白相关的致病机制

IF 3 3区生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of structural biology

Pub Date : 2025-09-01 Epub Date: 2025-06-23 DOI: 10.1016/j.jsb.2025.108229

Mia Argyrou , Eleni Pitsillou , Andrew Hung , Assam El-Osta , Tom C. Karagiannis

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the pathogenic agent responsible for the coronavirus disease 2019 (COVID-19) pandemic, uses the trimeric spike protein to gain entry into the host cell. Structural studies have revealed that the spike protein is comprised of the S1 and S2 subunits. The S1 subunit of the spike protein contains the receptor-binding domain (RBD), which binds to the human angiotensin-converting enzyme 2 (ACE2) receptor. The interaction between the RBD and ACE2 facilitates membrane fusion and host cell infection. The SARS-CoV-2 spike protein also contains a unique insertion of four amino acids that results in the 682-RRAR↓S-686 polybasic furin cleavage motif at the boundary of the S1 and S2 subunits. The furin cleavage motif contributes to the high infectivity and transmissibility of SARS-CoV-2. This review provides a comprehensive analysis of the molecular interactions of the spike protein, with a specific focus on the RBD and furin cleavage site. In addition to examining the binding characteristics with ACE2, the interactions with alternative receptors, such as neuropilin-1 (NRP1) and the nicotinic acetylcholine receptors (nAChRs) are highlighted. The ability of the spike protein to bind alternative receptors and host factors has been linked to the pathophysiology of COVID-19 and the persistence of symptoms in the post COVID-19 condition. Furthermore, we examine the impact of spike protein mutations on receptor affinity and disease severity. SARS-CoV-2 continues to evolve, with variants remaining an ongoing threat to public health. Understanding these molecular interactions is critical for the development of novel therapeutic interventions.

严重急性呼吸综合征冠状病毒2 （SARS-CoV-2）是导致2019冠状病毒病（COVID-19）大流行的病原体，它利用三聚体刺突蛋白进入宿主细胞。结构研究表明，刺突蛋白由S1和S2亚基组成。刺突蛋白的S1亚基含有受体结合域（RBD），与人血管紧张素转换酶2 （ACE2）受体结合。RBD与ACE2的相互作用促进了膜融合和宿主细胞感染。SARS-CoV-2刺突蛋白还包含一个独特的4个氨基酸插入，在S1和S2亚基的边界上形成682-RRAR↓S-686多碱基furin切割基序。furin切割基序与SARS-CoV-2的高传染性和传播性有关。这篇综述提供了刺突蛋白分子相互作用的全面分析，特别关注RBD和furin切割位点。除了研究与ACE2的结合特性外，还强调了与其他受体的相互作用，如神经匹林-1 （NRP1）和烟碱乙酰胆碱受体（nAChRs）。刺突蛋白结合替代受体和宿主因子的能力与COVID-19的病理生理和COVID-19后症状的持续存在有关。此外，我们研究了刺突蛋白突变对受体亲和力和疾病严重程度的影响。SARS-CoV-2继续演变，其变体仍然对公共卫生构成持续威胁。了解这些分子相互作用对于开发新的治疗干预措施至关重要。

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引用次数: 0

Binding of an N protein peptide to M protein of a bat coronavirus 一种蝙蝠冠状病毒N蛋白肽与M蛋白的结合

IF 3 3区生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of structural biology

Pub Date : 2025-09-01 Epub Date: 2025-07-13 DOI: 10.1016/j.jsb.2025.108234

Xiaodong Wang, Siqi Yang , Penghui Yang , Ziyi Sun, Xiaoming Zhou

The interaction between the membrane (M) protein and the nucleocapsid (N) protein of coronaviruses plays a crucial role in virus assembly and morphogenesis. Previous studies indicate that one M−N interaction occurs between M protein and the carboxy-terminus of N protein. However, the mechanistic details of M−N interactions remain unclear. Here, we present a complex structure of an N protein carboxy-terminal peptide bound to M protein from Pipistrellus bat coronavirus HKU5. The structure shows that the M−N peptide binding site includes a “horizontal” groove located between the carboxy-terminal domain and the transmembrane domain of M protein. Combined with molecular docking and binding analysis, our results provide structural insight into the binding mechanism between M and N proteins of a coronavirus.

冠状病毒的膜(M)蛋白与核衣壳(N)蛋白的相互作用在病毒的组装和形态发生中起着至关重要的作用。以往的研究表明，M蛋白与N蛋白的羧基端之间发生一次M - N相互作用。然而，M - N相互作用的机制细节仍不清楚。在这里，我们提出了一个复杂的结构的N蛋白羧基末端肽结合到M蛋白从pipistrelus蝙蝠冠状病毒HKU5。结构表明M - N肽结合位点包括位于M蛋白羧基末端结构域和跨膜结构域之间的“水平”凹槽。结合分子对接和结合分析，我们的研究结果为冠状病毒M蛋白和N蛋白的结合机制提供了结构性的见解。

引用次数: 0

Effects of base temperature, immersion medium, and EM grid material on devitrification thresholds in cryogenic optical super-resolution microscopy 基底温度、浸泡介质和EM栅格材料对低温光学超分辨显微镜反玻化阈值的影响

IF 3 3区生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of structural biology

Pub Date : 2025-09-01 Epub Date: 2025-07-17 DOI: 10.1016/j.jsb.2025.108231

Soheil Mojiri , Joseph M. Dobbs , Niko Faul , Thomas P. Burg , Julia Mahamid , Jonas Ries

Cryogenic correlative light and electron microscopy (cryo-CLEM) is an imaging strategy that integrates specific molecular labeling and molecular resolution structural information. However, there is a resolution gap of more than two orders of magnitude between diffraction-limited fluorescence microscopy and electron microscopy (EM). Single-molecule localization microscopy (SMLM) performed at cryogenic temperatures promises to bridge this resolution gap. Nevertheless, the high excitation laser powers required for SMLM risk the devitrification of frozen biological samples, leading to perturbation of their native-like state. Here, we investigate how base cooling temperature, immersion medium, and EM grid support materials influence sample devitrification. Using finite element simulations and experimental validation, we show that a cryo-immersion medium enhances heat dissipation for carbon supports, while metallic supports in a cold nitrogen gas medium tolerate higher laser intensities due to lower base temperatures. Gold supports illuminated at

640 nm

exhibit markedly high laser thresholds, similar to silver-coated grids. Additionally, metallic supports maintain efficient heat dissipation in vacuum-based cryostats. Our findings provide quantitative insights that aid in optimization of cryo-SMLM setups for improved cryo-CLEM imaging.

低温相关光电子显微镜（cryo-CLEM）是一种集成了特定分子标记和分子分辨率结构信息的成像策略。然而，在衍射极限荧光显微镜和电子显微镜（EM）之间存在两个数量级以上的分辨率差距。在低温下进行的单分子定位显微镜（SMLM）有望弥合这一分辨率差距。然而，SMLM所需的高激发激光功率有可能导致冷冻生物样品的反玻璃化，导致其原生态的扰动。在这里，我们研究了基底冷却温度、浸泡介质和EM网格支撑材料如何影响样品的脱玻化。通过有限元模拟和实验验证，我们发现低温浸泡介质增强了碳支架的散热，而低温氮气介质中的金属支架由于基底温度较低，可以承受更高的激光强度。在640nm照射下，金支架显示出明显的高激光阈值，类似于镀银网格。此外，金属支撑在真空低温恒温器中保持有效的散热。我们的研究结果提供了定量的见解，有助于优化冷冻- smlm设置，以改善冷冻- clem成像。

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引用次数: 0

Passage of ribosomes through microsprayer increases functional activity – Implications for activity assays in time-resolved cryo-EM 核糖体通过微喷雾器增加功能活性-时间分辨低温电镜活性分析的意义。

IF 3 3区生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of structural biology

Pub Date : 2025-09-01 Epub Date: 2025-07-04 DOI: 10.1016/j.jsb.2025.108232

Priyanka Garg , Xiangsong Feng , Swastik De , Joachim Frank

This study examines the validity of an assay that is used to report on the retainment of functional competence by ribosomes as they pass a microsprayer. We find a reproducible increase, rather than the expected decrease in GFP production as monitored by fluorescence, which may suggest heterogeneity or partial aggregation of ribosomes in solution. An even larger increase in functional activity is observed when sonication is used, pointing to mechanical agitation as the decisive factor in both scenarios. The results have a bearing on the design and interpretation of validation experiments in time-resolved cryo-EM based on microfluidic chips.

本研究检验了一种测定的有效性，该测定用于报告核糖体在通过微喷雾器时保留的功能能力。我们发现了可重复的增加，而不是预期的荧光监测的GFP产量减少，这可能表明溶液中核糖体的异质性或部分聚集。当使用超声时，观察到功能活动的更大增加，指出机械搅拌是两种情况下的决定性因素。这些结果对基于微流控芯片的时间分辨低温电镜验证实验的设计和解释具有一定的指导意义。

引用次数: 0

A generalist deep-learning volume segmentation tool for volume electron microscopy of biological samples 一个通用的深度学习体积分割工具，用于生物样品的体积电子显微镜。

IF 3 3区生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of structural biology

Pub Date : 2025-09-01 Epub Date: 2025-05-29 DOI: 10.1016/j.jsb.2025.108214

Yuyao Huang , Nickhil Jadav , Georgia Rutter , Lech Szymanski , Mihnea Bostina , Duane P. Harland

We present the Volume Segmentation Tool (VST), a deep learning software tool that implements volumetric image segmentation in volume electron microscopy image stack data from a wide range of biological sample types. VST automates the handling of data preprocessing, data augmentation, and network building, as well as the configuration for model training, while adapting to the specific dataset. We have tried to make VST more accessible by designing it to operate entirely on local hardware and have provided a browser-based interface with additional features for visualizations of the networks and augmented datasets. VST can utilise contour map prediction to support instance segmentation on top of semantic segmentation. Through examples from various resin-embedded sample derived transmission electron microscopy and scanning electron microscopy datasets, we demonstrate that VST achieves state of the art performance compared to existing approaches.

我们提出了体积分割工具（VST），这是一种深度学习软件工具，可在来自各种生物样品类型的体积电子显微镜图像堆栈数据中实现体积图像分割。VST自动处理数据预处理、数据增强和网络构建，以及模型训练的配置，同时适应特定的数据集。我们试图通过将VST设计为完全在本地硬件上运行来使其更易于访问，并提供了一个基于浏览器的界面，该界面具有用于网络可视化和增强数据集的附加功能。VST可以在语义分割的基础上利用等高线地图预测来支持实例分割。通过来自各种树脂包埋样品衍生的透射电子显微镜和扫描电子显微镜数据集的示例，我们证明与现有方法相比，VST实现了最先进的性能。

引用次数: 0

Structural insights into the RNA binding inhibitors of the C-terminal domain of the SARS-CoV-2 nucleocapsid 对 SARS-CoV-2 核头壳 C 端结构的 RNA 结合抑制剂的结构研究。

IF 3 3区生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of structural biology

Pub Date : 2025-06-01 Epub Date: 2025-03-18 DOI: 10.1016/j.jsb.2025.108197

Preeti Dhaka, Jai Krishna Mahto, Ankur Singh, Pravindra Kumar, Shailly Tomar

The SARS-CoV-2 nucleocapsid (N) protein is an essential structural element of the virion, playing a crucial role in enclosing the viral genome into a ribonucleoprotein (RNP) assembly, as well as viral replication and transmission. The C-terminal domain of the N-protein (N-CTD) is essential for encapsidation, contributing to the stabilization of the RNP complex. In a previous study, three inhibitors (ceftriaxone, cefuroxime, and ampicillin) were screened for their potential to disrupt the RNA packaging process by targeting the N-protein. However, the binding efficacy, mechanism of RNA binding inhibition, and molecular insights of binding with N-CTD remain unclear. In this study, we evaluated the binding efficacy of these inhibitors using isothermal titration calorimetry (ITC), revealing the affinity of ceftriaxone (18 ± 1.3 μM), cefuroxime (55 ± 4.2 μM), and ampicillin (28 ± 1.2 μM) with the N-CTD. Further inhibition assay and fluorescence polarisation assay demonstrated RNA binding inhibition, with IC₅₀ ranging from ∼ 12 to 18 μM and K_D values between 24 μM to 32 μM for the inhibitors, respectively. Additionally, we also determined the inhibitor-bound complex crystal structures of N-CTD-Ceftriaxone (2.0 Å) and N-CTD-Ampicillin (2.2 Å), along with the structure of apo N-CTD (1.4 Å). These crystal structures revealed previously unobserved interaction sites involving residues K261, K266, R293, Q294, and W301 at the oligomerization interface and the predicted RNA-binding region of N-CTD. These findings provide valuable molecular insights into the inhibition of N-CTD, highlighting its potential as an underexplored but promising target for the development of novel antiviral agents against coronaviruses.

SARS-CoV-2核衣壳蛋白(N)是病毒粒子的基本结构元件，在将病毒基因组包裹成核糖核蛋白（RNP）组装体以及病毒复制和传播中起着至关重要的作用。n蛋白的c端结构域（N-CTD）对于包封至关重要，有助于RNP复合物的稳定。在之前的一项研究中，筛选了三种抑制剂（头孢曲松、头孢呋辛和氨苄西林），因为它们有可能通过靶向n蛋白破坏RNA包装过程。然而，结合效果、RNA结合抑制机制以及与N-CTD结合的分子机制尚不清楚。在这项研究中,我们评估这些抑制剂使用的绑定疗效等温滴定量热法(ITC),揭示了亲和力的头孢曲松钠(18 ±1.3  μM),头孢呋辛(55 ±4.2  μM),和氨苄青霉素(28 ±1.2  μM) N-CTD。进一步的抑制实验和荧光极化实验显示RNA结合抑制，抑制剂的IC50范围为 ~ 12 ~ 18 μM， KD值分别为24 μM ~ 32 μM。此外，我们还确定了N-CTD-头孢曲松（2.0 Å）和N-CTD-氨苄西林（2.2 Å）的抑制剂结合复合物晶体结构，以及载子N-CTD （1.4 Å）的结构。这些晶体结构揭示了先前未观察到的相互作用位点，包括寡聚化界面上的残基K261， K266, R293， Q294和W301以及N-CTD预测的rna结合区。这些发现为N-CTD的抑制提供了有价值的分子见解，突出了其作为开发新型冠状病毒抗病毒药物的潜力。

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引用次数: 0

Improving CryoEM maps of symmetry-mismatched macromolecular assemblies: A case study on the flagellar motor 改进对称错配大分子组装的低温电镜图谱：鞭毛马达的案例研究。

IF 3 3区生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of structural biology

Pub Date : 2025-06-01 Epub Date: 2025-03-05 DOI: 10.1016/j.jsb.2025.108184

Prashant K. Singh , T.M. Iverson

Advances in cryo-electron microscopy instrumentation and sample preparation have significantly improved the ability to collect quality data for biomolecular structures. However, achieving resolutions consistent with data quality remains challenging in structures with symmetry mismatches. As a case study, the bacterial flagellar motor is a large complex essential for bacterial chemotaxis and virulence. This motor contains a smaller membrane-supramembrane ring (MS-ring) and a larger cytoplasmic ring (C-ring). These two features have a 33:34 symmetry mismatch when expressed in E. coli. Because close symmetry mismatches are the most difficult to deconvolute, this makes the flagellar motor an excellent model system to evaluate refinement strategies for symmetry mismatch. We compared the performance of masked refinement, local refinement, and particle subtracted refinement on the same data. We found that particle subtraction prior to refinement was critical for approaching the smaller MS-ring. Additional processing resulted in final resolutions of 3.1 Å for the MS-ring and 3.0 Å for the C-ring, which improves the resolution of the MS-ring by 0.3 Å and the resolution of the C-ring by 1.0 Å as compared to past work. Although particle subtraction is fairly well-established, it is rarely applied to problems of symmetry mismatch, making this case study a valuable demonstration of its utility in this context.

低温电子显微镜仪器和样品制备的进步显著提高了收集生物分子结构高质量数据的能力。然而，在对称不匹配的结构中，实现与数据质量一致的分辨率仍然具有挑战性。作为一个案例研究，细菌鞭毛马达是细菌趋化性和毒力所必需的大型复合体。该马达包含一个较小的膜上环（MS-ring）和一个较大的细胞质环（C-ring）。当在大肠杆菌中表达时，这两个特征有33:34的对称不匹配。由于紧密的对称失配是最难解卷积的，这使得鞭毛马达成为一个很好的模型系统来评估对称失配的改进策略。我们比较了掩码细化、局部细化和粒子减法细化在相同数据上的性能。我们发现，在细化之前的粒子减法对于正确地反卷积较小的ms环的对称性是必不可少的。额外的处理导致ms环的最终分辨率为3.1 Å， c环的最终分辨率为3.0 Å，与过去的工作相比，ms环的分辨率提高了0.3 Å， c环的分辨率提高了1.0 Å。虽然粒子减法是相当完善的，但它很少应用于对称不匹配的问题，使本案例研究成为其在这种情况下的实用性的有价值的演示。

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引用次数: 0

Structural and biophysical characterization of PadR family protein Rv0047c of Mycobacterium tuberculosis H37Rv 结核分枝杆菌H37Rv PadR家族蛋白Rv0047c的结构与生物物理特性

IF 3 3区生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of structural biology

Pub Date : 2025-06-01 Epub Date: 2025-05-20 DOI: 10.1016/j.jsb.2025.108211

Md Samsuddin Ansari , Muhammad Zohib , Meera Kumari , Vikash Yadav , Ravi Kant Pal , Sarita Tripathi , Anupam Jain , Bichitra Kumar Biswal , Ashish Arora

The members of the PadR family of transcriptional regulators are important for cell survival in toxic environments and play an important role in detoxification, pathogenicity, and multi-drug resistance. Rv0047c of Mycobacterium tuberculosis H37Rv is annotated as a PadR family protein. We have characterized the stability and structure of Rv0047c. Rv0047c forms a stable dimer in solution. Its stability is characterized by a thermal melting transition temperature (Tm) of 55.3 °C. The crystal structure of Rv0047c was determined at a resolution of 3.15 Å. The structure indicates the biological unit to be a dimer with each monomer having a characteristic N-terminal winged-helix-turn-helix DNA binding domain and a C-terminal dimerization domain. The N-terminal domain is composed of four helices, α1, α2, α3, and α4 and two beta strands β1 and β2. The C-terminal dimerization domain (CTD) consists two long helices α6 and α7. The two domains are connected by helix α5. A short helical turn (helix αa, residue 89–92), leads to compaction of the α4-α5 loop. Rv0047c exhibits specificity in binding to an upstream region having an inverted repeat sequence. This binding is dependent upon Y18 and Y40 residue of Rv0047c, which are highly conserved among the PadR family. Overall, our results suggest a transcription regulatory role for Rv0047c, similar to other PadR family proteins.

PadR转录调控家族成员对毒性环境下的细胞存活至关重要，在解毒、致病性和多药耐药等方面发挥重要作用。分枝杆菌H37Rv的Rv0047c被注释为PadR家族蛋白。我们对Rv0047c的稳定性和结构进行了表征。Rv0047c在溶液中形成稳定的二聚体。其稳定性表征为热熔转变温度（Tm）为55.3 °C。Rv0047c的晶体结构以3.15 Å的分辨率确定。该结构表明该生物单元为二聚体，每个单体具有典型的n端翼-螺旋-旋-螺旋DNA结合结构域和c端二聚结构域。n端结构域由α1、α2、α3和α4四个螺旋和两条β链β1和β2组成。c端二聚化结构域（CTD）由两个长螺旋α6和α7组成。两个结构域由螺旋α5连接。短螺旋旋转（螺旋αa，残基89-92）导致α4-α5环的压实。Rv0047c在与具有反向重复序列的上游区域结合方面表现出特异性。这种结合依赖于Rv0047c的Y18和Y40残基，这些残基在PadR家族中高度保守。总的来说，我们的研究结果表明Rv0047c具有转录调控作用，类似于其他PadR家族蛋白。

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引用次数: 0

Three-dimensional reconstruction of Magnetofaba australis strain IT-1: Magnetosome chain position with respect to flagella australis Magnetofaba菌株IT-1的三维重建：磁小体链在鞭毛上的位置。

IF 3 3区生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of structural biology

Pub Date : 2025-06-01 Epub Date: 2025-02-26 DOI: 10.1016/j.jsb.2025.108181

Eduardo Monteiro , Anderson S. Cabral , Viviana Morillo , Daniel Acosta-Avalos , Ulysses Lins , Fernanda Abreu

Magnetotactic bacteria (MTB) are a broad and diverse group of Gram-negative prokaryotes that biomineralize magnetosomes, organelles composed of a magnetic nanocrystal of magnetite (Fe₃O₄) or greigite (Fe₃S₄) and enveloped by a biological membrane. Magnetosomes are arranged in one or more chains intracellularly, which impart a magnetic moment to the cell. These structures permit a passive orientation of the MTB with the geomagnetic field lines (GML), which, when associated with swimming propelled by flagella, originate a phenomenon called magneto-aerotaxis, an important life strategy in a chemical stratified environment. There is a classical model based on elongated cells as vibrios and rods that tries to explain the magneto-aerotaxis. Still, this model raises questions when applied to other morphologies other than elongated cells. Here, we observe the spatial disposition of magnetosomes, motility behavior, and influence of magneto-aerotaxis in Magnetofaba australis strain IT-1, an MTB that achieves high swimming speeds and has some peculiarity in its motility. The three-dimensional reconstruction showed that Mf. australis strain IT-1′s magnetosome chain is misaligned with the swimming axis, which makes it impossible to use the classical model to explain magneto-aerotaxis in this MTB. Despite this, Mf. australis strain IT-1 was capable of swimming aligned to the GML. Also, this work studied the influence of the magnetosome and magneto-aerotaxis between populations of Mf. australis strain IT-1 with and without magnetosomes. Our results indicated that the magnetosome presence not only positively influences the movement in Mf. australis strain IT-1 but also can positively impact population growth in these MTB.

磁小体是由磁铁矿（Fe3O4）或灰铁矿（Fe3S4）的磁性纳米晶体组成的细胞器，由生物膜包裹。磁小体在细胞内排列成一条或多条链，给细胞带来磁矩。这些结构可使 MTB 与地磁场线（GML）被动定向，当与鞭毛推动的游动联系在一起时，就会产生一种称为磁气动的现象，这是在化学分层环境中的一种重要的生命策略。有一种基于拉长细胞（如振子和棒状细胞）的经典模型，试图解释磁气浮现象。然而，当这一模型应用于拉长细胞以外的其他形态时，就会产生问题。在此，我们观察了Magnetofaba australis菌株IT-1中磁小体的空间分布、运动行为以及磁气浮的影响。三维重建结果表明，Mf. australis strain IT-1 的磁小体链与游动轴错位，因此无法用经典模型来解释这种 MTB 的磁气动现象。尽管如此，Mf. australis 菌株 IT-1 仍能对准 GML 游动。此外，这项工作还研究了有磁小体和无磁小体的 Mf. australis 菌株 IT-1 群体之间磁小体和磁气浮的影响。我们的研究结果表明，磁小体的存在不仅会积极影响 Mf.australis 菌株 IT-1 的运动，还会对这些 MTB 的种群增长产生积极影响。

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引用次数: 0

MRGPRX2 ligandome: Molecular simulations reveal three categories of ligand-receptor interactions MRGPRX2配体：分子模拟揭示了配体与受体相互作用的三种类型。

IF 3 3区生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of structural biology

Pub Date : 2025-06-01 Epub Date: 2025-03-12 DOI: 10.1016/j.jsb.2025.108193

Philip Maier , Moritz Macht , Silvan Beck , Pavel Kolkhir , Magda Babina , Andreas E. Kremer , Dirk Zahn , Katharina Wolf

Introduction

Mas-related G protein-coupled receptor (MRGPR) X2 is a mast cell receptor known to be activated by a wide range of ligands of various size, charge and origin. Our aim is to gain a deeper understanding of the binding processes of the different MRGPRX2 ligands and the ligand-receptor interactions in order to identify crucial structural elements for receptor activation.

Materials and methods

We used the three-dimensional structure of MRGPRX2 described in Nature in 2021 by Cao et al. and Yang et al. to computationally model the interaction between MRGPRX2 and small molecule ligands under simulated physiological conditions.

Results

Docking and post-docking samplings of the MRGPRX2 ligandome within the GPCR binding pocket led to the identification of key structural features for protein–ligand interactions. On the ligand side, we obtained an overlay of different molecular patterns or chemical groups by comparing different ligands plotted on the receptor. These key features include at least one protonated amine moiety of MRGPRX2 ligands contributing to one salt-bridge and one π-cation interaction, as well as an extended non-polar domain of the ligand surface that offer hydrophobic segregation and/or π-stacking interactions. In the receptor, we identified amino acids (GLU164, ASP184, PHE101, PHE170, TRP243, PHE244 and PHE257) that specifically interact via hydrogen bonding, salt-bridges, π-cation interactions and π-π stacking with the ligands to direct binding and ultimately receptor activation.

Discussion

Our insights into ligand-receptor interaction obtained by molecular modeling can help to predict mast cell activation via MRGPRX2 including adverse reactions, and facilitate the development of MRGPRX2 antagonists for the treatment of mast cell-mediated diseases.

简介：肥大细胞相关G蛋白偶联受体（MRGPR） X2是一种已知可被各种大小、电荷和来源的配体激活的肥大细胞受体。我们的目标是更深入地了解不同MRGPRX2配体的结合过程和配体与受体的相互作用，以确定受体激活的关键结构元件。材料与方法：我们使用Cao等人、Yang等人在2021年Nature中描述的MRGPRX2的三维结构，在模拟生理条件下计算模拟MRGPRX2与小分子配体的相互作用。结果：对GPCR结合口袋内MRGPRX2配体的对接和对接后采样，鉴定了蛋白质-配体相互作用的关键结构特征。在配体方面，我们通过比较不同的配体绘制在受体上，获得了不同分子模式或化学基团的覆盖。这些关键特征包括MRGPRX2配体的至少一个质子化胺片段，有助于一个盐桥和一个π-阳离子相互作用，以及配体表面扩展的非极性结构域，提供疏水隔离和/或π-堆叠相互作用。在受体中，我们发现氨基酸（GLU164、ASP184、PHE101、PHE170、TRP243、PHE244和PHE257）通过氢键、盐桥、π-阳离子相互作用和π-π堆叠与配体特异性相互作用，直接结合并最终激活受体。讨论：我们通过分子建模获得的配体-受体相互作用的见解可以帮助预测MRGPRX2通过肥大细胞激活包括不良反应，并促进MRGPRX2拮抗剂的开发，用于治疗肥大细胞介导的疾病。

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引用次数: 0