185-3 Structural Evolution of Iron and Nickel Coordination in Proteins: Evidence of Adaptation to Earth’s Oxygenation

Session: New Advances and Voices in Geobiology (Posters)

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The co‑evolution of Earth’s redox state and biological metabolism is encoded not only in isotopic and mineral records, but also in the structural chemistry of proteins. Metal‑binding sites, which are central to catalysis and electron transfer, serve as molecular archives of life’s adaptation to changing environmental conditions through time. Here we compare mineralogical trends from iron (Fe)‑ and nickel (Ni)‑bearing minerals with protein structural data to show how changes in Earth’s surface chemistry and mineralogy are reflected in metalloprotein coordination environments.

Using the Coordination Sphere Analysis and Comparison (CSAC) workflow, we systematically examined Fe and Ni coordination spheres from Protein Data Bank structures relevant to biogeochemistry. CSAC quantifies the chemical environment of each metal center, including nearby atoms, electronegativity, amino acid frequencies, and hydropathy, allowing direct comparison of metal‑binding sites in aerobic and anaerobic proteins. We find significant differences in the hydropathy of Fe coordination environments, with aerobic proteins displaying more hydrophilic binding sites than anaerobic counterparts. Principal component analysis of amino acid frequency vectors further reveals that cysteine and glycine are key drivers of this separation, with cysteine use strongly reduced in aerobic Fe‑binding proteins (p = 4.98 × 10⁻¹⁰).

These results parallel mineralogical patterns: Fe‑bearing minerals show an expanding range of electronegativity associations through time as Earth’s surface became progressively more oxidized. Proteins in aerobic settings appear to have retained Fe while restructuring its binding environment to mitigate oxidative stress. By reducing reliance on cysteine thiolates, which are highly susceptible to oxidation, proteins can protect Fe‑binding sites and preserve catalytic function. In contrast, Ni mineralogy is more limited, with fewer species and narrower electronegativity associations through time. Ni protein folds likewise show lower hydropathy variation than Fe folds, reinforcing Ni’s role as a specialist cofactor in early anaerobic metabolisms such as methanogenesis and carbon fixation. Fe, by comparison, has been retained as a versatile cofactor, spanning both anaerobic and aerobic metabolisms.

Metal‑binding coordination spheres, like isotopes and minerals, preserve a record of ancient environmental change. By bridging protein bioinformatics and mineral chemistry, this work provides new tools for probing how life adapted its molecular machinery in concert with Earth’s evolving surface conditions.

Geological Society of America Abstracts with Programs. Vol. 57, No. 6, 2025

doi: 10.1130/abs/2025AM-8799

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