Hydration-Controlled Proton Transport in Respiratory Complex I

Proton pumping by respiratory Complex I is one essential element for generating the proton motive force that drives ATP synthesis in mitochondria. Although it is understood that electrons from NADH reduce ubiquinone at the peripheral arm and that four protons are transferred in the membrane domain, the mechanism by which this redox reaction initiates proton translocation remains unclear. A lateral pathway linking the quinone binding site to the membrane domain via ND1, ND3, and ND4L subunits has been proposed as the initial path of an excess proton. However, in experimental structures this region lacks a continuous water network between D66ND3 and E34ND4L, resulting in a hydration bottleneck that may regulate proton transfer. Using multiscale reactive molecular dynamics (MS-RMD) and a water wire connectivity metric, we directly simulate proton transport through this region as coupled the the hydration by water molecules. Our results reveal that proton transfer is thermodynamically feasible when transient hydration aligns with the presence of an excess proton, revealing the strong coupling between hydration and proton (PT) in this region of Complex I. These findings support a model where proton injection enhances local hydration, dynamically opening the pathway for proton transfer and regulating the onset of proton pumping in Complex I.