Figures index : Modeling and in Silico Analysis for Prediction of Epitopes Vaccine against Norwalk virus from Capsid Protein (VP1) through Reverse Vaccinology : Science and Education Publishing

Figures index

American Journal of Infectious Diseases and Microbiology. 2020, 8(1), 29-44 doi:10.12691/ajidm-8-1-5

Figure 1. Phylogenetic tree of the capsid protein (VP1) of the retrieved strains. The retrieved strains demonstrated divergence in their common ancestors

Figure 2. Multiple sequence alignment (MSA) of the retrieved strains of the capsid protein (VP1) using Bioedit software and ClustalW. Dots indicated the conservancy of the retrieved strains and letters within the rectangular indicated no conservancy (mutation) in amino acid

Figure 3. Prediction of B-cell epitopes by different IEDB scales (a- Bepipred linear epitope prediction, b- Emini surface accessibility, c- Kolaskar and Tongaonkar antigenicity prediction) for the capsid protein. Regions above threshold (red line) were proposed as a part of B cell epitope while regions below the threshold (red line) were not

Figure 4. Position of proposed eight conserved B cell epitopes in structural level of the capsid protein (VP1). The epitopes were shown in dark red ball and sticks shapes. These epitopes showed conservancy, high score in surface accessibility and antigenicity using IEDB software, nonallergic and nontoxic. The position of these epitopes was according to their position in the capsid protein

Figure 5. T cell proposed epitopes that interact with MHC-I alleles. Four epitopes (_140-AQATLFPHV-₁₄₈; _216-FLFLVPPTV_-224; _499-GVFVFVSWV_-507 and _410-YPPGFGEVL_-418) were shown in this figure since they interacted with MHC-1 alleles. The positions of these proposed epitopes was according to their position in the capsid protein

Figure 6. T cell proposed epitopes that interact with MHC-1I alleles. Three epitopes ( _216-FLFLVPPTV_-224; _499-GVFVFVSWV_-507 and _410-YPPGFGEVL_-418) were not shown in this figure since they were shown in figure (5) (interacted with MHC-1 and MHC-1I alleles). The other five epitopes (433-LPCLLPQEY-441; 90-NPFLLHLSQ-98; 394-NYGSSITEA-402; 247-PLPISSMGI-255 and 220-VPPTVEQKT-228) were only shown in this figure since they only interacted with MHC-1I alleles. The positions of these proposed epitopes was according to their position in the capsid protein