Origin of the tight binding mode to ACE2 triggered by multi-point mutations in the omicron variant: a dynamic insight.
PMID: 35373810
2022
Physical chemistry chemical physics
Abstract: This was due to the large number of positively charged patches (N440K, T478K, Q493R, Q498R, and Y505H) formed by the substitution of neutral amino acids at multiple sites.
SARS-CoV-2 BA.1 variant is neutralized by vaccine booster-elicited serum, but evades most convalescent serum and therapeutic antibodies.
PMID: 35380448
2022
Science translational medicine
Result: We compared the neutralization titers of these serum samples against pseudoviruses bearing spike proteins from the following variants: D614G, Omicron (A67V, del69-70, T95I, del142-144, Y145D, del211, L212I, ins214EPE, G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R,
Role of the Microbiome in the Pathogenesis of COVID-19.
PMID: 35433495
2022
Frontiers in cellular and infection microbiology
Table: Q493R
Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD.
Result: The same G339D, T478K, Q493R, G496S, and Q498R in the RBD region have also increased the antigen score, but these changes were not significant.
Computer Simulations and Network-Based Profiling of Binding and Allosteric Interactions of SARS-CoV-2 Spike Variant Complexes and the Host Receptor: Dissecting the Mechanistic Effects of the Delta and Omicron Mutations.
PMID: 35457196
2022
International journal of molecular sciences
Result: In the Omicron RBD-ACE2 complex, Q493R forms new salt bridges with E35, Q498R makes new contacts with D38 and Q42, and G496S and Y505H form new hydrogen bonds with K353 (Figure 4E,F).
Result: Interestingly, we found increased values for the distance fluctuation stability index of the Q493R, G496S and
Result: These observations are consistent with our hypothesis that key Omicron mutations, including Q493R, G496S and Q498R, display a stronger allosteric potential in the Omicron complex and therefore may allosterically modulate the stabilization of the RBD and ACE2 regions.
SARS-CoV-2 mutations acquired during serial passage in human cell lines are consistent with several of those found in recent natural SARS-CoV-2 variants.
PMID: 35474907
2022
Computational and structural biotechnology journal
Abstract: In the spike protein, Q493R and Q498R substitutions from passaged viruses were consistent with those in the B.1.1.529 (Omicron) variant.
Result: An additional Q493R mutation was found in one virus each passaged in A549 and Caco-2 cells.
Discussion: For example, Q493R and Q498R substitutions in the RBD were identified in this study and are consistent with key amino acid substitutions in the Omicron variant, which was first reported on November 24, 2021, in South Africa.
Binding Interactions between Receptor-Binding Domain of Spike Protein and Human Angiotensin Converting Enzyme-2 in Omicron Variant.
PMID: 35481766
2022
The journal of physical chemistry letters
Abstract: Other mutations, such as K417N, G446S, and Y505H, decrease the ACE2 binding, whereas S447N, Q493R, G496S, Q498R, and N501Y tend to increase it.
Discriminatory Weight of SNPs in Spike SARS-CoV-2 Variants: A Technically Rapid, Unambiguous, and Bioinformatically Validated Laboratory Approach.
Introduction: Last in order of arrival but certainly not least, the variant called Omicron (B.1.1.529) is characterized by more than thirty mutations on the spike gene only, many of these unique (E484A, Q493R, G496S, Q498R, N501Y, Y505H, T547K, H655Y, and N679K) while others are shared with other lineages (for example T478K with Delta and P681H with Alpha and Mu).
SARS_CoV_2 mutation literature information.
PMID: 
2022
Virus research
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