Immuno-informatics Characterization SARS-CoV-2 Spike Glycoprotein for Prioritization of Epitope based Multivalent Peptide Vaccine

Saba Ismail; Sajjad Ahmad; Syed Sikander Azam

The 3D model of the MEPVC was constructed using ab initio 3Dpro predictor as no appropriate template was available for homology modeling and threading methods. The 3D structure of MEPVC is shown in Fig.5B . The structure secured 85.4% of residues in the Ramachandran favored, 12.6%, 1.9% and 0% residues in additionally allowed, generously allowed and disallowed regions, respectively. As the predicted MEPVC unit has number of loop regions that need to be modeled proper before moving forward. In total, five sets of residues: Alas7-Lys32, Ile63-Gly69, Cys73-Arg77, Thr87-Pro102, and Asn113-Val119 were loop modeled. The loop modeled structure increased the Ramachandran favored residues percentage to 92.3%, residues in allowed region reduced to 6.7%, residues of generously allowed region to 1.0% and disallowed remained to 0%. The structure was subjected to structure perturbations and relaxations to obtain a refined model. Among the generated structures (S- Table 2 ), the first model was selected as it has improved Rama favored score, lowest stable galaxy energy of 0.96, improved clash score of 23.1 and good MolProbity value. Similarly, the structure lacks poor rotamers in contrast to the original structure. The Ramachandran statistics for the refined 3D structure are in following order: Ramachandran favored residues (93.2%), additionally allowed region (5.8%), generously allowed region (1.0%) and disallowed region (0 %). The Z-score of the refined MEPVC is -4.3 and within the score range of same size protein in structure data bases (S- Fig.1 ).