Molecular basis of H 2 O 2 /O 2 .- / . OH discrimination during electrochemical activation of DyP peroxidases: The critical role of the distal residues

• Published in: Journal of inorganic biochemistry 2025-03, Vol.264, p.112816
• Main Authors: Scocozza, Magalí F, Zitare, Ulises A, Cancian, Pablo, Castro, María A, Martins, Lígia O, Murgida, Daniel H
• Format: Article
• Language: English
• Subjects: Bacillus subtilis - enzymology; Bacterial Proteins - chemistry; Bacterial Proteins - genetics; Bacterial Proteins - metabolism; Catalytic Domain; Electrochemical Techniques - methods; Hydrogen Peroxide - chemistry; Hydrogen Peroxide - metabolism; Hydroxyl Radical - chemistry; Hydroxyl Radical - metabolism; Molecular Dynamics Simulation; Peroxidases - chemistry; Peroxidases - genetics; Peroxidases - metabolism; Pseudomonas putida - enzymology; Reactive Oxygen Species - metabolism; Superoxides - chemistry; Superoxides - metabolism
• ISSN: 1873-3344
• DOI: 10.1016/j.jinorgbio.2024.112816

Here, we show that the replacement of the distal residues Asp and/or Arg of the DyP peroxidases from Bacillus subtilis and Pseudomonas putida results in functional enzymes, albeit with spectroscopically perturbed active sites. All the enzymes can be activated either by the addition of exogenous H O or by in situ electrochemical generation of the reactive oxygen species (ROS) OH, O and H O . The latter method leads to broader and upshifted pH-activity profiles. Both WT enzymes exhibit a differential predominance of ROS involved in their electrochemical activation, which follows the order OH > O  > H O for BsDyP and O  > H O  >  OH for PpDyP. This ROS selectivity is preserved in mutants with unperturbed sites but is blurred out for distorted sites. The underlying molecular basis of the selectivity mechanisms is analysed through molecular dynamics simulations, which reveal distorted hydrogen bonding networks and higher throughput of the access tunnels in the variants exhibiting no selectivity. The electrochemical activation method provides superior performance for protein variants with a high prevalence of the alternative OH and O species. These results constitute a promising advance towards engineering DyPs for electrocatalytic applications.