Protein dynamics, free radical transfer and reaction cycle of ribonucleotide reductase

The molecules of a ribonucleotide reductase enzyme of class I contains a stable tyrosyl radical located 35 Angstrom from the substrate binding site. In the crystallographic structure several amino acid side chains have been identified with potential to form an array of hydrogen bonds from the tyrosyl radical to the substrate binding area The side chains may also orient so that p and pi orbital overlaps exist along the same array. The radical is supposed to make the reduction of the substrate possible by an initial one equivalent oxidation. The model presented here shows how the oxidizing equivalent can move in both directions along the side chain array with concomitant switching of the hydrogen bonds without any charge separation occurring and how the protein dynamics is controlling the process. The conformation(s) making radical transfer possible have appreciable probability only when substrate is bound to the complete enzyme. The model explains known properties of the enzyme, in particular the stability of the radical and the enzyme reaction kinetics.