Exploring the effects of N234 and N343 linked glycans to SARS CoV 2 spike protein pocket accessibility using Gaussian accelerated molecular dynamics simulations.

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Tác giả: Ronny L Cheng, Myrnel A Fortuna, Earl Adrian D R Hans, James Peter L Lim, Ricky B Nellas, Donnifer V Reyes

Ngôn ngữ: eng

Ký hiệu phân loại:

Thông tin xuất bản: England : Scientific reports , 2025

Mô tả vật lý:

Bộ sưu tập: NCBI

ID: 682080

The N234 and N343-linked glycans of the SARS-CoV 2 spike protein are known to stabilize the up-conformation of its receptor-binding domains (RBDs), enabling human angiotensin enzyme 2 (hACE2) receptor binding. However, the effect of spike-hACE2 binding on these important glycans remains poorly understood, and these changes could have implications in the development of drugs that inhibit viral entry. In this study, Gaussian accelerated molecular dynamics (GaMD) simulations of the hACE2-free and hACE2-bound spike protein are performed. Biophysical analyses were focused on the accessibility of three previously suggested druggable pockets underneath the three RBD subunits. A shielding effect by N234-linked glycans on the components of their adjacent pockets was observed. Although deshielding of central scaffold residues was observed in the hACE2-bound state, pocket A's accessibility was reduced due to an increase in NTD
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