Computation-aided novel epitope prediction by targeting spike protein's functional dynamics in Omicron

Bin Sun; Yong Zhang; Baofeng Yang

doi:10.2478/fzm-2023-0001

Computation-aided novel epitope prediction by targeting spike protein's functional dynamics in Omicron

doi: 10.2478/fzm-2023-0001

Bin Sun¹,
Yong Zhang^{2, 4},
Baofeng Yang^{2, 3, 4
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1.
Research Center for Pharmacoinformatics (The State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Department of Medicinal Chemistry and Natural Medicine Chemistry, College of Pharmacy, Harbin Medical University, Harbin 150081, China
2.
Department of Pharmacology (The State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), College of Pharmacy, Harbin Medical University, Harbin 150081, China
3.
Department of Pharmacology and Therapeutics, Melbourne School of Biomedical Sciences, Faculty of Medicine, Dentistry and Health Sciences University of Melbourne, Melbourne 3010, Australia
4.
Research Unit of Noninfectious Chronic Diseases in Frigid Zone, Chinese Academy of Medical Sciences, Harbin 150036, China

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Corresponding author: Baofeng Yang, yangbf@ems.hrbmu.edu.cn

摘要

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Figure 1. Sipke protein structure and dynamics

(A) The protomer of S protein showing S1 and S2 subunits. S1 contains the RBD and NTD domains. The RBD has "down" and "up" configurations, and the 'up' configuration is required for binding host ACE2; (B) Experimentally observed pH-regulated S protein conformational plasticity during the endosomal entry of SARS-CoV-2 into host cell^[6]; (C) The functional dynamics underlying the pH-regulated S protein plasticity is integral to SARS-CoV-2 infectivity. Computational simulations are able to decipher such dynamics and identify conserved regions that may have antigenicity; RBD, receptor binding domain; ACE2, angiotensin conversion enzyme 2; NTD, N-terminal domain.

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参考文献(20)

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