Figure 1. Root mean square deviations (RMSD) of the molecular dynamics (MD) simulations for the individual HLA-DR1 ensembles.

RMSD values for the α1/β1-domain are shown for the time course of the simulation. Different colors represent individual runs. A, The two peptide-loaded structures DR1_1DLH/HA306-318 and DR1_1SJE/GAG166-181 (left panels) and the P1-stabilized dipeptide-loaded model DR1_1DLH/Ac-FR-NH₂ were calculated for 15 ns (right panel). B, Empty HLA-DR1-models derived from PDB entries 1DLH (DR1_1DLH empty) and 1SJE (DR1_1SJE empty) were calculated for 30 ns.