ArticleInternational journal of molecular sciences2022
A Uniquely Stable Trimeric Model of SARS-CoV-2 Spike Transmembrane Domain.
Article in International journal of molecular sciences, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
What it found
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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
6 citing papers in PubMed.
- SARS-CoV-2 Spike Protein XBB.1.5 Mutations Altered Four Conserved Antigenic Determinants.International journal of molecular sciences · 2026Article
- Role of the transmembrane domain in severe acute respiratory syndrome (SARS) coronavirus 2 spike for palmitoylation and membrane fusion.Protein science : a publication of the Protein Society · 2026Article
- Cholesterol in viral envelope determines infectivity of SARS-CoV-2 and other coronaviruses.Frontiers in microbiology · 2025Article
- Inconspicuous Yet Indispensable: The Coronavirus Spike Transmembrane Domain.International journal of molecular sciences · 2023Review
- Prospecting native and analogous peptides with anti-SARS-CoV-2 potential derived from the trypsin inhibitor purified from tamarind seeds.Arabian journal of chemistry · 2023Article
- Progress of the "Molecular Informatics" Section in 2022.International journal of molecular sciences · 2023Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Understanding fusion mechanisms employed by SARS-CoV-2 spike protein entails realistic transmembrane domain (TMD) models, while no reliable approaches towards predicting the 3D structure of transmembrane (TM) trimers exist. Here, we propose a comprehensive computational framework to model the spike TMD only based on its primary structure. We performed amino acid sequence pattern matching and compared the molecular hydrophobicity potential (MHP) distribution on the helix surface against TM homotrimers with known 3D structures and selected an appropriate template for homology modeling. We then iteratively built a model of spike TMD, adjusting "dynamic MHP portraits" and residue variability motifs. The stability of this model, with and without palmitoyl modifications downstream of the TMD, and several alternative configurations (including a recent NMR structure), was tested in all-atom molecular dynamics simulations in a POPC bilayer mimicking the viral envelope. Our model demonstrated unique stability under the conditions applied and conforms to known basic principles of TM helix packing. The original computational framework looks promising and could potentially be employed in the construction of 3D models of TM trimers for a wide range of membrane proteins.
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Registered trials
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