title: 3-Layer-based analysis of peptide-MHC interaction: in silico prediction, peptide binding affinity and T cell activation in a relevant allergen-specific model.
abstract: CD4+ T cells recognize peptides bound to major histocompatibility complex (MHC) class II molecules on the surface of antigen presenting cells by their T cell receptor (TCR). Using a well-characterized allergen-specific model we studied peptide/MHC (pMHC) interactions by combining computational methods with experimental analyses. A 12-mer and an 18-mer peptide, both containing the human leukocyte antigen (HLA)-DR1-restricted, immunodominant T cell epitope of Art v 1, the major mugwort pollen allergen, were compared. A Molecular Dynamics simulation for a real time of 20 ns using GROMACS was performed. To this aim, the peptides were modelled into the binding groove of HLA-DRB1*0101 using different amino acid substitution tools. Binding of synthetic peptides to purified HLA-DRB1*0101 molecules was analysed in competition assays. The potency of the peptides to activate Art v 1-specific T cells was assessed using oligo- and monoclonal Art v 1-specific T cell cultures expanded from mugwort allergic individuals. All approaches revealed that the 18-mer peptide possessed higher HLA DR affinity as compared to the 12-mer. Computer modelling indicated that a loop-like structure within the additional N-terminal peptide flanking region of the 18-mer contributed to the pMHC interaction. Our approach, to combine computational methods validated by experimental results, demonstrates that Molecular Dynamics simulation may be a useful tool for the prediction of pMHC interactions in the future with possible applications in T cell-based immunotherapy e.g. in Type I allergy.
authors.affiliation: Department for Biomedical Computersimulation and Bioinformatics, Medical University of Vienna, Austria. bernhard.knapp@meduniwien.ac.at
authors.forename: Bernhard
authors.initials: B
authors.lastname: Knapp
authors.forename: Ulrich
authors.initials: U
authors.lastname: Omasits
authors.forename: Barbara
authors.initials: B
authors.lastname: Bohle
authors.forename: Bernard
authors.initials: B
authors.lastname: Maillere
authors.forename: Christof
authors.initials: C
authors.lastname: Ebner
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Schreiner
authors.forename: Beatrice
authors.initials: B
authors.lastname: Jahn-Schmid
mesh_terms: D000485:Allergens / Q000276:immunology; D000595:Amino Acid Sequence; D019943:Amino Acid Substitution; D017951:Antigen Presentation / Q000276:immunology; D003198:Computer Simulation; D018604:Epitope Mapping / Q000379:methods; D005544:Forecasting; D006684:HLA-DR Antigens / Q000737:chemistry / Q000235:genetics / Q000276:immunology / Q000378:metabolism*; D059811:HLA-DRB1 Chains; D006801:Humans; D021621:Imaging, Three-Dimensional / Q000379:methods; D008213:Lymphocyte Activation / Q000276:immunology*; D008285:Major Histocompatibility Complex / Q000276:immunology; D008958:Models, Molecular; D010455:Peptides / Q000737:chemistry / Q000276:immunology / Q000378:metabolism*; D011485:Protein Binding; D011487:Protein Conformation; D013379:Substrate Specificity; D013601:T-Lymphocytes / Q000276:immunology* / Q000378:metabolism
chemical_list: D000485:Allergens; D006684:HLA-DR Antigens; D059811:HLA-DRB1 Chains; D010455:Peptides