Skip to content
DraconiticResearch
Search Sources API
201,683 studies31 sourcesUpdated 18 min ago
Peer-reviewedCC BY 4.0The Febs Journal

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

  • Yi Ren1
  • Dale Ang2
  • Haluk Ertan3,4
  • Anne Poljak5
  • Janice R. Aldrich‐Wright6
  • Wallace J. Bridge3
  • Khawar Sohail Siddiqui3
6 affiliations
  1. 1Water Research Center, School of Civil and Environmental Engineering The University of New South Wales (UNSW) Sydney Australia
  2. 2Botanical Resources Australia Ulverstone Australia
  3. 3School of Biotechnology and Biomolecular Sciences (BABS) The University of New South Wales Sydney Australia
  4. 4Department of Molecular Biology and Genetics Istanbul University Turkey
  5. 5Bioanalytical Mass Spectrometry Facility The University of New South Wales Sydney Australia
  6. 6School of Science Western Sydney University (WSU) Penrith Australia
Read full textDOICite

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.

Related

  1. A multi-subunit autophagic capture complex facilitates degradation of ER-stalled MHC class I in pancreatic cancer
    Marine Berquez, Alexander L. Li, Matthew A. Luy +11
    Molecular CellPeer-reviewedLicence not stated10 citedCell biologyEpidemiology & public healthOpenAlex
  2. E3 ubiquitin ligase Smurf1 facilitates bacterial infection and regulates inflammatory responses via promoting MyD88 degradation in teleost
    Wen-Jing Dong, Tian-Jun Xu, Yue-Na Sun
    Zoological ResearchPeer-reviewedCC BY-NC 4.0Full textImmunologyPMC
  3. Fluorescence Correlation Spectroscopy To Study Diffusion and Reaction of Bacteriophages inside Biofilms
    R. Briandet, P. Lacroix-Gueu, M. Renault +6
    Applied and Environmental MicrobiologyPeer-reviewedLicence not stated157 citedEcologyHAL
  4. Fluorescence spectroscopy to monitor organic matter transformation during wet air oxidation of membrane-concentrated wastewater
    Emilie Gout, Fatimatou Toure Lo, Mathias Monnot +3
    HeliyonPeer-reviewedCC BY1 citedEcologyEnvironmental science & pollutionHAL
  5. Reactive molecular dynamics simulations of atenolol first steps degradation by 9CL6 ammonia monooxygenase
    Pascal Brault, Matthieu Wolf, Yana Gouzi +2
    HALPreprintCC BY 4.0Full textBioinformatics & computational biologyPhysical chemistryHALarXiv

Cite

BibTeXRIS
BibTeX
@article{ren2026molecular,
  title = {{Molecular dynamics simulations and fluorescence spectroscopy suggest reduced tryptophan‐to‐heme energy transfer facilitates lignin degradation in ClassII peroxidases}},
  author = {Yi Ren and Dale Ang and Haluk Ertan and Anne Poljak and Janice R. Aldrich‐Wright and Wallace J. Bridge and Khawar Sohail Siddiqui},
  journal = {The Febs Journal},
  year = {2026},
  month = may,
  doi = {10.1111/febs.70584},
  url = {https://doi.org/10.1111/febs.70584},
  note = {CC BY 4.0},
}
RIS
TY  - JOUR
TI  - Molecular dynamics simulations and fluorescence spectroscopy suggest reduced tryptophan‐to‐heme energy transfer facilitates lignin degradation in ClassII peroxidases
AU  - Yi Ren
AU  - Dale Ang
AU  - Haluk Ertan
AU  - Anne Poljak
AU  - Janice R. Aldrich‐Wright
AU  - Wallace J. Bridge
AU  - Khawar Sohail Siddiqui
PY  - 2026
DA  - 2026/05/15
JO  - The Febs Journal
DO  - 10.1111/febs.70584
UR  - https://doi.org/10.1111/febs.70584
AB  - 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.
SN  - 1742-464X
SN  - 1742-4658
ER  -