ArticleJournal of molecular graphics & modelling2022
Omicron BA.1 and BA.2 variants increase the interactions of SARS-CoV-2 spike glycoprotein with ACE2.
Article in Journal of molecular graphics & modelling, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 33 citations in OpenAlex.
- SARS-CoV-2 infection of domestic animals and their role in evolution and emergence of variants of concern.New microbes and new infections · 2024Review
- The mechanism and energetics of the dynein priming stroke.Structure (London, England : 1993) · 2024Article
- SARS-CoV-2 Omicron Subvariants Do Not Differ Much in Binding Affinity to Human ACE2: A Molecular Dynamics Study.The journal of physical chemistry. B · 2024Article
- Review
- SARS-CoV-2 omicron spike simulations: broad antibody escape, weakened ACE2 binding, and modest furin cleavage.Microbiology spectrum · 2023Article
- Determinants of species-specific utilization of ACE2 by human and animal coronaviruses.Communications biology · 2023Article
- SARS-CoV-2 Omicron Specific Mutations Affecting Infectivity, Fusogenicity, and Partial TMPRSS2-Independency.Viruses · 2023Article
- Heterologous boost with mRNA vaccines against SARS-CoV-2 Delta/Omicron variants following an inactivated whole-virus vaccine.Antiviral research · 2023Article
- Angiotensin-Converting Enzyme 2 Expression and Severity of SARS-CoV-2 Infection.Microorganisms · 2023Review
- A metabolic readout of the urine metabolome of COVID-19 patients.Metabolomics : Official journal of the Metabolomic Society · 2023Article
- SARS-CoV-2 and its impact on the cardiovascular and digestive systems - The interplay between new virus variants and human cells.Computational and structural biotechnology journal · 2023Review
- Article
- Probing Mechanisms of Binding and Allostery in the SARS-CoV-2 Spike Omicron Variant Complexes with the Host Receptor: Revealing Functional Roles of the Binding Hotspots in Mediating Epistatic Effects and Communication with Allosteric Pockets.International journal of molecular sciences · 2022Article
- Determinants of Spike infectivity, processing, and neutralization in SARS-CoV-2 Omicron subvariants BA.1 and BA.2.Cell host & microbe · 2022Article
- Are we moving toward ending SARS-CoV-2?Journal of medical virology · 2022Article
- Host chitinase 3-like-1 is a universal therapeutic target for SARS-CoV-2 viral variants in COVID-19.eLife · 2022Article
- Identifying vaccine escape sites via statistical comparisons of short-term molecular dynamics.Biophysical reports · 2022Article
- The puzzling mutational landscape of the SARS-2-variant Omicron.Journal of medical virology · 2022Article
- Omicron: What Makes the Latest SARS-CoV-2 Variant of Concern So Concerning?Journal of virology · 2022Review
- An infectious SARS-CoV-2 B.1.1.529 Omicron virus escapes neutralization by therapeutic monoclonal antibodies.Nature medicine · 2022Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
SARS-CoV-2 infection is initiated by binding of the receptor-binding domain (RBD) of its spike glycoprotein to the peptidase domain (PD) of angiotensin-converting enzyme 2 (ACE2) receptors in host cells. Recently detected Omicron variant of SARS-CoV-2 (B.1.1.529) is heavily mutated on RBD. First the BA.1 and later the BA.2 variant became the most dominant strains of the Omicron variant. To investigate how the mutations of these strains affect RBD-PD interactions, we performed all-atom molecular dynamics simulations of the BA.1 and BA.2 RBD-PD in the presence of full-length glycans, explicit water, and ions. Simulations revealed that RBDs of BA.1 and BA.2 variants exhibit a more dispersed interaction network and make an increased number of salt bridges and hydrophobic interactions with PD compared to wild-type RBD. Although BA.1 and BA.2 differ in two residues at the RBD-ACE2 interface, no major difference in RBD-PD interactions and binding strengths were observed between these variants. Using the conformations sampled in each trajectory, the Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) method estimated ∼34% and ∼51% stronger binding free energies to PD for BA.1 and BA.2 RBD, respectively, than wild-type RBD, which may result in higher binding efficiency of the Omicron variant to infect host cells.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.