A rigorous framework for detecting SARS-CoV-2 spike protein mutational ensemble from genomic and structural features.
PMID: 34806033
2021
Current research in structural biology
Result: Further, for the characteristic RBD mutations across VoCs (K417 T/N, L452R, S477N, T478K, E484K, and N501Y), we observed MTR scores between 0.68 and 0.91, suggesting these substitutions to be tolerant.
Result: Interestingly, five out of eight mutations of RBD are present in the epitope region, where L452Rand N501Y substitutions map to the RBD-loop epitope and S477N, T478K, and E484K are harboured in the RBD-ridge epitope.
Discussion: studied the effect of five prevalent
Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2.
4Method: In I2, R203K/G204R present an r- with LG_4, an r- with S194L, an r+ with LG_5 and an r+ with S477N (""Cor_mut.pdf"" in Data S1)."
Method: We first created 7-bp sequences by combining the nucleotide sequences of different strains at seven mutation sites (R203K/G204R (LG_3), N501Y (LG_5), A222V (LG_4), C313T, S477N, S194L and I120F).
Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms.
Method: We marked the important mutations S477N, T478K, E484K, D614G, P681H/R and T732A.
Result: A similar scenario with multiple combinations at the c
Discussion: Mutations T478K and S477N, involving changes from similar hydroxylated side-chains (T and S) into positively charged basic amino acids (K and N), may have analogous functional roles, reinforcing the ability of the virus to bind to the human ACE2 receptor.
Discussion: The first one is in the flexible loop of the RBD, and includes S477N, T478K and E484K.
Emergence of novel combinations of SARS-CoV-2 spike receptor binding domain variants in Senegal.
Abstract: Amongst these genomes, new combinations of SARS-CoV-2 spike mutations were identified, with E484K + N501T, L452R + N501Y, and L452M + S477N exclusively found in second wave specimens.
Additional Positive Electric Residues in the Crucial Spike Glycoprotein S Regions of the New SARS-CoV-2 Variants.
Result: In particular, Zahradnik et al., identified enhanced ACE2 binding by RBD's bearing Q498R and S477N when combined with the N501Y mutation [Zahradnik et al].
Structural models of SARS-CoV-2 Omicron variant in complex with ACE2 receptor or antibodies suggest altered binding interfaces.
Introduction: The Omicron spike in this study contained mutations A67V, Delta69-70, T95I, G142D, Delta143-145, Delta211, L212I, +214EPE, G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, Y505H, T547K,
The Development of SARS-CoV-2 Variants: The Gene Makes the Disease.
PMID: 34940505
2021
Journal of developmental biology
Introduction: Mutation Y453F, along with N439K, G446V, K444E, and S477N, among others, which are located at the interface between the S1 and ACE2, have been shown to partially interfere with antibody binding and neutralization.
Insights into the Binding of Receptor-Binding Domain (RBD) of SARS-CoV-2 Wild Type and B.1.620 Variant with hACE2 Using Molecular Docking and Simulation Approaches.
Abstract: Recently, a new variant, B.1620, with mutations (S477N-E484K) in the spike protein's receptor-binding domain (RBD) has been reported in Europe.
Abstract: The current findings based on protein complex modeling and bio-simulation methods revealed the atomic features of the B.1.620 variant harboring S477N and E484K mutations in the RBD and the basis for infectivity.
Introduction: A report published in Cell reported that these mutations (S477N-E484K) in the RBD increase the binding affinity for the host receptor ACE2.
Introduction: Recently, a new variant, B.1620, with mutations (S477N
SARS_CoV_2 mutation literature information.
PMID: 
2021
Current research in structural biology
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