Molecular dynamics simulations highlight the altered binding landscape at the spike-ACE2 interface between the Delta and Omicron variants compared to the SARS-CoV-2 original strain

Computers in Biology and Medicine, Год журнала: 2022, Номер 149, С. 106035 - 106035

Опубликована: Авг. 27, 2022

Язык: Английский

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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, Год журнала: 2022, Номер 23(19), С. 11542 - 11542

Опубликована: Сен. 29, 2022

In this study, we performed all-atom MD simulations of RBD-ACE2 complexes for BA.1, BA.1.1, BA.2, and BA.3 Omicron subvariants, conducted a systematic mutational scanning the binding interfaces analysis electrostatic effects. The free energy computations comprehensive examination interactions quantify driving forces provide new insights into energetic mechanisms underlying evolutionary differences between variants. A RBD residues determines protein stability centers hotpots in complexes. By employing ensemble-based global network analysis, propose community-based topological model that characterized functional roles sites mediating non-additive epistatic effects mutations. Our findings suggest contributions to affinity may be mediated by R493, Y498, Y501 are greater BA.1.1 BA.2 display strongest ACE2 among subvariants. network-centric adaptation reversed allosteric communication is unveiled which established robust connection hotspots potential pockets. Using approach, demonstrated long-range could anchor experimentally validated Through an array complementary approaches proposed models, multi-faceted computational study revealed quantified multiple key site R498, acting as hotspots, drivers well mediators communications with

Язык: Английский

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Structures of ACE2–SIT1 recognized by Omicron variants of SARS-CoV-2

Cell Discovery, Год журнала: 2022, Номер 8(1)

Опубликована: Ноя. 16, 2022

Язык: Английский

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Vitamin C promotes ACE2 degradation and protects against SARS‐CoV‐2 infection

EMBO Reports, Год журнала: 2023, Номер 24(4)

Опубликована: Март 6, 2023

Язык: Английский

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The receptor binding domain of SARS-CoV-2 Omicron subvariants targets Siglec-9 to decrease its immunogenicity by preventing macrophage phagocytosis

Nature Immunology, Год журнала: 2024, Номер 25(4), С. 622 - 632

Опубликована: Март 7, 2024

Язык: Английский

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