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
Introduction: A sub-lineage of Delta with an additional mutation, K417N is termed as AY.1 (Delta-plus).
Introduction: Another variant from South Africa (B.1.351) emerged independently with multiple mutations in the RBD (K417N and E484K) along with N501Y, however, lacked the 69/70 deletion mutations in the NTD segment.
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: Similarly, P.1
Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data.
PMID: 34806876
2021
Journal of chemical information and modeling
Abstract: However, Lys417Asn seems to have a compensatory mechanism of action increasing the S1 RBD-ACE2 free energy of binding.
Abstract: The N501Y and K417N mutations in the spike protein of SARS-CoV-2 and their combination gave rise to questions, but the data on their mechanism of action at the molecular level were limited.
Abstract: The K417N mutation in a combination with N501Y fully abolished the antibody effect.
Analysis of BNT162b2- and CVnCoV-elicited sera and of convalescent sera toward SARS-CoV-2 viruses.
Result: K417N by itself significantly reduces binding (Figure 3b).
Result: As in the direct ELISA, reduced CB6 binding was seen with the gamma and K417N RBDs.
Result: In contrast, 2E8 binding to RBDs with a single K417N or E484K mutation was not impaired (Figure 3a).
Result: The 2E8 ELISA bound to L, delta, the K417N mutant, kappa, and epsilon but not to any of the Y501-containing variant proteins: alpha, beta, and gamma.
Result: We also tested RBDs
Discussion: This is attributable to the K417N mutation, which alone reduces affinity 21.9-fold compared to a 13.8-fold reduction from the K417T change.
SARS-CoV-2 Variants, RBD Mutations, Binding Affinity, and Antibody Escape.
PMID: 34829998
2021
International journal of molecular sciences
Introduction: Surprisingly, the mutations of L452R, K417N, Y453F, E484K N501Y, and F490S transform the Ho-Hi interactions into Ho-Ho or ADD interactions at these positions, thus increasing the binding affinity with ACE2.
Introduction: There have been a number of missense mutations observed in the receptor-binding domain (RBD) of the SARS-CoV-2 S protein, which have presented in one or more of the VOCs, including the N440K, G446V, L452R, Y453F, E484Q, F490S, N501Y
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in a Dog in Connecticut in February 2021.
Result: The virus from this CT dog did not contain mutations related to the South African variant B.1.351 (N501Y, E484K and K417N in Spike) or the U.K.
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.
Introduction: Shortly after the appearance of D614G, other mutations in the Receptor Binding Domain (RBD
Result: Among these results, although not at a high frequency, cases of T478K co-occurring with other spike protein mutations of concern could be detected, including: (i) K417N, which is present in 20h/501Y.V2 or B.1.351, identified in one sample (February 2021, GISAID EPI ISL 1137473); (ii) L18F, which is present in 20J/501Y.V3 or P.1, identified in one sequence from the State of Oaxaca, in the parental lineage B.1 (January 2021, GISAID EPI ISL 1168605); and (iii) the deletion of an amino acid in position 144, which occurs in 20I/501Y.V1 or B.1.1.7 and 20A/S.484K or B.1.525, in one sample from Mexico City (February 2020, GISAID EPI ISL 1181713).
Molecular insights into receptor binding energetics and neutralization of SARS-CoV-2 variants.
Result: The same contact is more persistent in Alpha variant with freq ~ 0.9 and under mutations K417N and K417T in Beta and Gamma respectively, the contact frequency drops below 0.4, which correlates with the dramatic drop of the electrostatic contribution in the interfacial energy.
Differential Interactions between Human ACE2 and Spike RBD of SARS-CoV-2 Variants of Concern.
PMID: 34856802
2021
Journal of chemical theory and computation
Conclusion: K417N/T mutations of Beta and Gamma appear to make the RBD-ACE2 interactions less strong compared to the Alpha variant.
Method: From the WT RBD structure, each variant was modeled with the following mutations: Alpha (N501Y), Beta (K417N, E484K, N501Y), Gamma (
Result: As shown in Figure 2B and C, Alpha and Beta variants include the N501Y mutation, while the Beta variant involves two additional mutations, K417N and E484 K.
Result: The only difference between Gamma and Beta is the K417 mutation, i.e., K417T vs K417N.
Recognition of Variants of Concern by Antibodies and T Cells Induced by a SARS-CoV-2 Inactivated Vaccine.
Introduction: Furthermore, Beta and Gamma exhibit mutations in the residue K417 of the RBD but differ in the amino acid substitutions (K417N for Beta and K417T for Gamma), which may affect antibody binding.
SARS_CoV_2 mutation literature information.
PMID: 
2021
Current research in structural biology
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