Free radical transfer, fluctuating structure and reaction cycle of ribonucleotide reductase

Abstract

Our understanding of the nature and functional importance of protein dynamics is based on experimental and theoretical work on rather ‘simple’ systems. Here, the principles of the fluctuating structure of a protein is applied to the complex enzyme ribonucleotide reductase (RNR). This enzyme contains a stable tyrosyl radical, which is a strong oxidant. The radical initiates the enzymatic reaction by oxidizing the ribose moeity of the substrate, bound at a distance of ca. 35 Å away from the tyrosine harboring the radical. The transfer of the oxidation equivalent, the electron hole, requires a chain of overlapping electronic orbitals along the route, and is made energetically possible by the simultaneous switching of a series of H-bonds, making the transfer charge neutral. Only a fraction of the enormous number of accessible protein substates support this transfer. The probability of an enzyme molecule to obtain such a substate by thermal fluctuations is negligible, except for the case of a complete enzyme with bound substrate. When the radical has been transferred to the ribose, its 2′-OH is immediately reduced to 2′-H by the enzyme, and the electron hole goes back via the chains of orbital overlaps and H-bonds. This model is capable to explain all known kinetic properties of the wild type enzyme and its mutated forms. The analogy between this model of how the fluctuating protein structure controls and makes the radical transfer possible in RNR and recent ideas about the mechanism of the anomalously fast proton conduction in liquid water is considered.