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Fig. 2 | BMC Structural Biology

Fig. 2

From: DynaDom: structure-based prediction of T cell receptor inter-domain and T cell receptor-peptide-MHC (class I) association angles

Fig. 2

TCR and TCRpMHC complexes modeling pipeline. Center column: standard pipeline (see Methods) for the remodeling of the TCR Vα/Vβ association angles and for the pMHC positioning with respect to the TCR. Blue highlighted steps are performed in both modeling pipelines: only Vβ and combined Vβ/pMHC placement. Green highlighted steps are performed only if the pMHC is included in the remodeling process. The left and the right columns illustrate the individual steps of the pipeline. Steps with numbers circled in black: TCR Vα/Vβ association angle modeling pipeline, steps with numbers circled in green: combined Vβ/pMHC modeling pipeline. Steps 3 to 7 are performed for each of the 11 starting conformations. The protein domains represented in blue, red, and green color correspond to the Vα, Vβ, and pMHC units, respectively. In step 1 (both for TCR and TCRpMHC modeling), the different protein domains are described by unified cuboids and assembled. The illustration of steps 2 and 5 show the Q-flip correction/optimization. At step 2, each glutamine residue is optimized with respect to its direct environment only (only the corresponding variable domain is accounted for). Whereas in step 5, the two glutamine residues are optimized simultaneously, thus accounting for the whole TCR environment. In step 4 (only for TCRpMHC modeling), the pMHC unit is pre-placed, translated away from the TCR and optimized with respect to the fixed TCR variable domains. At step 6 (both for TCR and TCRpMHC modeling), the position of all cuboids as well as the orientation of the glutamine residues are optimized concurrently. The latter illustrations show the structure before and after optimization, with the target crystal structure depicted in gray

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