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研究奥密克戎受体结合域突变对抗体逃逸和受体结合的结构影响。

Investigating the structural impact of Omicron RBD mutation on antibody escape and receptor management.

机构信息

Department of Biological Sciences and Engineering (BSE), Netaji Subhas University of Technology (NSUT), New Delhi, India.

High Performance Computing (HPC) & AI Innovation Lab, Dell EMC, Bengaluru, India.

出版信息

J Biomol Struct Dyn. 2024 Jun;42(9):4668-4678. doi: 10.1080/07391102.2023.2222174. Epub 2023 Jun 19.

Abstract

The SARS-CoV-2 Variant B.1.1.5291 evolved rapidly in late November 2021 from the existing mutants sparking fear worldwide owing to its infamous immune escape from a varied class of neutralising antibodies. To assess the structural behaviour of Omicron-Receptor Binding Domain (RBD) upon interacting with cross-reactive CR3022 antibody, we investigated the computational approach of structural engagement in B.1.1529 RBD and wild-type RBD with CR3022 antibody. The current study investigates the interacting interface between the RBDs and CR3022 to decipher the key residues accompanying the potential mutational landscape of SARS-CoV-2 variants. We conducted docking followed by molecular dynamics simulation analysis to examine the dynamic behaviour of protein-protein interactions. Furthermore, the study unleashed possible interactions post energy decomposition analysis MM-GBSA. Conclusively, the mutational landscape of RBD eases in designing and discovering the effective neutralisation accompanied by development of a universal vaccine.Communicated by Ramaswamy H. Sarma.

摘要

SARS-CoV-2 变体 B.1.1.5291 于 2021 年 11 月迅速从现有突变体进化而来,由于其对多种中和抗体的著名免疫逃逸,引起了全球恐慌。为了评估 Omicron-受体结合域 (RBD) 与交叉反应性 CR3022 抗体相互作用时的结构行为,我们研究了 B.1.1529 RBD 和野生型 RBD 与 CR3022 抗体的结构结合的计算方法。本研究调查了 RBD 与 CR3022 之间的相互作用界面,以破译伴随 SARS-CoV-2 变体潜在突变景观的关键残基。我们进行了对接,随后进行了分子动力学模拟分析,以检查蛋白质-蛋白质相互作用的动态行为。此外,研究还通过能量分解分析 MM-GBSA 释放了可能的相互作用。总之,RBD 的突变景观简化了设计和发现有效的中和作用,同时开发了通用疫苗。由 Ramaswamy H. Sarma 传达。

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