Docking and molecular simulations reveal a quinone‐binding site on the surface of respiratory complex I

Abstract

The first component of the mitochondrial electron transport chain is respiratory complex I. Several high‐resolution structures of complex I from different species have been resolved. However, despite these significant achievements, the mechanism of redox‐coupled proton pumping remains elusive. Here, we combined atomistic docking, molecular dynamics simulations, and site‐directed mutagenesis on respiratory complex I from Yarrowia lipolytica to identify a quinone (Q)‐binding site on its surface near the horizontal amphipathic helices of ND1 and NDUFS7 subunits. The surface‐bound Q makes stable interactions with conserved charged and polar residues, including the highly conserved Arg72 from the NDUFS7 subunit. The binding and dynamics of a Q molecule at the surface‐binding site raise interesting possibilities about the mechanism of complex I, which are discussed.

On the role of ubiquinone in the proton translocation mechanism of respiratory complex I

“…Virtually all currently considered models (but see [22,27]) consider that reduced QH 2 then exits the tunnel in exchange for a molecule of oxidised Q from the membrane phase. By contrast, we have here highlighted the possibility of a piston‐like function where one molecule of Q remains in the tunnel and is oxidised when in the proximal position by another molecule of ubiquinone that may be bound to the complex I surface [27,35]. The perhaps greatest benefit of such a mechanism is, as it is coupled to reoxidation of QH 2 , that it provides local protons in a controlled fashion to annihilate the original negative charge that triggered the pump mechanism.…”

“…Most recently, and based on the strict distance requirements, Djurabekova et al. [35] proposed a potential binding site within the 14 Å edge‐to‐edge distance for an exchangeable Q by docking and molecular dynamics simulations (Fig. 2).…”

“…It should be noted, in particular, that the ‘Q piston’ mechanism includes unique oxidation of the QH 2 in the proximal position with specific deployment of the released protons to annihilate the primary structural proton extraction on forming Q 2− in the distal site. All other mechanisms (in which formed QH 2 exits the tunnel) must postulate proton uptake from the N‐side of the membrane to achieve the annihilation (see below), whereas in the Q‐piston model, the N‐side protons only neutralise the negative charge on the postulated exchangeable Q, which has been suggested to bind at membrane–protein interface based on docking and MD simulations [35].…”

“…Here, we would like to stress the importance of kinetic data and further development of freeze‐trapping the stages of catalytic turnover, possibly for structural analysis by cryoEM methodology. Another desired approach would be a focused cryoEM search of Q bound to the site external to the tunnel proposed here (see also [35]).…”

Tunnel dynamics of quinone derivatives and its coupling to protein conformational rearrangements in respiratory complex I

“…Latest high-resolution cryo EM data confirmed the existence of these sites (Kampjut & Sazanov, 2020; Parey et al, 2019). However, their functional meaning remains unclear, either they represent transient halts for Q upon its travel to and from the active site near N2 FeS cluster or they have a role in coupling Q-tunnel redox reactions to proton pumping in the membrane arm of complex I (Djurabekova et al, 2022; Haapanen & Sharma, 2021; Wikstrom, Sharma, Kaila, Hosler, & Hummer, 2015).…”