Kinetic model for reversible radical transfer in ribonucleotide reductase

Clorice R. Reinhardt, Daniel Konstantinovsky, Alexander V. Soudackov, Sharon Hammes-Schiffer

Research output: Contribution to journalArticlepeer-review

4 Scopus citations

Abstract

The enzyme ribonucleotide reductase (RNR), which catalyzes the reduction of ribonucleotides to deoxynucleotides, is vital for DNA synthesis, replication, and repair in all living organisms. Its mechanism requires long-range radical translocation over ∼32 Å through two protein subunits and the intervening aqueous interface. Herein, a kinetic model is designed to describe reversible radical transfer in Escherichia coli RNR. This model is based on experimentally studied photoRNR systems that allow the photochemical injection of a radical at a specific tyrosine residue, Y356, using a photosensitizer. The radical then transfers across the interface to another tyrosine residue, Y731, and continues until it reaches a cysteine residue, C439, which is primed for catalysis. This kinetic model includes radical injection, an off-pathway sink, radical transfer between pairs of residues along the pathway, and the conformational flipping motion of Y731 at the interface. Most of the input rate constants for this kinetic model are obtained from previous experimental measurements and quantum mechanical/molecular mechanical free-energy simulations. Ranges for the rate constants corresponding to radical transfer across the interface are determined by fitting to the experimentally measured Y356 radical decay times in photoRNR systems. This kinetic model illuminates the time evolution of radical transport along the tyrosine and cysteine residues following radical injection. Further analysis identifies the individual rate constants that may be tuned to alter the timescale and probability of the injected radical reaching C439. The insights gained from this kinetic model are relevant to biochemical understanding and protein-engineering efforts with potential pharmacological implications.

Original languageEnglish (US)
Article numbere2202022119
JournalProceedings of the National Academy of Sciences of the United States of America
Volume119
Issue number25
DOIs
StatePublished - Jun 21 2022
Externally publishedYes

All Science Journal Classification (ASJC) codes

  • General

Keywords

  • electron transfer
  • enzyme
  • kinetic model
  • proton-coupled electron transfer

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