Fig. 5: Conformational changes observed after binding of DQ.
From: Key role of quinone in the mechanism of respiratory complex I
a Overlay of CXIINT (grey) with CXIDQ structure (coloured subunits, Nqo4 in dark green, Nqo6 in red and Nqo8 in orange). The structures were aligned by the MDs. Note that upon DQ binding Nqo8 tilts in the direction of the arrow, with tilt developing further in the PA. b, d Zoom-in into the Q-site, the same alignment as in a, with CXIINT in grey and CXIDQ coloured. The Q cavity is indicated with a grey mesh (calculated in MOLE) and bound DQ is in violet. The movement of the key Nqo4 β-sheet is indicated by an arrow. Key loops flanking the Q-site (Nqo4 32–39, Nqo6 66–75 and Nqo8 223–229 residues) are shown as thick tubes, with key residues from these loops indicated. c The Q cavity shown as solvent-accessible surface (calculated in Pymol with 1.4 Å probe). Note that the cavity gets narrower around H384 residue in the CXIDQ structure (cyan) as compared with CXIINT (grey).
