Cryo-EM structures define ubiquinone-10 binding to mitochondrial complex I and conformational transitions accompanying Q-site occupancy

• Published in: Nature communications Vol. 13; no. 1; p. 2758
• Main Authors: Chung, Injae, Wright, John J., Bridges, Hannah R., Ivanov, Bozhidar S., Biner, Olivier, Pereira, Caroline S., Arantes, Guilherme M., Hirst, Judy
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 19.05.2022; Nature Publishing Group; Nature Portfolio
• Subjects: 101/28; 119/118; 631/45/173; 631/535/1258/1259; 82/16; 82/83; Animals; Binding Sites; Coenzyme Q10; Cryoelectron Microscopy; Electron transport chain; Electron Transport Complex I - metabolism; Energy transduction; Humanities and Social Sciences; Ions; Ligands; Mammals; Mammals - metabolism; Mitochondria; Mitochondrial Membranes - metabolism; Molecular dynamics; Molecular structure; multidisciplinary; NADH; NADH-ubiquinone oxidoreductase; Nicotinamide adenine dinucleotide; Oxidation-Reduction; Oxidative phosphorylation; Phospholipids; Phosphorylation; Protons; Residues; Science; Science (multidisciplinary); Substrates; Ubiquinone - metabolism
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-022-30506-1

Mitochondrial complex I is a central metabolic enzyme that uses the reducing potential of NADH to reduce ubiquinone-10 (Q 10 ) and drive four protons across the inner mitochondrial membrane, powering oxidative phosphorylation. Although many complex I structures are now available, the mechanisms of Q 10 reduction and energy transduction remain controversial. Here, we reconstitute mammalian complex I into phospholipid nanodiscs with exogenous Q 10 . Using cryo-EM, we reveal a Q 10 molecule occupying the full length of the Q-binding site in the ‘active’ (ready-to-go) resting state together with a matching substrate-free structure, and apply molecular dynamics simulations to propose how the charge states of key residues influence the Q 10 binding pose. By comparing ligand-bound and ligand-free forms of the ‘deactive’ resting state (that require reactivating to catalyse), we begin to define how substrate binding restructures the deactive Q-binding site, providing insights into its physiological and mechanistic relevance. Using cryo-EM, Chung et al . investigate conformational states of mammalian respiratory complex I to reveal an ubiquinone-10 molecule occupying the full length of the Q-binding channel. Molecular dynamics simulations suggest how the charge states of key residues influence the substrate binding pose.