Molecular electrostatic potential surfaces and PIPSA clustering of the dystrophin tandem-repeat models.
(A) The dendogram from the PIPSA analysis of the 21 dystrophin tandem repeats showed four clusters. The 4 tandem repeats used in the molecular dynamics simulation are underlined. (B) Representation of the electrostatic potential projected on the solvent accessible surface of the dystrophin repeats, separated into these 4 clusters. Each model was colored using the APBS electrostatic potential calculated for an ionic strength of 50 mM, and the surface colors were clamped at -3 (red) and +3 (blue) kTe-1. The molecules are presented with the same orientation as in Fig. 2A. (C) Graphical representation of the repartition of the electrostatic clusters along the rod domain. To take into account the overlapping repeats, the tandems are shown here in two lines, one for tandems starting with an odd number (R1-2, R5-6, etc.), and the other for the evens (R2-3 etc). Each tandem repeat is colored to indicate in which cluster it belongs: red for cluster 1, grey for 2, blue for 3 and green for 4. The uncolored repeats belong to tandem not studied because of the presence of a hinge. Dotted vertical lines are drawn to emphasize the presence of six specific regions.