Ribonucleotide reductases (RNRs) catalyze the conversion of all four ribonucleotides to deoxyribonucleotides and are essential for DNA synthesis in all organisms. The active form of E. coli Ia RNR is composed of two homodimers, α2 and β2, that associate and form the active α2β2 complex upon binding of substrate and effector molecules. Catalysis is initiated by long-range radical translocation over a ~32 Å proton-coupled electron transfer (PCET) pathway spanning the α/βinterface. Resolving the PCET pathway at the α/β interface between pathway residues Y356 in β and Y731 in α has been a long-standing challenge due to difficulty resolving the position of Y356. Molecular dynamics simulations were carried out on a recently solved cryogenic electron microscopy structure of an active α2β2 complex to examine the structure and fluctuations of interfacial water, as well as the hydrogen-bonding interactions and conformational motions of interfacial residues along the PCET pathway. Umbrella sampling simulations reveal that Y731 is able to sample both a flipped-out conformation, where it points toward the interface to facilitate interfacial PCET with Y356, and a stacked conformation, where it interacts with the adjacent tyrosine to enable collinear PCET. Y356 and Y731 can both exhibit hydrogen-bonding interactions with interfacial water molecules. These findings are consistent with biochemical and spectroscopic data and have implications for the interfacial PCET mechanism.

Conformational motions and water networks at the α/β interface in E. coli ribonucleotide reductase

ACS Spring Meeting 2021

The official archive and repository for all ACS Meetings & Expositions abstracts and select posters or presentations.