Construction of homology models of wild and mutant D614G spike protein
Investigating the functional effect of the frequently occurring D614G mutation is necessary for forecasting the emergence of more virulent and pathogenic viral strains. This information will elucidate whether the D614G mutant strains are more virulent than the wild type SARS-CoV-2. The structure of the SARS-CoV-2 spike glycoprotein will be retrieved from the PDB. Homology models of wild-type and the D614G mutant spike protein should be developed. Secondary structure prediction of target sequence needs be done. Finally, the model will be validated using Ramachandran andErrat plots. The stability of the models must be further validated in molecular dynamic (MD) simulations and energy of the system should be recorded in the trajectory at specific time interval (ps). The conformational changes, stability of the secondary structure of the protein, stability of the protein-inhibitor complexes should be assessed from the RMSD (< 3.5 Ǻ). The substrate binding free energy (ΔGbind) for the wild, as well as mutated proteins, is to be calculated and reported.