Nuclear inelastic scattering at the diiron center of ribonucleotide reductase from Escherichia coli

The enzyme ribonucleotide reductase R2 catalyzes an important step in the synthesis of the building blocks of DNA, and harbors a dinuclear iron center required for activity. Not only the iron valence states but also the protonation of the iron ligands govern the enzymatic activity of the enzyme. We have performed Nuclear Inelastic Scattering (NIS) experiments on the ⁵⁷Fe reconstituted ribonucleotide reductase R2 subunit from Escherichia coli (Ec R2a). Accompanying Mössbauer spectroscopic investigations show that the partial density of vibrational states (pDOS) of the ⁵⁷Fe reconstituted Ec R2a sample contained contributions from both ⁵⁷Fe-Ec R2a protein as well as unspecifically bound ⁵⁷Fe. Subtraction of a featureless pDOS as obtained from protein-coated iron oxide particles allowed modeling of the contribution of non-specifically bound iron and thus the pDOS of ⁵⁷Fe-Ec R2a could be obtained. Quantum-mechanics/molecular-mechanics (QM/MM) calculations of the whole ⁵⁷Fe-Ec R2a protein with variations of the cofactor protonation were performed in order to assign characteristic bands to their corresponding molecular vibrational modes.