Article Figures & Data
Figures
- Figure 1
- The workflow of methodology used in current work.
- Figure 2
- The present study involves the examination of various aspects related to a vaccine construct, including its 3D crystal structure (A), a refined 3D structure model of the vaccine (B), The refined model’s Z-score is -5.79, which falls within the score range of the residue’s score plot (C), The score plot of Residue by ProSA-web was employed to verify the quality of the local model (D). A ProSA-web validation of the vaccine’s 3D structure (E) An evaluation of the Ramachandran plot for the multi-epitope vaccine construct (F), The number of residues is indicated within brackets. The labeled entities are those that exhibit unfavorable conformations with a score of less than negative three. The utilisation of shading in the analysis of 163 structures at a resolution of 2.0A or higher (G), In conjunction with the properties of residues, reveals a favourable conformation (H).
- Figure 3
- Validation and optimization of designed candidate chimeric vaccine. A) The docked complex of the vaccine model and the toll-like receptro (TLR)4 immune receptor. (B) Root Mean square deviation (RMSD) and Root Mean square fluctuation (RMSF) of the vaccine with TLR-4. (C) Antibodies responses against chimeric vaccine predicted by C- immune simulation server. (D) Cytokines and different interferon response induce by chimeric vaccine.
Tables
- Table 1
- Displays the antigenic epitopes that have been filtered and predicted for the 4 vaccine proteins that have been prioritized.
B cell epitope T cell epitope Percentile score MHCPred Score (nM) Antigenicity MHCI MHCII NAGVNRNDAFNAEKYPDGQITRTN NAGVNRNDAFNAEKY 2.1 13 15.92 0.95 ELKLAKGLKFRSNFSMTQGFNNFKQFTTRVPEIGKPSNSNKLTLNDKRSSDI KGLKFRSNFSMTQGF 2.3 0.09 36.64 0.64 NSNKLTLNDKRSSDI 1.6 35 11.19 2.02 QIFMGNTPTRVTYLAETKRASTDLTWA YLAETKRASTDLTWA 26 0.53 26 1.06 GFDPEVGMDSYGMDSGRYP GFDPEVGMDSYGMDS 43 27 40.18 2.43 YTFHREDEKYFFDNIMPDYTGKDAFKLIS YTFHREDEKYFFDNI 1.7 0.19 67.76 0.67 NRRVDRPNEVDIRIFPKYDDAEIIKVGNPALRPQ DIRIFPKYDDAEIIK 4.6 1.8 2.61 1.33 MHCPred: Epitope binding’s value prediction, MHCI: Epitopes MHC-I binding prediciton, Allergenicity= non-allergen, toxicity= non-toxin, solubility= noluble - Table 2
- Showcases the antigenicity, allergenicity, solubility, and physicochemical properties of the primary sequence of our multi-epitope-based vaccine construct.
Features Assessment Number of amino acid 250 Molecular weight 26496.87 Chemical formula C1168H1837N325O363S8 Theoretical Pi 6.6 Instability index (II) 27.13 (stable protein) Aliphatic index 66.04 Grand average of hydropathicity (GRAVY) -0.531 Antigenicity Antigenic Allergenicity Non-allergen Solubility Soluble Total number (no.) of atoms 3701 No. of -ively charged residues (Asp+Glu) 30 No. of +ively charged residues (Arg+Lys) 29 Estimated half-life (Mammalian reticulocytes, in vitro) 30 hours (hrs) (Yeast, in vivo) >20 hrs (Escherichia coli, in vivo) >10 hrs Variables Vaccine-TLR4 momplex Energy component Average SD Err. of mean VDWAALS -14268.3 51.3606 5.1361 EEL -125777 160.9493 16.0949 EGB -23027.7 128.2908 12.8291 ESURF 616.7839 3.4972 0.3497 G gas -140045 155.5427 15.5543 G solv -22410.9 127.4705 12.7471 TOTAL -162456 110.4932 11.0493 TLR-4 VDWAALS -12136.3 50.2011 5.0201 EEL -104629 162.6708 16.2671 EGB -18516.2 136.2444 13.6244 ESURF 489.8555 3.2995 0.3299 G gas -116765 155.9755 15.5976 G solv -18026.3 135.2806 13.5281 TOTAL -134791 95.4058 9.5406 Chimeric vaccine VDWAALS -1902.44 19.2818 1.9282 EEL -21889.9 83.9904 8.399 EGB -4010.19 70.0089 7.0009 ESURF 156.9794 1.8144 0.1814 G gas -23792.4 88.4392 8.8439 G solv -3853.21 69.1563 6.9156 TOTAL -27645.6 41.7466 4.1747 Differences (complex –TLR4 – vaccine) VDWAALS -249.588 8.5386 0.8539 EEL 750.5124 66.0836 6.6084 EGB -402.319 60.9302 6.093 ESURF -25.0511 1.1245 0.1125 DELTA G gas 500.9245 66.2058 6.6206 DELTA G solv -427.37 60.2798 6.028 DELTA total -73.4452 9.8089 0.9809 VDWAALS: van der Waals, EEL: electrostatic, EGB: polar solvation energy, ESURF: solvation energy, TLR: toll-like receptor, std Dev: standard deviation, Err: error, delta G (net gas phase energy), delta total (net energy of system), G solv (net solvation energy), Model GDT-HA RMSD MolProbity Clash score Poor rotamers Rama favored Initial 1.000 0.000 1.878 24.4 0.0 99.0 Model 1 0.9806 0.296 1.549 10.8 0.0 99.0 Model 2 0.9733 0.367 1.365 6.0 1.1 99.0 Model 3 0.9830 0.326 1.527 10.2 0.0 99.0 Model 4 0.9757 0.348 1.491 8.4 1.1 99.0 Model 5 0.9709 0.358 1.479 9.0 0.0 99.0 Solution number Global energy Attractive VdW Repulsive VdW ACE HB 4 -16.61 -43.10 26.42 13.33 -5.54 3 -14.90 -10.02 2.52 2.49 -2.81 2 -0.65 -4.60 -4.60 0.20 0.00 9 -0.17 -0.80 0.00 -0.28 0.00 8 16.43 -46.47 63.30 19.55 -7.08 10 26.69 -4.41 0.03 3.19 0.00 6 47.44 -37.18 29.10 24.23 -4.90 1 251.52 -57.84 417.50 8.60 -11.08 7 315.13 -22.02 380.17 15.20 -1.15 5 580.83 -48.73 801.24 10.71 -5.45 VdW: Van der Waals force, ACE: atomic contact energy, HB: hydrogen bond, TLR: toll-like receptor
In this issue
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- Article
- Abstract
- Methods
- Results
- Discussion
- Acknowledgment
- Appendix 1 - Presents the results of the pan-genome analysis. (A) Depicts a phylogenetic tree, while (B) Illustrates the curves of the pan and core genome, and (C) Displays the frequency distribution of gene families within genes. (D) Illustrates the quantity of newly incorporated genes in each respective genome
- Appendix 2 - Prediction of models’ quality score by GalaxyWEB
- Appendix 3 - Quality scores for selected vaccine model. (A) The secondary structure of the vaccine construct. (B) A secondary structural analysis of the vaccine was conducted, which revealed the fluctuations of its structural atoms within a minimal range, indicating the stability of its structure
- Appendix 4 - Docking results of vaccine construct with TLR4 receptor
- Appendix 5 -3D model of the 7 predicted conformational B-cell epitopes. The yellow regions are the conformational B-cell epitopes, while the grey regions are the residue remnant. (A) 8 residues with 0.797 score. (B) 7 residues with 0.763 score. (C) 7 residues with 0.663 score. (D) 12 residues with 0.645 score. (E) 8 residues with 0.643 score. (F) 5 residues with 0.551 score. (G) 5 residues with 0.524 score
- Appendix 6 - Population coverage analysis predicted by immune database server
- Footnotes
- References
- Figures & Data
- eLetters
- References
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