In Fig. 3, Fig. 4, Fig. 5 , interactions between a selected three T-Cell epitopes with respective MHC Class I and II HLA-Alleles via hydrogen bond formation and van der Waals interactions is depicted. After positive docking results, these epitopes were subjected to further Molecular dynamic simulation and biochemical parameters assessment. Fig. 6 represents a graphical plot of binding scores for epitopes interacting with HLA-Alleles.
Fig. 3 FTIGTVTLK Epitope interaction with an antigen-binding pocket of HLA-A*68:01, of MHC I-HLA Allele. Here, Threonine at 2nd,5th, and 7th position in the epitope generate preferably a hydrogen bond due to the presence of partially charged positive and negative atoms, and also 4th position Glutamic acid and lysine at 8th position side chains can form a salt bridge, while other amino acids result in van der Waals interactions.
Fig. 4 ITLCFTLKR Epitope interaction with an antigen-binding pocket of HLA-A*68:01, of MHC I-HLA Allele. Here, Threonine at 2nd and 6th position, as well as cysteine at the 4th position in epitope, generate preferably a hydrogen bond due to the presence of partially charged positive and negative atoms, while other amino acids result in van der Waals interactions.
Fig. 5 VYQLRARSV Epitope interaction with an antigen-binding pocket of HLA-DRB1*07:01, of MHCII-HLA Allele, Here, Tyrosine at 2nd, Glutamine at 3rd position and Serine at 8th position in epitope generate preferably a hydrogen bond due to the presence of partially charged positive and negative atoms, and 5th and 7tharginine residue side chains can form a salt bridge, while other amino acids result in van der Waals interactions.
Fig. 6 Binding energy graphical plot for selected Epitope and HLA-Allelic pair.