Structure and dynamics of whole-sequence homology model of ORF3a protein of SARS-CoV-2: An insight from microsecond molecular dynamics simulations

Abstract

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

Keywords:

• ORF3a
• SARS-CoV-2
• homology modeling
• molecular dynamics simulation
• free energy landscape
• molecular docking
• steered molecular dynamics

Acknowledgements

We are grateful to our donors (http://grc-bd.org/donate/) who supported to build a computational platform. The authors like to acknowledge The World Academy of Science (TWAS) to purchase High-Performance Computers for molecular dynamics simulation. We also like to give special thanks Md. Minhas Hossain Sakib, Rumana Mahtarin and Shafiqul Islam for their cordial support and valuable suggestions.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Additional information

Funding

The author(s) reported there is no funding associated with the work featured in this article.