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

Saba Ismail; Sajjad Ahmad; Syed Sikander Azam

MD simulation was applied on the selected top complex for 50-ns to understand complex dynamics and stability for practical applications. This assay was categorized into three phases: (i) parameters file preparation (ii) pre-processing, and (iii) simulation production [68] . In first phase using an antechamber module of AMBER16 [69] , complex libraries and set of parameters for TLR3 and MEPVC were generated. The complex system was solvated into 12 Å TIP3P solvation box achieved through Leap module of AMBER. The intermolecular and intramolecular interactions of the system were determined by ff14SB force [70] field. Counter ions in the form of Na + were added to the system for charge neutralization. In the system pre-processing stage, complex energy was optimized through several rounds: minimization of complete set of 6 hydrogen atoms for 500 steps, minimization of system solvation box energy for 1000 steps with restraint of 200 kcal/mol -Å 2 on the remaining system, minimization of complete set of system atoms again for 1000 steps with applied restraint of 5 kcal/mol -Å 2 applied on system carbon alpha atoms, and 300 steps of minimization on system non-heavy atoms with restraint of 100 kcal/mol -Å 2 on other system components. The complex system then underwent a heating step where the complex was heated gradually to 300K through NVT ensemble, maintained through Langevin dynamics [71] and SHAKE algorithm [72] to restrain hydrogen bonds. Complex equilibration was achieved for 100-ps. Pressure on the system was maintained using NPT ensemble allowing restraint on Cα atoms of 5 kcal/mol -Å 2 . In the simulation production, trajectories of 50-ns were produced on time scale of 2-fs. Non-bounded interactions were differentiated by describing cut-off distance of 8.0 Å.CPPTRAJ module [73] was lastly used for statistical computation of different structure parameters to probe complex stability. The MD simulation trajectories were visualized and analyzed in Visual Molecular Dynamics (VMD) 1.9.3 [74] .