Fig. 3: Q-loop architecture of cyt. bdMtb.
a Left: The mycobacterial Q-loop is organized in a mostly disordered QN (blue) and a rigid, well-ordered QC segment (cyan). QN starts at Pro256.A and contains the horizontal helix Qh1 with the conserved residues Lys258.A and Glu263.A that covers heme b558, and a second small helix Qh2 comprising residues Tyr296.A to Ala303.A. The QC segment is exposed to the periplasm and consists of the third Q-loop helix Qh3 that covers the surface of the TMHs 6 and 7. Right: Van-der-Waals interaction cluster between Qh3 and the periplasmic loop 8 (PL8) of CydA. b Top view of a superposition of CydA snapshots obtained from MD simulations performed in presence and absence of the Cys266.A-Cys285.A disulfide bond. Positions of cysteine residues are indicated. The red dashed circle indicates the location of the intact disulfide bond. CydA (oxidized), yellow; CydA (reduced), violet. c Top: average root mean square fluctuation plot of CydA residues in MD simulations for 2 × 750 ns with reduced and oxidized disulfide bond (Cys266.A-Cys285.A) of the QN-loop. Middle: Data plots of Cα-Cα distance distribution between disulfide-forming cysteines during MD simulations. Bottom: Distribution of QN displacement in Z direction during MD simulations. Yellow data plots indicate a simulation setup with intact disulfide bond. Purple data points indicate a simulation setup with a reduced disulfide bond. d Sequence alignment of representative cytochrome bd oxidases.
