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

Figure 9

Interhelical distance and area of interhelical surface of MHC α-helices. (a) Mean distances between the two MHC α-helices as measured at 11 different points along the helices. -axis describes the running parameter of the helices with each helical axis divided into 100 equidistant points. The orientation of the running parameters of both helices is from N-terminus to C-terminus of G-ALPHA1. Distances are measured between corresponding points on each helical axis of G-ALPHA1 and G-ALPHA2. The standard deviation of the mean is shown in the error bars. This distance plot describes the shape and size of the peptide-binding pocket. B4403 and B4405 show a very similar pocket shape. (b) The two MHC α-helices span a ruled surface. Moving average of interhelical area along the MD simulation is shown. The magnitudes of interhelical area of B4403 (nonimmunogenic) and B4405 (immunogenic) are similar and slightly increasing, while B4402 shows a declining trend. The curvature integral (Figure 8) for individual helices shows a concomitant bending and relaxing, explaining the shrinkage of interhelical area.

(a)

(b)