Computational Identification and Characterization of a Promiscuous T-Cell Epitope on the Extracellular Protein 85B of Mycobacterium spp. for Peptide-Based Subunit Vaccine Design

Figure 3

Docking of the epitope with HLA-DRB10101 (a), HLA-DRB10901 (b), HLA-DRB10404 (c), HLA-DRB10701 (d), HLA-DPB10101 (e), HLA-DQB10301 (f), and HLA-DRA (g). The 3D structure of the Ag85B T-cell epitope was made in PyMol molecule builder. Docking of receptor MHC with epitope was performed in Molsoft ICM-pro 3.5. All 3D structures of HLA proteins were obtained from the PDB server unless noted. Homology models of HLA-DRB10701 and HLA-DRB10901 were prepared in MOE as described by Azad et al. [16]. MHC II structures are shown in gray ribbon and the amino acid residues involved in the hydrogen bonding interaction are shown as red sticks and labeled red. The epitope is shown as green ribbon and the amino acid residues involved in the hydrogen bonding network are shown as yellow sticks and labeled black. MHC II binding pockets are shown as an electrostatic sphere. Hydrogen bonds are displayed as blue spheres and the hydrogen bonding distances are labeled blue. Hydrogen bonding interaction between the amino acid residues of the epitope and those of MHC II are detailed in Additional File 5, Table  S4.

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