Fig 1.
Systemic flowchart of the multi-epitope subunit vaccines build against HCV.
Table 1.
Final selected CTL, HTL and LBL epitopes for multi-epitope vaccines construction.
Fig 2.
Prediction and assessment of the 3D structure of the multi-epitope vaccines.
(A) Schematic image of the final vaccine. (B) Ramachandran plot analysis of refined construct 1, showing 91.08%, 7.17% and 1.75% residues in favored, allowed and disallowed region, respectively, (C) ProSA validation of 3D construct 1, showing Z-score -3.28, (D) Ramachandran plot analysis of refined construct 2, showing 91.07%, 7.28% and 1.65% residues in favored, allowed and disallowed region, respectively, (E) ProSA validation of 3D construct 2, showing Z-score -3.88, (F and G) 3D structure of vaccines models showing α-helix (red cartoon), β-strand (yellow cartoon) and loop (green cartoon).
Table 2.
Various features of multi-epitope vaccines.
Fig 3.
MD simulations outputs of free vaccines and vaccines-TLRs complexes; A and B: The RMSD and RMSF values of Cα atoms for free vaccines, respectively; C and D: The RMSD values of Cα atoms for vaccines and TLRs in the complex states, respectively; E and F: The RMSF values of Cα atoms for vaccines and TLRs in the complex states, respectively; G: The Rg values of vaccines structures in the complex states.
Table 3.
Linear B-cell epitopes of the final vaccines.
Table 4.
Discontinuous B-cell epitopes of the final vaccines.
Fig 4.
The 3D view of the final system conformations.
The interface residues between two proteins TLRs (orange cartoon) and vaccines (magenta cartoon) residues (orange and magenta sticks) are labeled. Hydrogen bonds and hydrophobic contacts are presented as green dashed line and arc with spokes radiating, respectively. A and B indicate TLR4-construct 1 and TLR3-construct 2 complexes, respectively.
Table 5.
The contribution of various energy components in the ΔGbind (kJ/mol).