Electronic and Structural Heterogeneity in the Diiron Center of Sulerythrin: Insights From Hybrid QM/MM Calculations

Sulerythrins (SulE) are ferritin-like proteins from obligate aerobes such as Sulfolobus tokodaii, forming a domain-swapped dimer with a four-helix-bundle scaffold and a heterobimetallic Fe-Zn center. The diFe-SulE variant resembles diiron carboxylate proteins and contains two bimetallic active sites coordinated by histidines, glutamates, and bridging oxo ligands. High-resolution crystallography revealed slight differences in Fe-Fe distances and mixed-valence states, but the precise chemical nature of the oxo species remains unclear. To clarify the electronic and structural properties of diFe-SulE, we performed hybrid quantum mechanical/molecular mechanics (QM/MM) calculations on models varying in protonation, dioxo ligands, and iron redox states of the active site. Our results reveal at least three electronic states for diFe-SulE: (i) a diferrous center with an end-on di-μ-hydroperoxo ligand; (ii) a diferric center with hydroxo ligands interacting with protonated Glu95; and (iii) a diferrous center bridged by a di-μ-peroxo ligand, also interacting with protonated Glu95. These states are consistent with the structural heterogeneity observed experimentally. Overall, the hybrid QM/MM approach refines the crystallographic models and offers subatomic-level insight into the electronic structure and reactivity of the SulE diiron center, deepening our understanding of nonheme diiron enzymes.