ArticleJournal of chemical information and modeling2025
Exploring the Intrinsic Structural Plasticity and Conformational Dynamics of Human Beta Coronavirus Spike Glycoproteins.
Article in Journal of chemical information and modeling, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
1 citing paper in PubMed.
- Uncovering potent natural phytochemicals targeting SARS-COV-2 spike protein variants: molecular dynamics insights.Scientific reports · 2025Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The spike (S) glycoprotein of human beta coronaviruses (HCoVs) is central to viral entry, receptor engagement, and immune evasion. Here, we present an in-depth computational analysis of spike conformational dynamics across HCoVs, with a focus on SARS-CoV-2 and its variants. Leveraging a large cryo-EM structural ensemble and integrative modeling approaches, we dissect the intrinsic plasticity and variant-specific motions of the spike protein. Our results show that, despite substantial sequence divergence, HCoV spikes retain the ability to sample open and closed receptor-binding domain (RBD) states. For SARS-CoV-2, a hinge-like RBD opening motion dominates the conformational landscape, modulating ACE2 accessibility. Ensemble and single-structure normal modes revealed conserved dynamic domains and hinge regions and showed strong agreement with experimental structural transitions. Ligand binding rather than the D614G mutation was the principal driver of RBD opening, with multiple open RBDs observed predominantly in ligand-bound states. Notably, Omicron spike structures favored closed RBDs in the
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Registered trials
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