Journal of structural biology最新文献_第4页

NMR and semi-synthesis in synergy to study protein regulation 核磁共振和半合成协同研究蛋白质调控。

IF 3 3区生物学

Journal of structural biology Pub Date : 2025-03-13 DOI: 10.1016/j.jsb.2025.108192

Thibault Viennet

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

Journal of structural biology Pub 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

{"title":"MRGPRX2 ligandome: Molecular simulations reveal three categories of ligand-receptor interactions","authors":"Philip Maier , Moritz Macht , Silvan Beck , Pavel Kolkhir , Magda Babina , Andreas E. Kremer , Dirk Zahn , Katharina Wolf","doi":"10.1016/j.jsb.2025.108193","DOIUrl":"10.1016/j.jsb.2025.108193","url":null,"abstract":"<div><h3>Introduction</h3><div>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.</div></div><div><h3>Materials and methods</h3><div>We used the three-dimensional structure of MRGPRX2 described in <em>Nature</em> 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.</div></div><div><h3>Results</h3><div>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.</div></div><div><h3>Discussion</h3><div>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.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"217 2","pages":"Article 108193"},"PeriodicalIF":3.0,"publicationDate":"2025-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143630507","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Allosteric inhibition of cytosolic NADP+-dependent isocitrate dehydrogenase by oxaloacetate 草酰乙酸对胞浆内NADP+依赖性异柠檬酸脱氢酶的变构抑制作用。

IF 3 3区生物学

Journal of structural biology Pub Date : 2025-03-08 DOI: 10.1016/j.jsb.2025.108183

Dong Kyu Kim , Ha Yeon Cho , Hyo Je Cho , Beom Sik Kang

{"title":"Allosteric inhibition of cytosolic NADP+-dependent isocitrate dehydrogenase by oxaloacetate","authors":"Dong Kyu Kim , Ha Yeon Cho , Hyo Je Cho , Beom Sik Kang","doi":"10.1016/j.jsb.2025.108183","DOIUrl":"10.1016/j.jsb.2025.108183","url":null,"abstract":"<div><div>NADP<sup>+</sup>-dependent cytosolic isocitrate dehydrogenase (IDH1) plays a crucial role in providing reducing energy in response to oxidative stress through the oxidative decarboxylation of isocitrate. NADPH generated by IDH1 serves as an essential cofactor for fatty acid synthesis. The regulation of IDH1 activity is vital for the biological functions of NADPH within cells, and mutations in IDH1 have been implicated in various cancers. In an effort to identify small regulatory molecules for IDH1, we determined the crystal structures of mouse IDH1 complexed with isocitrate and with oxaloacetate. Each IDH1 comprises large and small domains that form an active site, along with a clasp domain that connects two IDH1 molecules for dimerization. Isocitrate was located at the active site in the presence of a magnesium ion, while oxaloacetate was found at a novel site formed by the two clasp domains, in addition to the active site. The activity of IDH1 was diminished in the presence of oxaloacetate and could not be restored by the addition of isocitrate, indicating the presence of allosteric regulation. The activity of the IDH1 H170A mutant, which is unable to bind oxaloacetate in the clasp domain, was unaffected by oxaloacetate. This allosteric regulatory site may serve as a potential target for novel IDH1 inhibitors.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"217 2","pages":"Article 108183"},"PeriodicalIF":3.0,"publicationDate":"2025-03-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143597205","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

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

Journal of structural biology Pub Date : 2025-03-05 DOI: 10.1016/j.jsb.2025.108184

Prashant K. Singh , T.M. Iverson

{"title":"Improving CryoEM maps of symmetry-mismatched macromolecular assemblies: A case study on the flagellar motor","authors":"Prashant K. Singh , T.M. Iverson","doi":"10.1016/j.jsb.2025.108184","DOIUrl":"10.1016/j.jsb.2025.108184","url":null,"abstract":"<div><div>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 <em>E. coli</em>. 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.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"217 2","pages":"Article 108184"},"PeriodicalIF":3.0,"publicationDate":"2025-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143585985","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Cryo-iCLEM: Cryo correlative light and electron microscopy with immersion objectives Cryo- iclem：带浸没物镜的低温相关光学和电子显微镜。

IF 3 3区生物学

Journal of structural biology Pub Date : 2025-03-01 DOI: 10.1016/j.jsb.2025.108179

Niko Faul , Shih-Ya Chen , Christian Lamberz , Mark Bruckner , Christian Dienemann , Thomas P. Burg

{"title":"Cryo-iCLEM: Cryo correlative light and electron microscopy with immersion objectives","authors":"Niko Faul , Shih-Ya Chen , Christian Lamberz , Mark Bruckner , Christian Dienemann , Thomas P. Burg","doi":"10.1016/j.jsb.2025.108179","DOIUrl":"10.1016/j.jsb.2025.108179","url":null,"abstract":"<div><div>Correlative light and electron microscopy (CLEM) is a powerful tool for investigating cellular structure and function at the molecular level. However, while electron microscopy is often performed to great advantage at cryogenic temperatures, this is not always the case for light microscopy. One key challenge is the lack of cryo-compatible immersion objectives. In recent years, multiple cryoimmersion light microscopy (cryo-iLM) approaches have been described, but these techniques have never been used in correlative approaches. Here we present a novel workflow for correlative cryoimmersion light microscopy and electron cryomicroscopy (cryo-iCLEM). Cryo-electron tomography conducted before and after cryo-iLM reveals that cryo-iCLEM maintains ultra-thin, electron-transparent samples mechanically intact and does not degrade the ultrastructural preservation achieved through plunge-freezing. For cryo-iLM, the sample is first embedded in a viscous immersion medium at cryogenic temperatures and examined with a custom cryo-immersion objective. After cryo-iLM, the immersion medium is dissolved in liquid ethane, allowing for subsequent cryo-EM imaging. We further show that cryo-iCLEM can be used on FIB-lamellae, demonstrating that mechanically sensitive samples remain undamaged. Embedding the sample in the immersion fluid reduces contamination and thus allows data acquisition over many hours. Samples can therefore be examined in detail with the advantage of low bleaching rates of fluorophores at cryogenic temperatures. In the future, we hope that our approach can help improve the performance of many advanced light microscopy techniques when they are applied in the context of cryo-CLEM.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"217 1","pages":"Article 108179"},"PeriodicalIF":3.0,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143458330","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Lack of embryonic skeletal muscle in mice leads to abnormal mineral deposition and growth 小鼠胚胎骨骼肌缺乏导致异常的矿物质沉积和生长。

IF 3 3区生物学

Journal of structural biology Pub Date : 2025-03-01 DOI: 10.1016/j.jsb.2025.108178

Isabella Silva Barreto , Marianne Liebi , Sophie Le Cann , Saima Ahmed , Leonard C. Nielsen , Tilman A. Grünewald , Hector Dejea , Viviane Lutz-Bueno , Niamh C. Nowlan , Hanna Isaksson

{"title":"Lack of embryonic skeletal muscle in mice leads to abnormal mineral deposition and growth","authors":"Isabella Silva Barreto , Marianne Liebi , Sophie Le Cann , Saima Ahmed , Leonard C. Nielsen , Tilman A. Grünewald , Hector Dejea , Viviane Lutz-Bueno , Niamh C. Nowlan , Hanna Isaksson","doi":"10.1016/j.jsb.2025.108178","DOIUrl":"10.1016/j.jsb.2025.108178","url":null,"abstract":"<div><div>Developing bones can be severely impaired by a range of disorders where muscular loading is abnormal. Recent work has indicated that the effects of absent skeletal muscle on bones are more severe early in development, with rudiment length and mineralization lengths being almost normal in muscle-less limbs just prior to birth. However, the impact of abnormal mechanical loading on the nanoscale structure and composition during prenatal mineralization remains unknown. In this exploratory study, we characterized the mineralization process of humeri from muscle-less limb embryonic mice using a multiscale approach by combining X-ray scattering and fluorescence with infrared and light microscopy to identify potential key aspects of interest for future in-depth investigations. Muscle-less humeri were characterized by initially less mineralized tissue to later catch up with controls, and exhibited continuous growth of mineral particles, which ultimately led to seemingly larger mineral particles than their controls at the end of development. Muscle-less limbs exhibited an abnormal pattern of mineralization, reflected by a more widespread distribution of zinc and homogenous distribution of hydroxyapatite compared to controls, which instead showed trabecular-like structures and zinc localized only to regions of ongoing mineralization. The decrease in collagen content in the hypertrophic zone due to resorption of the cartilage collagen matrix was less distinct in muscle-less limbs compared to controls. Surprisingly, the nanoscale orientation of the mineral particles was unaffected by the lack of skeletal muscle. The identified accelerated progression of ossification in muscle-less limbs at later prenatal stages provides a possible anatomical mechanism underlying their recovery in skeletal development.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"217 1","pages":"Article 108178"},"PeriodicalIF":3.0,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143433421","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Computational Engineering of siderocalin to modulate its binding affinity to the antihypertension drug candesartan 铁苷调节其与抗高血压药物坎地沙坦结合亲和力的计算工程。

IF 3 3区生物学

Journal of structural biology Pub Date : 2025-03-01 DOI: 10.1016/j.jsb.2025.108180

Kristina Vogel , Johanna Moeller , Nina G. Bozhanova , Markus Voehler , Anja Penk , Jens Meiler , Clara T. Schoeder

{"title":"Computational Engineering of siderocalin to modulate its binding affinity to the antihypertension drug candesartan","authors":"Kristina Vogel , Johanna Moeller , Nina G. Bozhanova , Markus Voehler , Anja Penk , Jens Meiler , Clara T. Schoeder","doi":"10.1016/j.jsb.2025.108180","DOIUrl":"10.1016/j.jsb.2025.108180","url":null,"abstract":"<div><div>Lipocalin family proteins have been shown to bind a vast array of small molecules and have subsequently been adapted to selectively bind specific ligands. In this study, candesartan, an antihypertension drug, was identified to bind mouse and human siderocalin in biomolecular NMR experiments, allowing for structural insights into the candesartan-siderocalin interaction. The ligand binding site was determined through an integrative structural biology approach using <em>in silico</em> ligand docking guided by NMR experiments. Building on this structurally informed binding model, we used rational protein design to modulate the binding pocket for increased or decreased ligand binding affinity. The predicted mutations were evaluated <em>in vitro</em> using isothermal titration calorimetry. This resulted in a mutant with a 50-fold increase in binding affinity in addition to a second mutant with a five-fold decrease in binding affinity. Thus, siderocalins have potential as a scaffold for creation of various ligand binding-based tools, including drug scavengers.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"217 1","pages":"Article 108180"},"PeriodicalIF":3.0,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143468251","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Effects of Gα C-terminal deletion on the intrinsic GDP release/GTPase activity and conformational dynamics Gα C 端缺失对固有 GDP 释放/GTP 酶活性和构象动态的影响

IF 3 3区生物学

Journal of structural biology Pub Date : 2025-02-27 DOI: 10.1016/j.jsb.2025.108182

Junyoung Kim, Ka Young Chung

{"title":"Effects of Gα C-terminal deletion on the intrinsic GDP release/GTPase activity and conformational dynamics","authors":"Junyoung Kim, Ka Young Chung","doi":"10.1016/j.jsb.2025.108182","DOIUrl":"10.1016/j.jsb.2025.108182","url":null,"abstract":"<div><div>Heterotrimeric G proteins (G proteins) serve as key signaling mediators downstream of G protein-coupled receptors (GPCRs). Comprised of Gα, Gβ, and Gγ subunits, the activation state of Gα, determined by GDP or GTP binding, governs G protein activity. While high-resolution structures of GPCR-G protein complexes have identified the Gα C-terminal 5 residues (<em>i.e.,</em> wavy hook) as critical for GPCR binding and coupling selectivity, its influence on Gα’s intrinsic biochemical properties remains unclear. Here, we investigated the role of wavy hook truncation in the intrinsic GDP/GTP turnover rate, GTPase activity, and conformational dynamics of Gαs and Gαi1 using BODIPY-labeled nucleotides and hydrogen/deuterium exchange mass spectrometry (HDX-MS). Truncation of the wavy hook significantly altered the GDP/GTP turnover rate, GTPase activity, and conformational flexibility of Gαs, particularly at the p-loop through α1 region, but had minimal impact on Gαi1. These findings reveal subtype-specific effects of the wavy hook on G protein stability and conformational dynamics, highlighting the importance of structural elements in regulating G protein function and their implications for GPCR signaling studies.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"217 2","pages":"Article 108182"},"PeriodicalIF":3.0,"publicationDate":"2025-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143537316","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

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

Journal of structural biology Pub 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

{"title":"Three-dimensional reconstruction of Magnetofaba australis strain IT-1: Magnetosome chain position with respect to flagella","authors":"Eduardo Monteiro , Anderson S. Cabral , Viviana Morillo , Daniel Acosta-Avalos , Ulysses Lins , Fernanda Abreu","doi":"10.1016/j.jsb.2025.108181","DOIUrl":"10.1016/j.jsb.2025.108181","url":null,"abstract":"<div><div>Magnetotactic bacteria (MTB) are a broad and diverse group of Gram-negative prokaryotes that biomineralize magnetosomes, organelles composed of a magnetic nanocrystal of magnetite (Fe<sub>3</sub>O<sub>4</sub>) or greigite (Fe<sub>3</sub>S<sub>4</sub>) 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 <em>Magnetofaba australis</em> strain IT-1, an MTB that achieves high swimming speeds and has some peculiarity in its motility. The three-dimensional reconstruction showed that <em>Mf. australis</em> 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, <em>Mf. australis</em> 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 <em>Mf. australis</em> strain IT-1 with and without magnetosomes. Our results indicated that the magnetosome presence not only positively influences the movement in <em>Mf.australis</em> strain IT-1 but also can positively impact population growth in these MTB.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"217 2","pages":"Article 108181"},"PeriodicalIF":3.0,"publicationDate":"2025-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143531298","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Computational identification of B and T-cell epitopes for designing a multi-epitope vaccine against SARS-CoV-2 spike glycoprotein 设计抗SARS-CoV-2刺突糖蛋白多表位疫苗的B细胞和t细胞表位的计算鉴定

IF 3 3区生物学

Journal of structural biology Pub Date : 2025-02-11 DOI: 10.1016/j.jsb.2025.108177

Truc Ly Nguyen , Thong Ba Nguyen , Heebal Kim

{"title":"Computational identification of B and T-cell epitopes for designing a multi-epitope vaccine against SARS-CoV-2 spike glycoprotein","authors":"Truc Ly Nguyen , Thong Ba Nguyen , Heebal Kim","doi":"10.1016/j.jsb.2025.108177","DOIUrl":"10.1016/j.jsb.2025.108177","url":null,"abstract":"<div><div>Although the peak of the COVID-19 pandemic has passed, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to pose a significant global threat and remains a public health concern. Given the ongoing risk and the substantial loss of life caused by the virus, continuous research into vaccine development is essential. This study employs immunoinformatics approaches to identify T-cell and B-cell epitopes for designing a multi-epitope peptide vaccine candidate targeting the Omicron variant. The proposed vaccine construct comprises 1435 amino acids, including eight linear B lymphocyte, seven cytotoxic T lymphocyte, and five helper T lymphocyte epitopes, along with appropriate adjuvants and linkers. The evaluation of the vaccine revealed high antigenicity, non-allergenicity, non-toxicity, and favorable physicochemical properties. To further assess its efficacy, molecular docking studies were performed to investigate interactions between the vaccine and key immune components, including Toll-like receptors and major histocompatibility complex molecules. Stability of these interactions was confirmed using molecular dynamics simulations in triplicate, conducted over 100 ns using GROMACS 2023 to compute key metrics, such as root mean square deviation, root mean square fluctuation, solvent-accessible surface area, and radius of gyration. The results demonstrate that the multi-epitope vaccine has the potential to elicit strong immune responses against the Omicron variant, providing a promising foundation for further experimental validation and clinical development in COVID-19 vaccine research.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"217 2","pages":"Article 108177"},"PeriodicalIF":3.0,"publicationDate":"2025-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143414501","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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