Ubiquinone Binding and Reduction by Complex I-Open Questions and Mechanistic Implications

Abstract

NADH: ubiquinone oxidoreductase (complex I) is the first enzyme complex of the respiratory chain. Complex I is a redox-driven proton pump that contributes to the proton motive force that drives ATP synthase. The structure of complex I has been analyzed by x-ray crystallography and electron cryo-microscopy and is now well-described. The ubiquinone (Q) reduction site of complex I is buried in the peripheral arm and a tunnel-like structure is thought to provide access for the hydrophobic substrate from the membrane. Several intermediate binding positions for Q in the tunnel were identified in molecular simulations. Structural data showed the binding of native Q molecules and short chain analogs and inhibitors in the access pathway and in the Q reduction site, respectively. We here review the current knowledge on the interaction of complex I with Q and discuss recent hypothetical models for the coupling mechanism.

Keywords: NADH dehydrogenase; electron transfer; inhibitor; oxidative phosphorylation; proton pumping; respiratory chain; semiquinone.

Figure 1

Architecture of complex I. The primary electron acceptor FMN is connected by a chain of FeS clusters with the Q reduction site near FeS cluster N2. Q moves in a tunnel between the active site and the membrane. A hydrophilic axis (red dots) connects the Q module with the proton pumps. Its initial section is called the E channel due to the presence of several strictly conserved glutamates in subunit ND1. Loops of subunits NDUFS2 (green), NDUFS7 (blue), ND1 (red), and ND3 (yellow) line the Q access pathway and the interface between the membrane arm and the peripheral arm. Concerted conformational changes in the loop cluster are thought to play a key role in the coupling mechanism.

Figure 2

Q binding positions. (A) The Q reduction site in the peripheral arm of complex I (PDB: 6RFR) is formed by subunits NDUFS2 (green) and NDUFS7 (blue). A tunnel for Q access from the membrane traverses subunit ND1 (pink). The tunnel was calculated using the CAVER3 software (Chovancova et al., 2012) (starting point conserved Y144, PDB: 6RFR, probe radius 1.3 Å). Intermediate Q binding positions determined by computational methods are indicated by Arabic numbers according to Haapanen et al. (2019). The positions of Q molecules (head group) modeled into X-ray or cryo-EM structures are indicated by Roman numbers and are shown in detailed views in separate panels; the direction of view is consistent for panels in the same row. (B) DBQ bound to complex I from T. thermophilus (PDB: 6I0D) (Y, Y87; H, H38); (C) DBQ bound to complex I from Ovis aries in the closed state during turnover (PDB: 6ZKC) (Y, Y108; H, H59); (D) PL9 bound to ndh complex I from T. elongatus BP-1 (PDB: 6KHJ) (Y, Y72; H, H23; A, A237; R₃, R329); (E) Q9 bound to complex I from Y. lipolytica (PDB: 6RFR) (R₁, R27; R₂, R108, R₃, R297; F, F228); (F) DBQ bound to complex I from O. aries in the closed state during turnover (PDB: 6ZKC) (R₁, R25; R₂, R77, R₃, R274; F, F224); (G) DBQ bound to complex I from O. aries in the open state with NADH bound in the N module (PDB 6ZKH) (R₁, R25; R₂, R77, R₃, R274; F, F224); (H) DBQ bound to complex I from O. aries in the open state during turnover (PDB 6ZKD) (R₁, R25; R₂, R77, R₃, R274; F, F224).

Figure 3

Inhibitor binding positions. (A) Rotenone bound to complex I from O. aries in the closed state (PDB 6ZKK) (Y, Y108; H, H59); (B) Piericidin A bound to complex I from Mus musculus (PDB 6ZTQ) (Y, Y108; H, H59); (C) Rotenone bound to complex I from O. aries in the open state (PDB 6ZKL) (R₁, R25; R₂, R77, R₃, R274; F, F224). Binding positions in the Q tunnel are indicated by Roman numbers and correspond to Figure 2A but note that rotenone occupies a larger area. For colors, see the legend of Figure 2.