Figure 1

Complex I may work like a semi-automatic shotgun. The cartoon model previously published by Efremov et al.,⁴ with the variation of not having the subunit equivalent to ND2 as a proton pump,²⁴ was first tilted vertically and then horizontally by 180° as in Figure 1 of Treberg and Brand.⁷ The silhouette, which respects the dimension of the X-ray structure of Thermus complex I,⁴ was then used to outline the modular assembly of the equivalent mitochondrial ND subunits (Table 1). The ND2 subunit is shown behind other subunits for it is postulated to have an ancillary role in proton pumping.²⁵ The major hotspots for the pathogenic mutations of different ND subunits are noted by the indicated symbol and arrows (Table 1, see also Bridges et al.¹⁷ for further details on pathogenic ND mutations). Helix HL of subunit ND5⁴ is represented by the long spring that may be analogous to the spring-loaded helices of viral agglutinins and similarly undergo proton-associated conformational changes.^{26, 27} Here, these changes are considered to be analogous to the re-loading movements of semi-automatic shotguns. The ND1 subunit, perhaps together with adjacent subunits of the hydrophilic domain (e.g. NQO6⁴), provides the short spring that converts the inertia of the recoiling process into automatic forward movement of the ‘bolt’, which is proposed to be essentially formed by the ND6 subunit as depicted in the top right part of the figure (in subsequent parts, the image of the short spring and bolt device is not shown for sake of clarity). (a) Static view, in which The ND3 and ND4L subunits are labeled with lower font size to indicate that they may not form the core of the functional bioenergetic machinery of mitochondrial complex I, because they are not present in the mitochondrial genomes of some algae¹² and have fewer damaging mutations (Table 1). Cluster N2 is in light blue to denote its oxidized state. The images on the right illustrate the mechanical devices of complex I that are proposed to be analogous to those essential in semi-automatic shotguns. (b) Dynamic view in four snapshots (Supplementary Movie 1, for a cartoon showing these and other steps in motion). Step 1 – Reduction of Q via cluster N2, in turn reduced (dark blue) by NADH via other redox groups (only FMN is shown), is accompanied by the uptake of two protons from the matrix. Step 2 – The formation of the ubiquinol (QH2) product induces a large conformational change in the hydrophilic domain and the adjacent ND1 and ND6 subunits leading to the forward movement of the ‘bolt’, represented by the acute angle of the rhombic shape of ND6 along the membrane plane. This ‘fires’ the outward release of two protons by the ND4 and ND5 subunits, while compressing the long HL helix. Step 3 – The ubiquinol product leaves the complex allowing the decompression of helix HL and the re-loading of another molecule of Q substrate from a membrane reservoir (not pictured) into the Q-reacting cavity. In the recoil process, additional protons are taken up from the matrix side, while the spring and bolt mechanism is ‘armed’ again. This arming uses the mechanical energy provided by the relaxation of the long HL, which is connected to the short helix behind the ‘bolt’ by a lever device primarily formed by the ND1 and ND6 subunits, in analogy with the mechanics of semi-automatic shotguns. Step 4 – The automatic relaxation of the short helix pushes the ND6 ‘bolt’ forward again, converting the mechanical energy driven by the HL helix recoil into an ‘automatic’ round of proton release by the ND4 and ND5 pumps, perhaps assisted by the ND2 subunit as well. Conformational type A inhibitors (Table 2) are predicted to block the recoiling of step 3 and 4, in particular