Key role of quinone in the mechanism of respiratory complex I

Javier Gutiérrez-Fernández,Rozbeh Baradaran,Leonid A Sazanov,Gurdeep S Minhas,Margherita Tambalo,Karol Kaszuba,David T Gallagher

doi:10.1038/s41467-020-17957-0

Abstract

Complex I is the first and the largest enzyme of respiratory chains in bacteria and mitochondria. The mechanism which couples spatially separated transfer of electrons to proton translocation in complex I is not known. Here we report five crystal structures of T. thermophilus enzyme in complex with NADH or quinone-like compounds. We also determined cryo-EM structures of major and minor native states of the complex, differing in the position of the peripheral arm. Crystal structures show that binding of quinone-like compounds (but not of NADH) leads to a related global conformational change, accompanied by local re-arrangements propagating from the quinone site to the nearest proton channel. Normal mode and molecular dynamics analyses indicate that these are likely to represent the first steps in the proton translocation mechanism. Our results suggest that quinone binding and chemistry play a key role in the coupling mechanism of complex I.

Highlights

Complex I is the first and the largest enzyme of respiratory chains in bacteria and mitochondria
Each set likely comprises half of a proton channel, with the N-terminal set linked to the bacterial cytoplasm/mitochondrial matrix and the C-terminal set linked to the periplasm/inter-membrane space (IMS)
Previously we observed that the exposure of crystals of the isolated peripheral arm (PA) of the complex to NADH led to shifts of some helices in Nqo4/6 subunits[32]

Summary

Introduction

Complex I is the first and the largest enzyme of respiratory chains in bacteria and mitochondria. 1234567890():,; Complex I (NADH:ubiquinone (UQ) oxidoreductase) is the first and the largest enzyme of the respiratory chain, catalysing the transfer of two electrons from NADH to UQ, coupled to the translocation of four protons across the bacterial or inner mitochondrial membrane[1,2,3,4,5]. T. thermophilus complex I crystal structure, comprising 16 subunits of a total molecular weight of 550 kDa, is the most complete highresolution structure[5,16] and it provides a reliable basis and a simpler model to study the catalytic mechanism as well as the effect of substrates and inhibitors on this enzyme. In this work we address this question by building and analyzing atomic structures of nine different conformational states of complex I, which were obtained by X-ray crystallography and single-particle cryo-EM. Preliminary information on the mode of binding of DQ and piericidin A was reported[16], at that time the models were not fully refined and so were not deposited in the PDB

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Results

Conclusion