Molecular dynamics simulations and fluorescence spectroscopy suggest reduced tryptophan‐to‐heme energy transfer facilitates lignin degradation in ClassII peroxidases

Abstract

A key step in the evolution of lignin‐degrading enzymes is revealed by the observation that, unlike other heme proteins studied to date, ClassII peroxidases exhibit minimal energy transfer from tryptophan to heme residues. Bioinformatics analyses and molecular dynamics simulations (MDS) of ClassII peroxidases (manganese peroxidase, MnP and versatile peroxidase, VP) and the ClassIII enzyme horseradish peroxidase indicate that the tryptophan residue in horseradish peroxidase has the highest orientational factor and corresponding fluorescence resonance energy transfer (FRET) propensity. In contrast, tryptophan residues in manganese peroxidase and versatile peroxidase display lower FRET propensity due to unfavorable orientation factors, despite their proximity to the heme. Steady‐state fluorescence experiments support this prediction, showing strong emission in manganese peroxidase and versatile peroxidase but weak emission in horseradish peroxidase. This decreased tryptophan‐to‐heme energy transfer appears to minimize competition between direct fluorescence resonance energy transfer and long‐range electron transfer (LRET), allowing electrons to flow from bulky lignin substrates to the heme center. Such a mechanism likely provided a selective advantage during the evolution of ClassII peroxidases, facilitating efficient lignin degradation at the enzyme surface.