Table 1.
Physiochemical parameters of structural and non-structural protein of West Nile virus.
Fig 1.
B cell Epitope prediction of Capsid C protein at IEDB linear epitope prediction tool.
Predicted peptide regions above the threshold values (yellow region) are shown in red arrow. Methods used for prediction are enlisted as: (A) BepiPred 2.0, (B) Emini Surface Accessibility tool, (C) Karplus & Schulz Flexibility tool, and (D) Parker Hydrophilicity tool.
Fig 2.
B cell Epitope prediction of prM protein at IEDB linear epitope prediction tool.
Predicted peptide regions above the threshold values (yellow region) are shown in red arrow. Methods used for prediction are enlisted as: (A) BepiPred 2.0, (B) Emini Surface Accessibility tool, (C) Karplus & Schulz Flexibility tool, and (D) Parker Hydrophilicity tool.
Fig 3.
B cell Epitope prediction of Envelope protein at IEDB linear epitope prediction tool.
Predicted peptide region above the threshold values (yellow region) are shown in red arrow. Methods used for prediction are enlisted as: (A) BepiPred 2.0, (B) Emini Surface Accessibility tool, (C) Karplus & Schulz Flexibility tool, and (D) Parker Hydrophilicity tool.
Fig 4.
Population coverage analysis of finalized epitopes (MHC-I and MHC-II).
Europe, England, North America, United States, and West Africa showed the highest (100%) population coverage.
Fig 5.
Schematic representation of WNV vaccine construct: A 488 amino acids long multi-epitope vaccine sequence consisting an adjuvant at N-terminal end linked with a multi-epitope sequence with the help of EAAAK linker (Red) followed by PADRE sequence.
CTL epitopes were linked through GGGS linkers (blue). HTL epitopes were linked through GPGPG linkers (Sky). BCL epitopes were linked through KK linkers (Yellow). Invasin molecule linked through EGGE linker (Green).
Table 2.
Physiochemical, immunogenic and solubility properties of vaccine protein.
Fig 6.
Tertiary structure and Ramachndran plot assessment of the refined vaccine protein.
a) Model-5 from Robetta server (Homology modelling server) after refinement; b) Ramachandran plot analysis of refined vaccine protein by PROCHECK server. Refined model contains 88.1% residues in most favored region, 5.3% residues in additionally allowed region, 0.5% in generously allowed region and only 0.3% in disallowed region.
Fig 7.
Ligand-receptor docked complex of vaccine protein with human toll like receptor (TLR)-3, 4, 7 and 8.
Vaccine protein is represented as purple color while TLR-3, 4, 7, 8 as aqua color. The global energy of vaccine protein with other toll like receptors were found -22.08 for TLR3, -26.96 for TLR4, -0.06 for TLR7 and -6.29 for TLR respectively.
Fig 8.
Molecular dynamics simulation of the vaccine protein with human toll like receptor-4.
(A) RMSD-Root Mean Square Deviation of docked complex shows very minor deviation reflecting the stable interaction between vaccine protein and TLR-4 molecule. (B) RMSF-Root Mean Square Fluctuation plot of docked protein complex remained fairly flat reflecting the flexibility of side chain of docked protein complex. (C) Rg plot of docked complex shows a relatively flat curve suggesting stable vaccine-receptor complex.