Simulation and comparison of the tertiary structure of spike protein belong SARS-CoV-2, Bat-SL-CoVZC21, PCoV_GX-P4L, and identification the hotspot amino acids in the trimeric structure of protein

 Covid-19 disease with acute respiratory symptoms appeared in 2019. The disease was associated with fever, cough, and severe respiratory distress. The causative agent of the disease belonged to the beta-coronavirus family and was named SARS-CoV-2. The outbreak of Covid-19 and the creating of a global epidemic led to many attempts to understand the structure and function of the virus. The spike protein is a relatively heavy glycosylated protein consisting of three identical subunits that appear as a homo-trimmer on the virus's surface. After binding to the surface cell receptor (angiotensin-converting enzyme), the protein conformational changes and eventually causes the virus to enter the host cell. This process is necessary for viruses to enter human cells and infect them. Therefore, investigating the structural details of the spike protein through molecular dynamics simulation can play an influential role in understanding how the subunits connect and identifying the hotspot amino acids.

 First, the tertiary structure of spike proteins related to SARS-CoV-2, bat-SL-CoVZC21 (Bat Coronavirus), and PCoV_GX-P4L (Pangolin coronavirus) was constructed through modeling homology. After evaluation and validation, these structures were simulated using NAMD software. The structural properties of spike proteins were evaluated in the level of 3D structure, measurement of the interface area between monomers, thermodynamic parameters, trimmer structures' stability, and hotspot amino acids' identification in making connections between subunits.

 Evaluation of the trimeric structure of spike protein showed that this protein in SARS-CoV-2 has the highest ΔGdiss value (113.2 kcal/mol), which indicates the stability of the oligomeric protein structure among other spike proteins. The lowest ΔGdiss (100.6 kcal/mol) was obtained for the spike protein of PCoV_GX-P4L. The interface area between the subunits was almost the same in all spike proteins. Y369, D405, Y707 in subunit A, Y369, D574, Y707, Y837, D985 in subunit B, and Y707 in subunit C were identified as red hotspot amino acids for SARS-CoV-2 spike protein.

 The study of the structure of virus surface proteins at the atomic scale, and the recognition of hotspot residues that play an essential role in establishing monomeric connections, has created a window to further recognition and function of the virus. Thus, it can provide new information about neutralizing the virus.