Molecular nature of the conformational and electrostatic coupling in the proton pumping mechanism of complex I

Complex I (NADH–ubiquinone oxidoreductase) in the respiratory chains of mitochondria and bacteria catalyzes the transfer of electrons from NADH to ubiquinone (UQ), and couples the free energy of the reaction to proton pumping across the membrane. The established proton electrochemical gradient is then used to drive the synthesis of ATP — the energy currency of the cell. Site-directed mutagenesis, kinetic experiments as well as equilibrium redox titrations have shown that the UQ reduction reaction is linked with the proton pumping through a long-range indirect coupling mechanism. Some of the key elements involved in long-range coupling have indeed been identified in the recently solved crystal structure of the entire complex I from the thermophilic bacterium Thermus thermophilus. However, despite these advances the molecular level description of the proton pumping mechanism of complex I has remained elusive. Here, with the help of state-of-the-art classical molecular dynamics (MD) simulations performed on the entire crystal structure of complex I immersed in a lipid-solvent environment, we present molecular level insights to the coupling between UQ reduction and proton pumping. The data from simulations performed in different redox and protonation states suggest that the coupling involves both long-range conformational transitions and electrostatic effects.