From the ‘black box' to ‘domino effect' mechanism: what have we learned from the structures of respiratory complex I

Abstract

My group and myself have studied respiratory complex I for almost 30 years, starting in 1994 when it was known as a L-shaped giant ‘black box' of bioenergetics. First breakthrough was the X-ray structure of the peripheral arm, followed by structures of the membrane arm and finally the entire complex from Thermus thermophilus. The developments in cryo-EM technology allowed us to solve the first complete structure of the twice larger, ∼1 MDa mammalian enzyme in 2016. However, the mechanism coupling, over large distances, the transfer of two electrons to pumping of four protons across the membrane remained an enigma. Recently we have solved high-resolution structures of mammalian and bacterial complex I under a range of redox conditions, including catalytic turnover. This allowed us to propose a robust and universal mechanism for complex I and related protein families. Redox reactions initially drive conformational changes around the quinone cavity and a long-distance transfer of substrate protons. These set up a stage for a series of electrostatically driven proton transfers along the membrane arm (‘domino effect'), eventually resulting in proton expulsion from the distal antiporter-like subunit. The mechanism radically differs from previous suggestions, however, it naturally explains all the unusual structural features of complex I. In this review I discuss the state of knowledge on complex I, including the current most controversial issues.

A computational study to assess the pathogenicity of single or combinations of missense variants on respiratory Complex I

“…The p.T536A/ND5 mutation affects the ND5 subunit, which is in contact with subunit ND4. Visual inspection of the trajectories and both the RMSD and RMSF analyses on the dynamics of these two subunits show that there are no significant changes in their secondary structure between closed and open system, as observed in previous experimental studies (20,23,27). Then, the focus was placed on the remaining two variants, p.M64V/ND6 and p.A71T/ND4L, which are close to each other in the putative E-channel.…”

“…1) (1, 2, [21][22][23][24][25]. Further, subunits ND1, ND3, ND6 and ND4L form the proximal part of the P module at the interface with the Q module (22)(23)(24)27) and create together the E-channel, a region containing several conserved glutamates (Fig. 1) (28,29).…”

“…Specifically, in the open conformation the third trans-membrane helix (TMH3) of ND6 forms a π-bulge (Fig. 1), which breaks the hydrophilic axis in the E-channel region and is proposed to be crucial for CI mechanism, preventing a futile proton leaking towards the Q-cavity (20,27). Despite the structural and biochemical advances, the mechanism of the proton pumping coupled to the reduction of ubiquinone is still debated (27,31,32).…”

“…1), which breaks the hydrophilic axis in the E-channel region and is proposed to be crucial for CI mechanism, preventing a futile proton leaking towards the Q-cavity (20,27). Despite the structural and biochemical advances, the mechanism of the proton pumping coupled to the reduction of ubiquinone is still debated (27,31,32). The complexity of CI structure implies that many amino acids have a crucial role in the conformational changes required for its activity.…”

Using cryo-EM to understand the assembly pathway of respiratory complex I

“…Proton-pumping NADH:ubiquinone oxidoreductase is a large membrane-protein complex with a central role in aerobic energy metabolism (Galemou Yoga et al, 2020;Parey et al, 2020;Chung, Grba et al, 2022;Sazanov, 2023). The enzyme is also called complex I because it is the first complex in the respiratory chain.…”