Complex I in the respiratory chain. The structure of the L-shaped molecule (4) has been placed in the membrane. The positions of the seven membrane subunits L, M, N, K, J, A, and H are roughly indicated. Each of the subunits L, M, and N is proposed to translocate one proton per turnover (blue arrows); translocation of a fourth proton might be catalyzed by the subunits in the heel of the boot-like structure (see text). The position of iron-sulfur cluster N2 is indicated by a yellow circle. The rough positions of two proposed ubiquinone molecules, Q_A and Q_B, are indicated. Q_A transmits electrons from N2 to Q_B. The latter is reduced to ubiquinol (QH₂) with uptake of two “substrate protons” (black arrow). QH₂ enters the membrane in exchange for an oxidized ubiquinone. The program VMD was used for visualization of the structure (5).

Proposed oxidoreduction function of two ubiquinone molecules in complex I. Q_A is the ubiquinone proposed to be bound near iron-sulfur cluster N2, whereas Q_B is another ubiquinone bound more weakly near the membrane domain (see Fig. 1). Q_A is insulated from protonation and its one-electron reduction is thermodynamically unfavorable (see text). Uptake of the second electron to yield the doubly negatively charged pair is again unfavorable. The doubly charged ubiquinone pair is proposed to drive conformational changes in the LMN subunit triad (see Fig. 3 A and B), which are reversed on protonation of Q_B. Reduced Q_B then exchanges with the membrane pool for oxidized Q.

Two possible scenarios for proton pumping by complex I. The corners of the cube represent eight different states distinguished by (i) the cooperative sidedness of the proton-transferring groups of subunits L, M, and N (x axis; P or N connectivity), (ii) the presence or absence of negative charge at the catalytic ubiquinone(s) (y axis; red arrows indicating electron uptake), and (iii) the protonation state of the key groups in subunits L, M, and N (z axis; uptake and release of H⁺). The four P and N states have protonic connectivity to the P and N side of the membrane, respectively. In case A, the orientation with proton access from the N side has the lowest energy in the absence of electrons or protons at the respective active sites (state 1), and the protonatable groups in the L, M, and N subunits have a pK_a well above the pH of the aqueous N phase. In case B, the lowest energy state (state 1) has the L, M, and N subunits protonically accessible to the P side, and electron transfer to the quinone(s) is required for the switch to the N orientation. Note that the states marked with the red minus sign correspond to those where electron transfer to ubiquinone yields net negative charge that drives conformational transitions in the L, M, and N subunits (i.e., state in Fig. 2). refers to the chemical protons taken up into reduced Q_B to form the quinol, QH₂, whereby the negative charge is neutralized. We stress that cycles A and B here are only two examples out of several possible ones.