Hydrogen Tunneling and Conformational Motions in Nonadiabatic Proton-Coupled Electron Transfer between Interfacial Tyrosines in Ribonucleotide Reductase

Abstract

Ribonucleotide reductase (RNR) is essential for DNA synthesis and repair in all living organisms. The mechanism of E. coli RNR requires long-range radical transport through a proton-coupled electron transfer (PCET) pathway spanning two different protein subunits. Herein, the direct PCET reaction between the interfacial tyrosine residues, Y356 and Y731, is investigated with a vibronically nonadiabatic theory that treats the transferring proton and all electrons quantum mechanically. The input quantities to the PCET rate constant expression are computed with a combination of density functional theory and molecular dynamics simulations. The calculations highlight the importance of hydrogen tunneling in this PCET reaction. Compression of the distance between the proton donor and acceptor oxygen atoms of the interfacial tyrosine residues is essential to facilitate hydrogen tunneling by increasing the overlap between the reactant and product proton vibrational wave functions. This compression occurs by thermal conformational fluctuations of these interfacial tyrosine residues. N733 and R411 are identified as key residues that can hydrogen bond to Y731 and Y356, respectively, and thereby compete with the hydrogen-bonding interaction between Y731 and Y356 required for direct PCET. Understanding the roles of hydrogen tunneling and conformational motions in this interfacial PCET reaction, as well as identifying other residues that may impact the kinetics, is important for targeted protein engineering efforts to modulate RNR activity.