Fig. 3.

Ion-pair dynamics at the subunit interfaces in the membrane domain of complex I. A) The Nqo13 – Nqo14 interface. Upper panel: Distances of the Lys₁₃-204/Glu₁₃-123 ion pair (in black), the Lys₁₄-345/Glu₁₃-123 ion pair (in red) during 0.6 μs of MD simulation (simulation 5). The flip of the ion pair correlates with a decrease in the Lys₁₃-204/Lys₁₃-235 distance (in blue). Lower panel: Lys₁₃-235/Lys₁₃-204 distances and their distribution during 2.8 μs of dynamics (simulations 1 to 5). The dark blue curve represents a ‘repulsive’ regime where both residues are positively charged, whereas deprotonation of Lys₁₃-204 leads to sampling of shorter distances (light blue curve). Vertical grey lines indicate boundaries between separate simulations. B) The Nqo11 – Nqo14 interface. Distances of the Glu₁₁-67/Lys₁₄-186 (in blue) and Lys₁₄-186/Lys₁₄-216 (in red) ion pairs during 2 μs MD simulations (simulations 1, 2, 5) and the distribution of the distances between Glu₁₁-67/Lys₁₄-186 during the MD simulations. Upon deprotonation of Glu₁₁-67 at 1.4 μs, the inter-subunit contact forms, which correlates with an increase in the Lys₁₄-186/Lys₁₄-216 distance. Deprotonation of Glu₁₁-67 leads to formation of contact with Lys₁₄-186. C) The Nqo12 – Nqo13 interface. Upper panel: Distances of the Arg₁₂-163/Glu₁₃-377 (in blue) and the Arg₁₂-163/Asp₁₂-166 (in red) ion pairs during 0.6 μs of MD simulation (simulation 5). Arg₁₂-163 forms inter- and intra-subunit salt-bridges. Lower panel: Distances between Arg₁₂-163/Glu₁₃-377 during 2.8 μs of simulation (simulations 1 to 5) and their respective distribution. Intra-subunit and intermediate states are drawn in dark-blue and the inter-subunit state in light blue. Vertical grey lines indicate boundaries between separate simulations.