NADH-Quinone Oxidoreductase Mechanisms in Membrane Proteins

NADH-quinone oxidoreductases are membrane-bound enzymes that catalyse the oxidation of NADH and concomitant reduction of quinone molecules, forming the entry point for electrons into the respiratory chain. Two major classes exist: the multi-subunit complex I (NDH-1) that couples electron transfer to proton pumping, and the single-subunit alternative type II enzymes (NDH-2) which contribute indirectly to the electrochemical gradient. Both classes rely on a flavin cofactor to mediate hydride transfer from NADH and transfer electrons to membrane-soluble quinones. Despite extensive study, the precise sequence of substrate binding, electron flow and proton translocation remains debated, with evidence supporting both ping-pong and ternary complex mechanisms. These oxidoreductases operate within a dynamic lipid environment, where membrane composition and quinone availability modulate activity. Their broad phylogenetic distribution and absence of type II in mammals render them prime targets for antimicrobial therapy and models for bioenergetic engineering.

Research from Nature Portfolio

Recent studies have delineated the catalytic versatility of type II NADH:quinone oxidoreductases, demonstrating that the NADH and quinone substrates engage independently at distinct active sites and that stochastic routing between ping-pong and ternary complex pathways is dictated by substrate concentrations and dissociation constants. Large-scale sequence and structural analyses across bacterial and eukaryotic enzymes revealed conserved amino acid motifs and predicted proton-transfer channels, identifying a key glutamate residue as a proton donor to the quinone bound pocket. High-resolution crystallography of yeast alternative dehydrogenase in complex with competitive and mixed-type inhibitors has further resolved overlapping binding modes near the flavin adenine dinucleotide cofactor, offering a structural basis for substrate positioning and inhibitor design.

NADH-Quinone Oxidoreductase Mechanisms in Membrane Proteins publication trend

The graph below shows the total number of articles in nadh-quinone oxidoreductase mechanisms in membrane proteins across all publications each year (not limited to Nature Index journals).

Technical terms

Ping-pong mechanism: A catalytic pathway in which substrates bind and products are released sequentially, and the enzyme is temporarily modified between substrate turnovers.

Ternary complex mechanism: A mechanism in which both substrates bind simultaneously to the enzyme, forming a three-component complex before electron transfer occurs.

Flavin adenine dinucleotide (FAD): A redox-active cofactor embedded in the enzyme that facilitates hydride transfer from NADH.

Quinone-binding site: A pocket within the protein structure where the quinone substrate docks to accept electrons.

Proton pathway: A chain of amino acids or structural channels that enable proton transfer to the quinone during catalysis.

References

1. The mechanism of catalysis by type-II NADH:quinone oxidoreductases. Scientific Reports (2017).
2. Structural and Functional insights into the catalytic mechanism of the Type II NADH:quinone oxidoreductase family. Scientific Reports (2017).
3. Structure of the NDH-2 – HQNO inhibited complex provides molecular insight into quinone-binding site inhibitors. Biochimica et Biophysica Acta (BBA) - Bioenergetics (2018).
4. Ubiquinone binding site of yeast NADH dehydrogenase revealed by structures binding novel competitive- and mixed-type inhibitors. Scientific Reports (2018).
5. HDQ (1-Hydroxy-2-dodecyl-4(1H)quinolone), a High Affinity Inhibitor for Mitochondrial Alternative NADH Dehydrogenase EVIDENCE FOR A PING-PONG MECHANISM*. Journal of Biological Chemistry (2004).
6. Reaction Mechanism of Single Subunit NADH-Ubiquinone Oxidoreductase (Ndi1) from Saccharomyces cerevisiae EVIDENCE FOR A TERNARY COMPLEX MECHANISM*. Journal of Biological Chemistry (2011).
7. The Profound Influence of Lipid Composition on the Catalysis of the Drug Target NADH Type II Oxidoreductase. Membranes (2021).
8. Review of NAD(P)H-dependent oxidoreductases: Properties, engineering and application. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics (2017).