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

Mitochondrial complex I is a major source of reactive oxygen species (ROS), but whether radical pair spin dynamics contribute to the regulation of ROS-associated reactions remains unknown. Here we integrate cryo-electron microscopy structure-guided oxygen sampling with radical pair quantum dynamics to determine how the molecular architecture surrounding flavin mononucleotide (FMN) shapes modelled spin-dependent radical-pair reaction yields. Monte Carlo sampling revealed a broad ensemble of sterically accessible oxygen configurations, whereas spin sensitivity was concentrated within a restricted near-contact region centred at approximately 3.3-3.4 [A] from the FMN reference centre. This localisation was defined by the integration of structural accessibility with magnetic field and spin dephasing sensitivities and spatially overlapped with an exchange-hyperfine crossover regime favourable for singlet-triplet interconversion. Simulations of structural fluctuations further show that equivalent perturbations generated greater variability in singlet reaction yields within a hotspot than outside it, identifying a localized regime of enhanced structural responsiveness. These results suggest that the FMN binding pocket may act as a structure-dependent amplification layer that converts small changes in radical pair geometry into heterogeneous spin-dependent reaction outcomes. Our findings establish a framework linking experimentally resolved protein architecture to radical pair spin dynamics and identify structural constraints that may shape spin-dependent ROS chemistry in mitochondrial complex I.