Fig. 3.

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.