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