Modeling of the TCR-MHC-peptide complex

The methodology for generating a homology model of the T1 TCR-PbCS-K-d clas s I major histocompatibility complex (MHC) class I complex is presented. Th e resulting model provides a qualitative explanation of the effect of over 50 different mutations in the region of the complementarity determining reg ion (CDR) loops of the T cell receptor (TCR), the peptide and the MHC's alp ha(1)/alpha(2) helices. The peptide is modified by an azido benzoic acid ph otoreactive group, which is part of the epitope recognized by the TCR. The construction of the model makes use of closely related homologs (the A6 TCR -Tax-HLA A2 complex, the 2C TCR, the 14.3.d TCR V beta chain, the 1934.4 TC R V alpha chain, and the H-2 K-b-ovalbumine peptide), ab initio sampling of CDR loops conformations and experimental data to select from the set of po ssibilities. The model shows a complex arrangement of the CDR3 alpha, CDR1 beta, CDR2 beta and CDR3 beta loops that leads to the highly specific recog nition of the photoreactive group. The protocol can be applied systematical ly to a series of related sequences, permitting the analysis at the structu ral level of the large TCR repertoire specific for a given peptide-MHC comp lex. (C) 2000 Academic Press.