Coenzyme Q10 trapping in mitochondrial complex I underlies Leber's hereditary optic neuropathy

Abstract

How does a single amino acid mutation occurring in the blinding disease, Leber's hereditary optic neuropathy (LHON), impair electron shuttling in mitochondria? We investigated changes induced by the m.3460 G>A mutation in mitochondrial protein ND1 using the tools of Molecular Dynamics and Free Energy Perturbation simulations, with the goal of determining the mechanism by which this mutation affects mitochondrial function. A recent analysis suggested that the mutation's replacement of alanine A52 with a threonine perturbs the stability of a region where binding of the electron shuttling protein, Coenzyme Q10, occurs. We found two functionally opposing changes involving the role of Coenzyme Q10. The first showed that quantum electron transfer from the terminal Fe/S complex, N2, to the Coenzyme Q10 headgroup, docked in its binding pocket, is enhanced. However, this positive adjustment is overshadowed by our finding that the mobility of Coenzyme Q10 in its oxidized and reduced states, entering and exiting its binding pocket, is disrupted by the mutation in a manner that leads to conditions promoting the generation of reactive oxygen species. An increase in reactive oxygen species caused by the LHON mutation has been proposed to be responsible for this optic neuropathy.

Keywords: Coenzyme Q10; blinding genetic disease; mitochondria; molecular dynamics simulation; quantum electron tunneling.

Fig. 1.

(A) The full complex I taken from the cryo-EM structure 5XTD, with the chains used in the simulations shown in color. (B) The periodic image of the fully solvated structure, including the colored part of the images in A, the membrane, and the Fe/S clusters. (C) Image with the solvent and electrolyte ions removed for clarity.

Fig. 2.

Simulations show that the mutant binds CoQ10 less strongly by ~4 kcal/mol. (A) The distance between the center of the CoQ10 headgroup and the center of N2 (black dashed arrow) monitored throughout the molecular dynamics simulation showing (B) that shorter distances are accessible to CoQ10 in the mutated pocket (red curve), facilitating a higher rate of electron transfer. (C) Thermodynamic cycle for the FEP simulations to compute the relative binding affinity of CoQ10 in WT and A52T.

Fig. 3.

CoQ10 extraction from its ND1 binding pocket. The ND1 protein forms part of the 38-Å-long CoQ10 binding tunnel of respiratory complex I. (A) CoQ10 (shown in green) is fully inserted, with the electron receiving end (reducible oxygens shown in red) in close proximity to the terminal Fe-S complex in the Fe-S cluster chain (shown as yellow/orange group). The mutation site is labeled in the Inset. The pulling reaction coordinate is shown as the red dashed arrow in the inset (52A/T). (B) The reduced CoQ10H₂ has been “pulled” out by the tail (red arrow at lower right). Unbound CoQ10H₂ diffuses within the membrane bilayer to complex 3 where it is oxidized. The full extraction simulation over 48 Å is done over the course of 30 ns (Left). The inset corresponds to the tail of CoQ10 (15 Å) passing the mutation site. (Right) The head of CoQ10 (15 Å) passing the mutation site, performed over the course of 30 ns, showing a more pronounced hindrance caused by the mutation. The legends indicate whether the trajectory is WT or A52T mutant and whether CoQ10 is oxidized or reduced (SI Appendix).