Proton translocation channels in respiratory complex I probed by molecular dynamics simulations

Abstract

Energy production is one of the vital functions in living cells. In oxidative phosphorylation, the nutrients in foodstuff are converted to the energy currency of cells, adenosine triphosphate (ATP). Five respiratory complexes embedded in the inner mitochondrial membrane in eukaryotes, and in the inner cell membrane of bacteria, perform oxidative phosphorylation. The first enzyme in the respiratory chain, NADH(nicotinamide adenine dinucleotide)-ubiquinone oxidoreductase (complex I) is one of the largest known protein assemblies. Complex I is L-shaped and consists of two domains: the hydrophilic domain in the matrix and the hydrophobic domain in the membrane. The enzyme transfers two electrons from NADH to quinone, utilises the released free energy in pumping four protons across the membrane and thus participates in the generation of the proton electrochemical gradient. Dysfunctions and mutations in complex I have been connected to several incurable neurodegenerative diseases, for instance Alzheimer's disease. Understanding the molecular function of complex I is the key to unravel the dysfunctions and develop cures against these lethal diseases. The mechanism of complex I is elusive, and many questions concerning the coupling mechanism and proton pumping remain unsolved. The objective of this thesis is to study the possible proton translocation pathways in the antiporter-like subunits Nqo12-14 in the membrane arm of complex I. The research question is addressed using a computational method, known as atomistic molecular dynamics (MD) simulations. The results reveal a set of conserved hydrophilic residues coordinating the water wire formation. Additionally, a strong water mediated connection through the middle plane of the membrane arm in subunits Nqo12-14 is observed, giving rise to a tentative coupling element. Water dynamics along the long horizontal helix HL unique in subunit Nqo12 is also analysed, and a stabilising mechanism of subunits Nqo12-14 is proposed.