Division of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh.
Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, GA, USA.
J Biomol Struct Dyn. 2024 Aug;42(13):6726-6739. doi: 10.1080/07391102.2023.2236715. Epub 2023 Aug 1.
The ORF3a is a large accessory protein in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which plays an important role in virulence and viral replication; especially in inflammasome activation and apoptosis. However,, the existing cryo-EM structure of SARS-CoV-2 ORF3a is incomplete, . making it challenging to understand its structural and functional features. The aim of this study is to investigate the dynamic behaviors of the full-sequence homology model of ORF3a and compare it with the cryo-EM structure using microsecond molecular dynamics simulations. The previous studies indicated that the unresolved residues of the cryo-EM structure are not only involved in the pathogenesis of the SARS-CoV-2 but also exhibit a significant antigenicity. The dynamics scenario of homology model revealed higher RMSD, Rg, and SASA values with stable pattern when compared to the cryo-EM structure. Moreover, the RMSF analysis demonstrated higher fluctuations at specific positions (1-43, 97-110, 172-180, 219-243) in the model structure, whereas the cryo-EM structure displayed lower overall drift (except 1-43) in comparison to the model structure.Secondary structural features indicated that a significant unfolding in the transmembrane domains and β-strand at positions 166 to 172, affecting the stability and compactness of the cryo-EM structure , whereas the model exhibited noticeable unfolding in transmembrane domains and small-coiled regions in the N-terminal. , The results from molecular docking and steered molecular dynamics investigations showed the model structure had a greater number of non-bonding interactions, leading to enhanced stability when compared to the cryo-EM structure. Consequently, higher forces were necessary for unbinding of the baricitinib and ruxolitinib inhibitors from the model structure.. Our findings can help better understanding of the significance of unresolved residues at the molecular level. Additionally, this information can guide researchers for experimental endeavors aimed at completing the full-sequence structure of the ORF3a.Communicated by Ramaswamy H. Sarma.
ORF3a 是严重急性呼吸综合征冠状病毒 2（SARS-CoV-2）中的一种大型辅助蛋白，在毒力和病毒复制中发挥重要作用；特别是在炎症小体激活和细胞凋亡中。然而，SARS-CoV-2 ORF3a 的现有冷冻电镜结构不完整，使得难以理解其结构和功能特征。本研究旨在利用微秒分子动力学模拟研究全序列同源模型的动态行为，并将其与冷冻电镜结构进行比较。先前的研究表明，冷冻电镜结构中未解决的残基不仅参与了 SARS-CoV-2 的发病机制，而且具有显著的抗原性。与冷冻电镜结构相比，同源模型的动力学情况显示出更高的 RMSD、Rg 和 SASA 值以及更稳定的模式。此外，RMSF 分析表明，模型结构中特定位置（1-43、97-110、172-180、219-243）的波动较大，而冷冻电镜结构的整体漂移较小（除 1-43 外）与模型结构相比。二级结构特征表明，跨膜结构域和位置 166 至 172 处的 β-链发生显著展开，影响冷冻电镜结构的稳定性和紧凑性，而模型在跨膜结构域和 N 端的小卷曲区域显示出明显的展开。分子对接和导向分子动力学研究的结果表明，模型结构具有更多的非键相互作用，与冷冻电镜结构相比，其稳定性更高。因此，从模型结构中解联巴瑞替尼和鲁索利替尼抑制剂需要更大的力。我们的研究结果可以帮助更好地理解分子水平上未解决残基的重要性。此外，这些信息可以指导研究人员进行旨在完成 ORF3a 全长序列结构的实验工作。由 Ramaswamy H. Sarma 传达。
