ArticleComputational and structural biotechnology journal2023
Reversal of the unique Q493R mutation increases the affinity of Omicron S1-RBD for ACE2.
Article in Computational and structural biotechnology journal, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 37 citations in OpenAlex.
- Differential Impact of Substrate Peptides on Interdomain Interactions in Severe Acute Respiratory Syndrome Coronavirus 2 Main Protease.Computational and structural biotechnology journal · 2026Article
- Convergent Evolution and Host-Limiting Impacts of SARS-CoV-2 Revealed by Cellular Experiments.Molecular biology and evolution · 2025Article
- Selective Endocytosis-Mediated Omicron S1-RBD Internalization Revealed by Reconstitution of ACE2-S1-RBD Interaction on Micropatterned Membrane Substrates.International journal of molecular sciences · 2025Article
- What Has SARS-CoV-2 Taught Us About Evolution?Cureus · 2025Review
- An Italian Single-Center Genomic Surveillance Study: Two-Year Analysis of SARS-CoV-2 Spike Protein Mutations.International journal of molecular sciences · 2025Article
- Is SARS-CoV-2 facing constraints in its adaptive evolution?Biomolecules & biomedicine · 2025Review
- Structural and Energetic Insights into SARS-CoV-2 Evolution: Analysis of hACE2-RBD Binding in Wild-Type, Delta, and Omicron Subvariants.International journal of molecular sciences · 2025Article
- Coevolving residues distant from the ligand binding site are involved in GAF domain function.Communications chemistry · 2025Article
- Decoding the cross-immune pressure: Dengue's role in SARS-CoV-2 evolution.Computational and structural biotechnology journal · 2025Article
- Structural basis for receptor-binding domain mobility of the spike in SARS-CoV-2 BA.2.86 and JN.1.Nature communications · 2024Article
- The Recognition Pathway of the SARS-CoV-2 Spike Receptor-Binding Domain to Human Angiotensin-Converting Enzyme 2.Molecules (Basel, Switzerland) · 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
- Unraveling the binding mechanisms of SARS-CoV-2 variants through molecular simulations.Heliyon · 2024Article
- AlphaFold2-Enabled Atomistic Modeling of Structure, Conformational Ensembles, and Binding Energetics of the SARS-CoV-2 Omicron BA.2.86 Spike Protein with ACE2 Host Receptor and Antibodies: Compensatory Functional Effects of Binding Hotspots in Modulating Mechanisms of Receptor Binding and Immune Escape.Journal of chemical information and modeling · 2024Article
- SARS-CoV-2 Omicron (BA.4, BA.5) variant: Lessons learned from a new variant during the COVID-19 pandemic.Health science reports · 2024Article
- BRET-based biosensors for SARS-CoV-2 oligonucleotide detection.Frontiers in bioengineering and biotechnology · 2024Article
- A potential allosteric inhibitor of SARS-CoV-2 main protease (MFrontiers in molecular biosciences · 2024Article
- Computational Investigation of Selected Spike Protein Mutations in SARS-CoV-2: Delta, Omicron, and Some Circulating Subvariants.Pathogens (Basel, Switzerland) · 2023Article
- Impact of mutations defining SARS-CoV-2 Omicron subvariants BA.2.12.1 and BA.4/5 on Spike function and neutralization.iScience · 2023Article
- Functional Characterization of NovelInternational journal of molecular sciences · 2023Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The SARS-CoV-2 Omicron variant containing 15 mutations, including the unique Q493R, in the spike protein receptor binding domain (S1-RBD) is highly infectious. While comparison with previously reported mutations provide some insights, the mechanism underlying the increased infections and the impact of the reversal of the unique Q493R mutation seen in BA.4, BA.5, BA.2.75, BQ.1 and XBB lineages is not yet completely understood. Here, using structural modelling and molecular dynamics (MD) simulations, we show that the Omicron mutations increases the affinity of S1-RBD for ACE2, and a reversal of the unique Q493R mutation further increases the ACE2-S1-RBD affinity. Specifically, we performed all atom, explicit solvent MD simulations using a modelled structure of the Omicron S1-RBD-ACE2 and compared the trajectories with the WT complex revealing a substantial reduction in the Cα-atom fluctuation in the Omicron S1-RBD and increased hydrogen bond and other interactions. Residue level analysis revealed an alteration in the interaction between several residues including a switch in the interaction of ACE2 D38 from S1-RBD Y449 in the WT complex to the mutated R residue (Q493R) in Omicron complex. Importantly, simulations with Revertant (Omicron without the Q493R mutation) complex revealed further enhancement of the interaction between S1-RBD and ACE2. Thus, results presented here not only provide insights into the increased infectious potential of the Omicron variant but also a mechanistic basis for the reversal of the Q493R mutation seen in some Omicron lineages and will aid in understanding the impact of mutations in SARS-CoV-2 evolution.
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