Geometry Dynamics of α-Helices in Different Class I Major Histocompatibility Complexes

Figure 16

Dynamics of secondary structure. The TCR/pMHC systems B4402, B4403, and B4405 comprise 829 amino acids. The following list shows which residues belong to which protein: MHC, residues 1–276; β-2-microglobulin, residues 277–375; ABCD3 peptide, residues 376–384; TCR α, residues 384–584; TCR β, residues 585–825. The graph on the right-hand side displays the structural behaviour of amino acid residues along the simulation time. Different secondary structural elements are assigned different colours as shown in the legend. Secondary structures are stable along the 250 ns MD simulation for all three TCR/pMHC systems. The graph on the left-hand side displays the relative simulation time that an amino acid residue is part of an α-helix. Extended and stable α-helices in these TCR/pMHC systems are only present in the MHC molecule.