Structure-defined amplification of spin-dependent radical-pair reactivity in mitochondrial complex I

Mitochondrial complex I generates reactive oxygen species (ROS), but whether radical pair spin dynamics shape these reactions is unknown. We combined cryo-electron microscopy-guided oxygen sampling with radical pair quantum dynamics to examine how the protein environment around flavin mononucleotide (FMN) shapes spin-dependent reaction outcomes. Sterically accessible oxygen positions clustered near FMN, and spin sensitivity concentrated in a narrow region about 3.3 angstroms away, where magnetic coupling between radicals is strong. This hotspot was robust across varying reaction rates, although its magnitude fell sharply with faster spin dephasing, implying observable effects require unusually slow dephasing. Magnetic sensitivity itself showed no sharp peak near FMN, rising instead to a plateau farther away, indicating the hotspot reflects accessibility rather than a localized maximum. Structural fluctuations produced greater yield variability within the hotspot, suggesting the FMN pocket amplifies small geometric changes into heterogeneous ROS outcomes, linking structure to spin-dependent chemistry in complex I.