Saura, P. | Search bioRxiv

bioRxiv2024

Molecular principles of redox-coupled sodium pumping of the ancient Rnf machinery

The Rnf complex is the primary respiratory enzyme of several anaerobic prokaryotes that transfers electrons from ferredoxin to NAD+ and pumps sodium ions (Na+) across a membrane, powering ATP synthesis. Rnf is widespread in primordial organisms and the evolutionary predecessor of the Na+-pumping NADH-quinone oxidoreductase (Nqr)1. By running in reverse, Rnf reduces ferredoxin with NADH as reductant at the expense of the transmembrane electrochemical ion gradient and provides low potential electrons for nitrogenases as well as CO2 reductases. Yet, the molecular principles that couple the long-range electron transfer to the Na+ translocation across the membrane remain elusive. Here we resolve key functional states along the electron transfer pathway using redox-controlled cryo-electron microscopy (cryo-EM) that, in combination with biochemical functional assays and atomistic molecular simulations, provide key insight into the redox-driven Na+ pumping mechanism. We show that the reduction of the unique membrane-embedded [2Fe2S] cluster in the vestibule between the RnfA/E subunits electrostatically attracts the sodium ions, and in turn, triggers an inward/outward transition with alternating membrane access driving the Na+ pump and the reduction of NAD+. Our study unveils an ancient mechanism for redox-driven ion pumping, and provides key understanding of the fundamental principles governing energy conversion in biological systems.

biochemistry↗

bioRxiv2022

Structural basis of mammalian Complex IV inhibition by steroids

The mitochondrial electron transport chain maintains the proton motive force that powers ATP synthesis. The energy for this process comes from oxidation of NADH and succinate, with the electrons from this oxidation passed via intermediate carriers to oxygen. Complex IV (CIV), the terminal oxidase, transfers electrons from the intermediate electron carrier cytochrome c to oxygen, contributing to the proton motive force in the process. Within CIV, protons move through the K- and D-pathways during turnover. The former is responsible for transferring two protons to the enzymes catalytic site upon reduction of the site, where they eventually combine with oxygen and electrons to form water. CIV is the main site for respiratory regulation, and although previous studies showed that steroid-binding can regulate CIV activity little is known about how this regulation occurs. Here we characterize the interaction between CIV and steroids using a combination of kinetic experiments, structure determination, and molecular simulations. We show that molecules with a sterol moiety, such as glyco-diosgenin and cholesteryl hemisuccinate, reversibly inhibit CIV. Flash photolysis experiments probing the high-speed equilibration of electrons within CIV demonstrate that binding of these molecules inhibits proton uptake through the K-pathway. Single particle cryo-EM of CIV with glyco-diosgenin reveals a previously undescribed steroid-binding site adjacent to the K-pathway, and molecular simulations suggest that the steroid binding modulates the conformational dynamics of key residues and proton transfer kinetics within this pathway. The binding pose of the sterol group sheds light on possible structural gating mechanisms in the CIV catalytic cycle. SIGNIFICANCE STATEMENTMammalian complex IV (CIV), the final complex of the mitochondrial electron transport chain, uses electrons from cytochrome c to reduce oxygen to water, driving aerobic life. Although CIV functions as the main site for respiratory regulation, there is little structural or biochemical information on how this regulation occurs. Previous studies provided evidence of CIV regulation by steroids, but the steroid binding site and regulatory mechanism remain unclear. Using single particle cryogenic electron microscopy, we discover the binding site of the steroid-derived detergent, glyco-diosgenin. Results from flash photolysis kinetic experiments with CIV in the presence of glyco-diosgenin and cholesterol hemisuccinate are combined with cryo-EM and molecular simulations to elucidate how steroid binding limits proton uptake by the complex.

biophysics↗