In silico Evolutionary Divergence Analysis Suggests the Potentiality of Capsid Protein VP2 in Serotype-Independent Foot-and-Mouth Disease Virus Detection

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  Figure 1. Visualization of amino acid divergence in VP2 protein of foot-and-mouth disease virus serotypes O, A, and Asia1. (A) Wu–Kabat protein variability plot for VP2 protein using Protein Variability Server (PVS). The plot was generated using the protein alignment of 279 VP2 sequences. The marked regions indicate the previously reported antigenic sites of VP2. The X and the Y axis of the plot, respectively, delineates the amino acid positions of VP2 and Wu–Kabat variability coefficient. (B) Graphical representation for the overall mutation score of the mutated sites in VP2. The protein alignment of 279 VP2 sequences was used to carry out the mutational study. For each position, the frequency of most common and mutated amino acids is represented with black and gray color, respectively. The X axis shows the amino acid position of VP2, and the Y axis shows the frequency of mutated and most common amino acids. Only the previously reported antigenic sites were taken into consideration for the mutational study. (C) Graphical representation for overall mutational score of the mutated positions in the conserved fragments of VP2 protein. The protein alignment of 360 Asian VP2 sequences was used…

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  Figure 2. Screening of surface-accessible conserved antigenic regions in VP2 and designing of consensus VP2 sequence along with mapping of possible B cell epitopes. (A) Graphical representation of the surface accessibility and the structural properties of VP2 protein. Relative surface accessibility is presented in blue and red elevation and inclination (), where red indicates the exposed surface and blue indicates the buried regions; threshold was kept at 25%. Curved (), arrowed (), and lined () cartoons depict the secondary structure of different regions of the protein, indicating helical, stranded, and coiled structure, respectively. The disorderliness of residues in the protein is shown by gray-colored curvature, where the thickness of the gray line equals the probability of the disordered residue. (B) Designed consensus VP2 protein sequence and its predicted 2D and 3D models. The sequence was designed by combining the most common amino acids at positions 1–130 of VP2 protein. The green arrows highlight the predicted β-strands. Cylinders and lines, shown in cyan and orange colors, highlight the α-helices and connecting loops, respectively. The underlined amino acid residues represent…