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

Figure 7

Curvature integral and helix conformations. Three case studies showing the time course of the curvature integral for G-ALPHA1 (b and c) and G-ALPHA2 (a). Upper row shows curvature integral along the 250 ns MD simulation. Phases of increasing or decreasing trends are highlighted in orange and red. Middle row shows 3D conformations of MHC α-helices ( atoms) and polynomials derived by fragment-fitting. Colours correspond to the highlighted phases in the upper row. We see that the red bundle of conformations differs from the orange bundle, especially near the ends. Lower row shows that RMSD matrices between helix conformations were calculated and frequencies of RMSD values plotted. Red and orange lines represent frequency distribution of RMSD values between configurations within red and orange phases, respectively. Black lines represent RMSD distributions between configurations in the red and configurations in the orange phases. The difference between lower RMSD within phases and higher RMSD between phases confirms a conformational change between these phases.

(a)

(b)

(c)