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

Figure 11

Stability of MHC α-helices and protein-protein contacts. (a) Histogram of amino acids that form α-helices in the MHC and β-2-microglobulin protein complex. α-helical stability of 0 means that a given atom is never part of an α-helix during the MD simulation. On the contrary, an α-helical stability of 1 means that this atom is part of an α-helix in every time step of the MD simulation and thus is part of a very stable α-helix. The histogram shows a distinctly bimodal distribution. (b) Histogram of atoms forming stable close contacts (atoms being less than 1.4 nm apart) at the protein-protein interface. The distribution is also distinctly bimodal. Contact stability of 0 means that a atom never forms a close contact during the MD simulation. A contact stability of 1 means that this atom forms very stable contacts throughout the MD simulation. (c) The number of stable residues on -axis is calculated by intersecting both sets of stable helix atoms and stable close contacts atoms. In Section 2.3, we claim that, due to the distinctly bimodal distributions, neither stable α-helices nor the number of close contacts is insensitive to the choice of the cut-off. The resulting number of stable residues will roughly stay constant for a wide range of cut-off values (from 0.2 to 0.8), therefore justifying our choice of 0.5 as the stability cut-off.

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