ArticleCommunications biology2022
SARS-CoV-2 spike opening dynamics and energetics reveal the individual roles of glycans and their collective impact.
Article in Communications biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed, 71 citations in OpenAlex.
- Disulfide bonds stabilize the SARS-CoV-2 RBD and preserve binding to ACE2 following thermal denaturation.Bioscience reports · 2026Article
- Flavonoids as Structural Probes Reveal Conformationally Dependent Ligand Recognition in the SARS-CoV-2 JN.1 Spike Protein.International journal of molecular sciences · 2026Article
- DeepPath: overcoming data scarcity for protein transition pathway prediction using physics-based deep learning.Chemical science · 2026Article
- Generating 3D models of complex carbohydrates with GLYCAM-Web.Nature methods · 2026Article
- Mutation and ACE2-induced allosteric network rewiring in Delta and Omicron SARS-CoV-2 spike proteins.Biophysical journal · 2026Article
- Mutation and ACE2-induced Allosteric Network Rewiring in Delta and Omicron SARS-CoV-2 Spike Proteins.bioRxiv : the preprint server for biology · 2025Article
- Article
- A Reflection on the Use of Molecular Simulation to Respond to SARS-CoV-2 Pandemic Threats.The journal of physical chemistry letters · 2025Review
- Conformational and Stability Analysis of SARS-CoV-2 Spike Protein Variants by Molecular Simulation.Pathogens (Basel, Switzerland) · 2025Article
- Exploring the effects of N234 and N343 linked glycans to SARS CoV 2 spike protein pocket accessibility using Gaussian accelerated molecular dynamics simulations.Scientific reports · 2025Article
- Article
- Comprehensive analysis of SARS-CoV-2 Spike evolution: epitope classification and immune escape prediction.Virus evolution · 2025Article
- Article
- Article
- Enhanced Surface Accessibility of SARS-CoV-2 Omicron Spike Protein Due to an Altered Glycosylation Profile.ACS infectious diseases · 2024Article
- Article
- Testing the feasibility of targeting a conserved region on the S2 domain of the SARS-CoV-2 spike protein.Biophysical journal · 2024Article
- Ensemble-Based Mutational Profiling and Network Analysis of the SARS-CoV-2 Spike Omicron XBB Lineages for Interactions with the ACE2 Receptor and Antibodies: Cooperation of Binding Hotspots in Mediating Epistatic Couplings Underlies Binding Mechanism and Immune Escape.International journal of molecular sciences · 2024Article
- Review
- Many Roles of Carbohydrates: A Computational Spotlight on the Coronavirus S Protein Binding.ACS applied bio materials · 2024Review
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The trimeric spike (S) glycoprotein, which protrudes from the SARS-CoV-2 viral envelope, binds to human ACE2, initiated by at least one protomer's receptor binding domain (RBD) switching from a "down" (closed) to an "up" (open) state. Here, we used large-scale molecular dynamics simulations and two-dimensional replica exchange umbrella sampling calculations with more than a thousand windows and an aggregate total of 160 μs of simulation to investigate this transition with and without glycans. We find that the glycosylated spike has a higher barrier to opening and also energetically favors the down state over the up state. Analysis of the S-protein opening pathway reveals that glycans at N165 and N122 interfere with hydrogen bonds between the RBD and the N-terminal domain in the up state, while glycans at N165 and N343 can stabilize both the down and up states. Finally, we estimate how epitope exposure for several known antibodies changes along the opening path. We find that the BD-368-2 antibody's epitope is continuously exposed, explaining its high efficacy.
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