Landscape-Based Mutational Sensitivity Cartography and Network Community Analysis of the SARS-CoV-2 Spike Protein Structures: Quantifying Functional Effects of the Circulating D614G Variant.
Introduction: Other studies examined dynamics and energetics of the S-D614 and S-G614 proteins in the closed and partially open conformations, suggesting that the S-G614 mutant can improve the interprotomer interactions between S1 and S2 regions.- MD simulations of other circulating variants revealed that the N501Y mutation increases ACE2-binding affinity.
Emergence in southern France of a new SARS-CoV-2 variant harbouring both N501Y and E484K substitutions in the spike protein.
Introduction: 3 of the 85 non-B.1.1.7 samples (B.1.258 lineage) were positive for del-HV69/70, but not N501Y, which was confirmed by the TIB MOL reference assays (Table 3 ).
Introduction: 50 B1.1.7 lineage samples were classified as positive for N501Y and del-HV69/70.
Introduction: Additionally, all samples were tested with a set of commercial assays to confirm the relevant mutations (TIB MOL, VirSNiP Spike N501Y and Del69/70, Berlin, Germany).
Introduction: An additional assay was designed (using Beacon designer and PrimerQuest software) and integrated into the multiplex to detect the N501Y SNP.
Introduction: In particular, non-synonymous spike-gene mutations such as the N501Y SNP (single nucleotide polymorphism) may
COVID-19 mRNA vaccine induced antibody responses against three SARS-CoV-2 variants.
Result: The amino acid changes in the spike protein, especially the aforementioned E484K, K417N, and N501Y have recently been reported to affect the neutralizing efficacy of the antibodies.
Result: The three B.1.351 variant substitutions E484K, K417N, and N501Y are in the groove of the RBD-ACE2 interaction domain.
Discussion: The critical amino acid changes linked to escape from humoral immunity in the B.1.351 variant appear to be K417N, E484K, and N501Y.
Evolution, correlation, structural impact and dynamics of emerging SARS-CoV-2 variants.
PMID: 34188776
2021
Computational and structural biotechnology journal
Abstract: However, reported greater binding affinity of N501Y Spike with ACE2 does not seem to be entirely due to increased hydrophobic interactions, given that Spike mutation R417T in P.1 or K417N in B.1.351 results in the loss of a salt-bridge interaction between ACE2 and S-RBD.
Abstract: Structural analysis indicated that the N501Y mutation may increase hydrophobic interactions at the ACE2/Spike interface.
Ultrapotent miniproteins targeting the SARS-CoV-2 receptor-binding domain protect against infection and disease.
Abstract: Importantly, LCB1v1.3 protected in vivo against a historical strain (WA1/2020), an emerging B.1.1.7 strain, and a strain encoding key E484K and N501Y spike protein substitutions.
Discussion: Based on the cryoelectron microscopy (cryo-EM) structure of the parent LCB1 binder in complex with SARS-CoV-2 RBD, only the N501Y mutation is expected to affect binding.
Discussion: Because structural data suggested that the N501Y mutation might affect LCB1 binding, we tested LCB1v1.3 against a virus encoding this mutation in vivo.
Discussion: In comparison, LCB1v1.3 showed efficacy against historical (WA1/2020) and emerging (B.1.1.7 and E484K/N501Y/D614G) S
SARS-CoV-2 mRNA vaccination induces functionally diverse antibodies to NTD, RBD, and S2.
Discussion: However, recent expansion of B.1.526, a lineage also featuring E484K but without N501Y in New York City, suggests that this fitness loss may be overcome by other, yet uncharacterized, changes in the virus as well.
Discussion: In fact, the B.1.351 RBD, which carries N501Y and E484K (as well as N417K) showed binding to hACE2 that was similar to wild-type RBD.
Discussion: Interestingly, Discussion: Interestingly, binding of convalescent sera to the N501Y RBD was also increased, suggesting that changes that increase affinity for the receptor may also increase affinity of a set of antibodies that may mimic the receptor.
A Unique SARS-CoV-2 Spike Protein P681H Variant Detected in Israel.
Introduction: Mutations in the SARS-CoV-2 genome affecting the S protein have emerged in numerous differentially-reported variants, such as the N501Y mutation that is shared by the currently known VOCs, B.1.1.7, B.1.351, and P.1, and which increase the affinity of the S protein to its receptor binding domain (RBD).
SARS-CoV-2 Infectivity and Severity of COVID-19 According to SARS-CoV-2 Variants: Current Evidence.
Introduction: The major changes are the mutation N501Y in the receptor-binding domain (RBD); the deletion 69-70 which may increase transmissibility and produces a false negative in certain RT-PCR-based diagnostic assays; and the mutation P681H, next to the furin cleavage site, that could impact antigenicity and enhance viral infectivity.
Immune Evasion of SARS-CoV-2 Emerging Variants: What Have We Learnt So Far?
Introduction: A combination of del H69/V70 and N501Y was shown to increase infectivity in vitro.
Introduction: Five mutations are located within NTD (L18F, T20N, P26S, D138Y, R190S), three in RBD (K417T, E484K, N501Y), two in the C-terminal domain of S1 and near the furin cleavage site (D614G, H655Y), and one in S2 (T1027I) (Figure 3).
Introduction: However, a combination of K417N and N501Y was shown to enhance the binding with ACE2 and reduce binding with a
SARS_CoV_2 mutation literature information.
PMID: 
2021
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