Structure constrained spin responses of an FMN superoxide radical-pair model in mitochondrial complex I

Abstract

Mitochondrial complex I produces reactive oxygen species at its flavin mononucleotide (FMN) cofactor. We combined steric sampling of oxygen positions in human complex I with radical-pair spin simulations to examine how the FMN pocket shapes reaction yield sensitivity, which provided singlet yields across FMN O2 centroid separations, magnetic fields and spin dephasing conditions. When candidate oxygen positions overlapping the FMN cofactor itself were excluded, almost no accessible positions remained within 3.3 A of the isoalloxazine centre (0.2%), and a composite score combining geometric accessibility with normalised field and dephasing responses had no near-contact maximum. In the reference structure (PDB 5XTD), the highest-scoring 10% of accessible configurations had a mean separation of 5.8 A (2.5th~97.5th percentiles, 5.6~6.0 A); in the independently determined 9TI4 structure, the corresponding mean was 7.9 A (7.7~8.0 A), reflecting differences in the modelled pocket. Within each structure, this location changed little when the dephasing model, flavin hyperfine parameters, steric radii and recombination/dephasing rates were varied. Over 2.5~20 A, the exchange only score formed a broad plateau without a localized maximum. Small prescribed fluctuations in separation produced less singlet yield variability in the high scoring configurations than elsewhere in the accessible ensemble. A near contact score maximum reported in an earlier version of this analysis arose because positions overlapping FMN had been counted as accessible. The accessibility-weighted spin-response map of the complex I flavin site is therefore set mainly by pocket geometry and should be evaluated over structural ensembles rather than a single model.