Dynamics of Peptides Bound to Class I Major Histocompatibility Complex Proteins: Implications for T-Cell Receptor Recognition in the Immune Response

T cell receptor (TCR) recognition of peptides bound and presented by major histocompatibility complex (MHC) proteins initiates a cellular immune response. The stability of the peptide/MHC molecule is correlated with TCR recognition and the resulting immune response. Residual dynamics of peptides within MHC binding grooves have also been suggested to influence TCR recognition, yet NMR studies which could address this most rigorously have been hindered by the prohibitive expense of isotopically labeled peptide and the large size of the peptide/MHC complex. This study describe methodologies for characterizing peptide dynamics within MHC binding grooves via NMR, using a biosynthetic approach for producing labeled peptide in which the peptide is fused to ubiquitin and a ubiquitin dehydrolase used to liberate the peptide. Using the Tax11-19 peptide bound to the 45 kD human class I MHC HLA-A2 as a model system, it is evident that peptides generated in this manner can be well characterized in MHC binding grooves by NMR, providing the opportunity to more precisely study the role of peptide dynamics in TCR recognition, specificity, and cross-reactivity.Using both NMR and molecular dynamics simulations, the principles governing conformational changes observed in Tax (LLFGYPVYV) and P6A-Tax (LLFGYAVYV) peptide/MHC upon TCR binding were examined. NMR results indicated that despite nearly identical crystallographic structures, there are differences in the conformations of the two peptide/HLA-A2 complexes as a function of increasing temperature. Analysis of unrestrained molecular dynamics simulation at 300 and 330 K provided insight into these differences, showing that the central region of both peptides sampled alternative conformations. In addition, the studies suggested that conformational changes observed upon TCR binding to MHC cannot be explained solely as an induced-fit or selection of a pre-existing equilibrium conformation but rather a combination of these two binding mechanisms.In the case of the MART-1 melanoma antigen (AAGIGILTV), despite improving peptide binding 40-fold, replacement of the suboptimal alanine at position 2 with leucine (ALGIGILTV) completely abolished T cell recognition. Although crystallographic structures indicated similar backbone conformations of both peptides, molecular dynamics simulations and NMR at multiple temperatures showed alternative conformations in the modified peptide. This tracked closely with the crystallographic results, showing that the modified peptide samples all the conformations observed crystallographically. Collectively, these observations reveal that contrary to the usual considerations regarding peptide antigenicity, antigen dynamical properties can profoundly influence T cell recognition. Further, these observations demonstrate that seemingly minor modifications within a peptide can have dramatic unanticipated consequences such as increasing antigenic peptide dynamics, with implications for TCR binding and kinetics.