Proton transfer through a charged conduit in respiratory complex I - long range effects and conformational gating

Energy coupling processes in respiratory complex I - a large redox-driven proton pump in the inner mitochondrial membrane - remains one of the most enigmatic problems in modern bioenergetics. Recent high-resolution cryo EM structures of complex I revealed extensive hydration in the interior of the protein, including the buried E channel, which is an acidic charged conduit that bridges the quinone binding cavity with the extended membrane domain of the enzyme. Despite the general agreement that E channel participates in proton transfer, absence of proton density in the cryo-EM maps pose a significant challenge to develop viable models of proton pumping. By adhering to the hypothesis that E channel catalyzes transfer of proton(s) from the quinone binding cavity to the membrane-bound proton pumping site(s), we performed hybrid quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations using the ~2.4 A cryo-EM structure of mitochondrial complex I from Mus musculus. By combining classical atomistic MD simulations with the hybrid QM/MM free energy calculations, we identify several energetically favorable Grotthuss-competent proton transfer paths in the E channel region. As part of the long-range coupling in complex I, our calculations show that protonation of a single acidic amino acid residue in the distal MM surroundings can alter the dynamics of proton transfer in the E channel region. Additionally, we pinpoint the gating function of a highly conserved tyrosine residue in the E channel, which undergoes conformational flipping to establish an energetically favorable proton transfer path. In the context of the redox-coupled proton pumping mechanism of complex I, we propose a stepping-stone model of proton transfer through the E channel.