ArticleNature chemistry2021
A glycan gate controls opening of the SARS-CoV-2 spike protein.
Article in Nature chemistry, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 222 papers.
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222 citing papers in PubMed.
- Disulfide bonds stabilize the SARS-CoV-2 RBD and preserve binding to ACE2 following thermal denaturation.Bioscience reports · 2026Article
- Structural dynamics and allosteric communication of a SARS-like bat coronavirus spike glycoprotein.Biophysical journal · 2026Article
- Mass spectrometry-based mapping of conformational epitopes on SARS-CoV-2 antigens targeted by monoclonal antibodies.International journal of biological macromolecules · 2026Article
- Machine Learning-Driven Simulations of the SARS-CoV-2 Fitness Landscape from Deep Mutational Scanning Experiments.Journal of chemical information and modeling · 2026Article
- Large-scale protein conformational transitions revealed by weighted ensemble simulations and EPR.Chemical science · 2026Article
- Concanavalin A targets phylogenetically conserved N-linked glycans on coronavirus spike proteins for broad-spectrum antiviral activity.Journal of virology · 2026Article
- D614G reshapes allosteric networks and opening mechanisms of SARS-CoV-2 spikes.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Glycosite mapping and in situ mass spectrometry imaging of MUC2 glycopeptides via on-slide mucinase digestion.Nature communications · 2026Article
- Generation of Pathway Signatures by Combining Normal Modes with Weighted Ensemble Simulations.bioRxiv : the preprint server for biology · 2026Article
- N-Glycans modulate tilting of HIV-1 envelope glycoprotein.Nature communications · 2026Article
- The Open Molecular Software Foundation (OMSF) and the Growing Role of Open Source Software in Molecular Modeling.Journal of chemical information and modeling · 2026Review
- Glycans Modulate the Adsorption of RBD Glycoproteins on Polarizable Surfaces.Journal of chemical information and modeling · 2026Article
- Structural basis for bat receptor recognition by SARS-CoV-2 and bat SARS2-like coronaviruses.Communications biology · 2026Article
- Recent advances in machine learning and coarse-grained potentials for biomolecular simulations.Biophysical journal · 2026Review
- Mutation and ACE2-induced allosteric network rewiring in Delta and Omicron SARS-CoV-2 spike proteins.Biophysical journal · 2026Article
- Discovery of thiadiazole-based small-molecule inhibitors of SARS-CoV-2 spike-ACE2 interaction through integrated computational prediction and experimental validation.Scientific reports · 2026Article
- The roles of post-translational modifications in the pathogenesis of RNA viruses: allies or adversaries?Frontiers in microbiology · 2026Review
- Identification and genomic characterization of BA.3.2: a highly divergent BA.3-related SARS-CoV-2 lineage from southern Africa.Virus evolution · 2026Article
- Comparing cryo-EM methods and molecular dynamics simulation to investigate heterogeneity in ligand-bound TRPV1.Nature communications · 2025Article
- Weighted Ensemble Simulations Reveal Novel Conformations and Modulator Effects in Hepatitis B Virus Capsid Assembly.Journal of chemical theory and computation · 2025Article
162 more citing papers are in PubMed but not listed here.
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17 authors.
Funding
Abstract
SARS-CoV-2 infection is controlled by the opening of the spike protein receptor binding domain (RBD), which transitions from a glycan-shielded 'down' to an exposed 'up' state to bind the human angiotensin-converting enzyme 2 receptor and infect cells. While snapshots of the 'up' and 'down' states have been obtained by cryo-electron microscopy and cryo-electron tomagraphy, details of the RBD-opening transition evade experimental characterization. Here over 130 µs of weighted ensemble simulations of the fully glycosylated spike ectodomain allow us to characterize more than 300 continuous, kinetically unbiased RBD-opening pathways. Together with ManifoldEM analysis of cryo-electron microscopy data and biolayer interferometry experiments, we reveal a gating role for the N-glycan at position N343, which facilitates RBD opening. Residues D405, R408 and D427 also participate. The atomic-level characterization of the glycosylated spike activation mechanism provided herein represents a landmark study for ensemble pathway simulations and offers a foundation for understanding the fundamental mechanisms of SARS-CoV-2 viral entry and infection.
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