Scrutinizing the SARS-CoV-2 protein information for the designing an effective vaccine encompassing both the T-cell and B-cell epitopes

Neha Jain; Uma Shankar; Prativa Majee; Amit Kumar

Refined structure of the model construct was further check for its stability in real environment by simulating it for 20 ns in a water sphere. 10,000 steps energy minimization was performed to minimize the potential energy of the system. Unnecessary or false geometry of the protein structures are repaid by performing energy minimization resulting in a more stable stoichiometry. Before energy minimization, the potential energy was observed to be -447451.2005 Kcal/mol. After 10,000 steps the protein was minimized with a potential energy of -676040.4692 kcal/mol ( Figure 7A) . The system was subsequently heated from 0 K to 310 K and then 10 ns molecular dynamic simulation was performed. The temperature remained constant throughout the simulation process ( Figure 7B ). The DCD trajectory file was analysed for analysing the movement of the atoms during the simulation course and RMSD was calculated. Upon analysing the RMSD of SARS-CoV-2 vaccine construct, it was observed that, the system gained equilibrium at ~4 ns and then remained constant till 10 ns depicting the stability of the vaccine construct ( Figure 7C ). Furthermore, upon analysing the change in kinetic, potential and total energy of the system, it was observed that after a quick initial change in all the three, they remained constant throughout the simulation further strengthening the stability of the vaccine construct ( Figure 7D-F) . Furthermore, the bond energy, VdW energy, dihedral and improper dihedral energy analysis revealed no change throughout the 10 ns dynamics simulation. Root mean square fluctuation (RMSF) analysis revealed the rigidness of the atoms in vaccine construct with a slight mobility observed at ~ 120 and 501 residues (Supplementary Figure S4) . Thus, simulation analysis revealed the stability of the vaccine construct in the real environment. The refined vaccine construct structure was therefore used for interaction analysis with immunological receptor TLR3.