Water Gated Transitions in Proton Pumping of Respiratory Complex I

Abstract

Respiratory Complex I or NADH:ubiquinone oxidoreductase is a redox-driven proton-pump. Powered by quinone reduction, Complex I drives the energetically uphill translocation of protons across the mitochondrial inner membrane and bacterial cytoplasmic membrane. The established electrochemical proton gradient provides the driving force for active transport and synthesis of ATP and is thus crucial for biological energy conversion. Complex I comprises a membrane domain that includes three antiporter-like subunits, involved in the proton-pumping process, and a soluble domain, responsible for reduction of quinones by electron transfer from NADH. Remarkably, site-directed mutagenesis experiments show that mutations of titratable residues in the antiporter-like subunits, ∼200 A away from site of quinone reduction, inhibit both proton pumping and quinone reduction. To explain this long-range proton-coupled electron transfer mechanism, both indirect and direct coupling models have been suggested. However, despite the recent elucidation of the complete intact structure of Complex I, the molecular principles of the coupling principles remain elusive. We present here results of large-scale classical and hybrid quantum-classical (QM/MM) molecular dynamics (MD) simulations of Complex I, embedded in biologically realistic environments. Our simulations indicate that water molecules provide important elements in the proton-pumping process. Our findings may form a basis for understanding long-range energy transduction in Complex I, and mechanistic similarities to other redox-driven proton-pumps such as cytochrome c oxidase and bacteriorhodopsin.