Miller, M.; Loewenthal, D.; Kukura, P.; Gould, N.

Human quinone reductase 2 (QR2, NQ02) is a cytosolic flavoprotein involved in cell physiology and metabolism, and implicated in several diseases. However, the mechanisms that govern its oligomeric assembly and diverse functional outcomes remain incompletely understood. Here, we employ native mass spectrometry to directly resolve the dynamic oligomeric landscape of recombinant human QR2 expressed in Escherichia coli, preserving non-covalent interactions and enabling analysis of assembly behavior under native conditions. QR2 is predominantly observed as a dimer stabilized by multiple non-covalently bound ligands, giving rise to discrete species. Top-down native mass spectrometry reveals a single intact proteoform, excluding covalent modification or covalently bound flavins as drivers of oligomerization. Binding of flavin adenine dinucleotide (FAD) robustly stabilizes the dimer, while unexpectedly, flavin mononucleotide (FMN) also promotes dimer formation. As FMN and FAD differ structurally by the presence of an adenine dinucleotide moiety, we hypothesized that purine nucleotide binding itself may modulate QR2 assembly. Consistent with this, we identify a new concentration-dependent effect of guanosine-triphosphate (GTP) on QR2 dimerization. Functional reductase assays show that flavin-stabilized dimers exhibit the highest catalytic activity, whereas GTP-induced dimers retain reduced activity. Binding of the inhibitor YB537 abolishes activity despite promoting dimer formation. Together, these findings reveal a ligand-dependent structural plasticity in QR2 oligomerization that is decoupled from reductase function, suggesting that QR2 dimerization serves a wider regulatory role beyond simply supporting reductase catalysis.