Terminal Electron–Proton Transfer Dynamics in the Quinone Reduction of Respiratory Complex I

Abstract

Complex I functions as a redox-driven proton pump in aerobic respiratory chains. By reducing quinone (Q), complex I employs the free energy released in the process to thermodynamically drive proton pumping across its membrane domain. The initial Q reduction step plays a central role in activating the proton pumping machinery. In order to probe the energetics, dynamics, and molecular mechanism for the proton-coupled electron transfer process linked to the Q reduction, we employ here multiscale quantum and classical molecular simulations. We identify that both ubiquinone (UQ) and menaquinone (MQ) can form stacking and hydrogen-bonded interactions with the conserved Q-binding-site residue His-38 and that conformational changes between these binding modes modulate the Q redox potentials and the rate of electron transfer (eT) from the terminal N2 iron-sulfur center. We further observe that, while the transient formation of semiquinone is not proton-coupled, the second eT process couples to a semiconcerted proton uptake from conserved tyrosine (Tyr-87) and histidine (His-38) residues within the active site. Our calculations indicate that both UQ and MQ have low redox potentials around -260 and -230 mV, respectively, in the Q-binding site, respectively, suggesting that release of the Q toward the membrane is coupled to an energy transduction step that could thermodynamically drive proton pumping in complex I.

Redox-coupled quinone dynamics in the respiratory complex I

“…This site is stabilized further by a hydrogen bond to protonated His-38 Nqo4 ( Fig. 5 B ), consistent with previous studies ( 30 ), and our equilibrium MD simulations. A shoulder in the PMF (site 1′) indicates a metastable site at a distance of ∼10–15 Å to Tyr-87 Nqo4 , where the Q headgroup forms interactions with Phe-63 Nqo6 ( Fig.…”

“…200 mV (Q ox /SQ •/− couple; SI Appendix , Fig. S14 ), which arises from differences in local protein surroundings, especially by interaction or proximity to positively charged residues (Arg-62 Nqo6 , Arg-36 Nqo8 , and Lys-69 Nqo8 ), and dissociation from the N2 center ( 30 ). Moreover, approximate electrostatic binding free energies further suggest that the motion of the Q ox /QH 2 toward the second binding site is coupled with an energy release of ca .…”

“… 24 ), a low (Q L ) and a high (Q H ) potential site. The Q L site is near center N2 that was initially characterized biochemically ( 27 – 29 ) and later confirmed computationally ( 26 , 30 ). The Q H site could be located somewhere in the Q tunnel, albeit its precise location as well as its molecular architecture remains undescribed ( Fig.…”

“…To date, however, a bound Q molecule has not been resolved in any of the crystal or recent cryo-EM structures of complex I ( 11 , 12 , 31 , 32 ). Two conformations have been reported for Q bound to the conserved Tyr-87 Nqo4 ( 30 ), and recent studies also show that the mammalian complex I can operate with different numbers of isoprene units, Q 1 –Q 10 ( 33 ). Earlier reports from labeling experiments ( 34 , 35 ) also support the existence of multiple Q-binding sites in complex I.…”

Exploring the quinone/inhibitor-binding pocket in mitochondrial respiratory complex I by chemical biology approaches

“…It is conceivable that decoupling UQs accept electrons from the Fe-S cluster N2, but at somewhat different positions from that of ordinary short-chain UQs, such as UQ 2 , because of their unique sidechain structures. Accordingly, the catalytic reduction of decoupling UQs may be unable to induce the predicted structural changes inside the quinone-binding pocket, which is essential for transmitting the redox energy released in the electron transfer reaction to the membrane domain for driving proton translocation (39,41). However, the channel models exclude the possibility that quinones possessing various chemical frameworks bind to the narrow reaction site in different positions or manners (5)(6)(7)(8)(9).…”