(A and B) Helical wheels of the C-terminal (A) and penultimate
C-terminal (B) helices. Residues are color coded according to the type of amino
acid: nonpolar (yellow); polar (purple or pink); positively charged (blue);
negatively charged (red). Arrows represent hydrophobic moments. Analysis was
performed using heliQuest (http://heliquest.ipmc.cnrs.fr/) (Gautier et al., 2008).
(C) The cartoon diagram provides a view from the membrane interior of
the C-terminal and penultimate C-terminal helices (white), adjacent loop regions
(green), and DCQ (sticks); nonpolar residues are shown as balls and sticks with
carbons colored yellow. The decyl tail of DCQ points toward the membrane-facing
surface; the tip of the tail (colored magenta) protrudes from the CoQ binding
cavity.
(D) Crystallographic packing constraints on the C-terminal helix
(Ala439-Glu452). Chain A from one asymmetric unit and an adjacent
symmetry-related chain D are shown as cartoons colored green and yellow,
respectively, except for a portion of a loop (400-405), which is colored white
in both chains. The C-terminal helix touches loop 400-405, but makes no specific
contacts. Glu452, the Arg411- Ser413 peptide backbone, and the side chains of
Arg411 and Ser413 are shown as sticks. Hydrogen bonds are indicated by the
yellow dotted lines.
(E) The cartoon diagram shows the spatial position of SQOR in the inner
mitochondrial membrane (white spheres) that was calculated using the PPM server
(http://opm.phar.umich.edu/server.php) (Lomize et al., 2011). The C-terminal and penultimate
C-terminal helices are colored green; all other regions are colored blue. FAD
and DCQ are shown as spheres, colored yellow and gold, respectively.