6b(1)). The selected peptide–H-2Kb interface as the template from crystal structures is presented in Fig. 6b(2).50 NS2:114–121, GQ and FG

peptides are simulated with the same H-2Kb and TCR from the template crystal structure (Fig. 6b(3,4,5)). As the backbones of several H-2Kb-bound peptides adopt the same conformation, we have speculated on many features of the critical contact residues to be the main factors to affect specific recognition by TCR (Figs 6a(2),b). At the fifth anchor motif, substitution of phenylalanine (F) with glycine (G) could undermine the binding forces of GQ to H-2Kb because of the lack of an inward benzyl group without compromising the recognition of the outward side chain via TCR (Fig. 6b(3,4)). The substitution of glutamine (Q) with glycine (G) at the sixth TCR contact site has removed the outward amide side chain find more from recognition by specific TCR (Fig. 6b (3,5)). Simulation results are compatible with those obtained

from laboratory experiments (Tables 2 and 3; Figs 2 and 5). The simulation approach with TCR contact information has more accurate prediction results on epitope identification than all previous computing programmes. Respiratory syncytial virus causes bronchiolitis and pneumonia in infants and young children.51 Influenza A virus still represents one of the major respiratory viruses causing significant morbidity and mortality in severe respiratory tract infections.52 selleck inhibitor In the 1960s, the trials of formalin-inactivated vaccines not only failed to protect those people who were vaccinated from RSV infection but induced deviant pathological consequences.53 The lack of CD8 T-lymphocyte responses has been associated with pulmonary eosinophilia that was observed in vaccinated people or experimental animals.7,53,54 Antigenic drifts and heterotypic influenza A viruses continue to

cause annual epidemics and pandemic outbreaks.4,6 It is critical to identify the important elements constituting the epitope to enable CD8 T-lymphocyte recognition as well as to map mutant epitopes from mutable pathogens, either for experimental research or for immunoinformatical programmes. The role of anchor motifs Thiamet G of peptides in the binding to MHC class I molecules is known and well-studied.19–22 Immunologists and microbiologists have long relied on these anchor motifs to predict MHC class I-restricted epitopes from the protein sequences of viral pathogens. Several peptide–MHC class I binding methods have been developed to map CD8 T-lymphocyte epitopes. Consistent with the previous publication of competitive binding experiments, M2:82–90 had the highest binding affinity to H-2Kd molecules to be detected by RMA-S-Kd cells22 (Figs 1a,c and Supplementary material, Fig. S2).