MHC-related applications. In this figure we tested the applicability of PyTMs with respect to altered peptide ligands (APLs). As described in the implementation, we started with the crystal structure of a native gp34 LCMV epitope complexed within the mouse MHC class I molecule H-2Kb. We introduced nitration into the p3TYR residue and refined the structure locally to resolve resulting clashes. The results were aligned and compared to the experimentally determined crystal structure. A) Orientation of the native gp34 in the resolved crystal structure [PDB: 3ROO]. The view is focused on the peptide-binding cleft. B) The refined model of a nitrated gp34 APL derived from the same crystal structure. Alternative backbone-dependent rotamers for GLU152 (steric displacement) and TYR116 (hydrogen bonding) have been chosen to accommodate this APL. C) The aligned gp34 APL and MHC pocket from the experimentally resolved crystal structure [PDB: 3ROL]. The essential adaptations are surprisingly similar. We therefore conclude that modeling APLs can be a valid predictive approach. However, the ligation of this APL induces more pronounced and global conformational changes that cannot be accounted for by local refinement. D) Relative positioning of the aligned peptides. Black and blue: Two nitrated gp34 epitopes according to modeling which correspond to 180° rotamers of each other. The first variant (model 1, black) clashed significantly with the helix of the MHC and TYR159, a feature that may contribute to the reduced affinity of the nitrated epitope (complete model not shown). The alternatively positioned model 2 was used for the modeling above and fits significantly better, especially after local refinement. Note how the orientation of this APL is essentially identical to that of the experimentally resolved variant (green).