Fig. 10.

Illustration of the rotation of NBD-I with respect to NBD-II which brings NBD-β close to the back side of NBD-II. (A) 2KHO structure in which NBD-I crosses NBD-II (δ = 65°), (B) 3C7N structure in which NBD-I moves closer to a parallel orientation with respect to NBD-II (δ = 47°). (C) The structure from the trajectory shown in Figure 6A after 10 ps of simulations, in which NBD-II is nearly parallel to NBD-II (δ = 26°) (where δ is the angle between the long axes of NBD-I and NBD-II). It can also be seen that the “switch” (SW) α-helix which runs from E369 to G380 rotates with respect to NBD-II, following the rotation of NBD-I, with which it is associated through interactions with the E171-Y179 “holder” (HO) α-helix. The SW α-helix is connected to SBD-β by a linker. Consequently, its motion switches the orientation of SBD-β from the top of NBD to the back side of this domain and brings it closer to NBD-I; it also brings the linker segment closer to the β-sheet of NBD-II and enables it to join it as a β-strand in the 3C7N structure, thus fixing SBD at a short distance from the NBD. The drawings were done with PyMOL (http://www.pymol.org) and the backbones of the UNRES conformations were converted to all-atom representation by using the knowledge-based algorithm developed by Gront et al.⁴³ to enable to draw the structures in ribbon representation.