Designing a multi-epitope vaccine against coxsackievirus B based on immunoinformatics approaches

Figures

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  Figure 1. Flow diagram of the multi-epitope vaccine design in this study.

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  Figure 2. (A) The complete sequence of the coxsackievirus B (CVB) vaccine. (B) Prediction of the secondary structure of the multi-epitope vaccine construct.

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  Figure 3. In-silico immune simulation of the CVB vaccine by the C-ImmSim tool. (A) Antibody production in response to antigen injections (vertical black lines). (B) Level of B-cell population. (C) Level of helper T-cell population. (D) Level of cytotoxic T-cell population. (E) Level of cytokine expression.

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  Figure 4. The refinement and quality assessment of the CVB vaccine construct. (A) The refinement model of the CVB vaccine construct. (B) (a) The Ramachandran plot of the primary model and (b) the Ramachandran plot of the refined model. (C) (a) The Z-score of the initial model was −3.52, and (b) the Z-score of the refined model is −4.06; both models were not in the range of native protein conformation. The Z-score plot contains Z-scores of all experimental protein chains in PDB determined by NMR spectroscopy (dark blue) and X-ray crystallography (light blue).

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  Figure 5. Molecular docking of the CVB vaccine (pink color) with human immune receptors. (A) CVB vaccine and MHC-I. (B) CVB vaccine and MHC-II. (C) CVB vaccine and TLR3. (D) CVB vaccine and TLR4.

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  Figure 6. Molecular dynamics simulation of the CVB vaccine–immune receptor complex at 50 ns. (A) Molecular dynamics system (prepared for the simulation); (B) RMSD (root mean square deviation) of the docked complex reflects the stability between the vaccine. (C) RMSF (root mean square fluctuation) reflects the flexibility and fluctuation of the amino-acid residues in the side chain of docked complexes. (D) Time evolution of the radius of gyration (rRyr) during 50 ns of MD simulation.