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

Saba Ismail; Sajjad Ahmad; Syed Sikander Azam

The stability of MEPVC with TLR3 was further investigated through MD simulations. The trajectories of MD simulations were used in vital statistical analysis to decode backbone stability and residual flexibility. Root mean square deviation (RMSD) [92, 93] was performed first that compute average distance of backbone carbon alpha atoms of superimposed frames (Fig.10A) . The average RMSD for the system is 3.23 Å with max of 4.4 Å at 24-ns. An initial sudden change in RMSD can be seen up to 2.7-ns that may be due to adjustments adopted by the complex when exposed to dynamics forces and milieu. The second minor RMSD shift can be noticed between 22-ns to 26-ns. Afterward, the system is quite stable with not global and local conformational changes specified. Next, root mean square fluctuations (RMSF) [94] was applied on the system trajectories (Fig.10B) . RMSF is the average residual mobility of complex residues from its mean position. Mean RMSF for the MEPVC-TLR3 complex calculated is 1.60 Å with max of 8.6 Å pointed at the N-terminal of the MEPVC. Most of the interacting residues of the MEPVC with TLR3 are subject to minor fluctuations, a fact in analogy to complex high stability. The thermal residual deviation was assessed afterward by beta-factor (β-factor) [95] , the outcomes of which is strongly correlated to the RMSF and hence further affirming system stability (Fig.10C) . The average β-factor of the system analyzed is 88.64 Ų with max of 1956.23 Ų. Lastly, we evaluated the compactness of the system by means of radius of gyration (Rg) [96] analysis (Fig.10D) . High Rg and low Rg illustrate the magnitude of system compactness and system less tight packing. It further tell us the whether the system of interest in order or not. Highly compact system is an indication of system stability and vice versa. The mean Rg for our system is 55.8411 Å with max score of 74.884 reflecting higher ordered and compact nature of the system. author/funder. All rights reserved. No reuse allowed without permission.