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Studying the binding mechanisms of veratryl alcohol to P. chrysosporium lignin peroxidase: insights from theoretical approaches

  • Rodrigo Recabarren
  • Isabel Fuenzalida-Valdivia
  • Jans Alzate-Morales
Regular Article
Part of the following topical collections:
  1. CHITEL 2015 - Torino - Italy

Abstract

Veratryl alcohol (VA) is the main substrate of lignin peroxidase (LiP), a key lignin-degrading enzyme. A redox mediator role, in the lignin degradation process, has been attributed to this molecule; however, many unanswered questions remain about its action mechanism. In this investigation, the basic aspects of a plausible action mechanism, this means VA binding modes to Phanerochaete chrysosporium LiP, were addressed. Docking calculations were used to obtain LiP–VA complexes near to Trp171, the active redox residue where VA is oxidized. Our results show that VA interacts at Trp171 helped by hydrogen bonding interactions with the acidic amino acids Asp264 and Glu168, as well as by hydrophobic interactions with Phe267, confirming previous experimental findings. MM–GBSA calculations, molecular dynamics simulations, and cluster analysis gave further insights into the energetic preferences of the different binding modes and the stability of LiP–VA complexes. A hydrophobic concave ditch, next to Trp171, was observed to stabilize VA at LiP surface, confirming previous suggestions based on the LiP crystal structure. A detailed analysis of the interactions in this site is provided. These findings are expected to be the basis for site-directed mutagenesis and QM/MM experiments that will prove the importance of the identified residues.

Keywords

Lignin-degrading enzymes LiP Biotransformations Molecular dynamics MM/GBSA Value-added products 

Notes

Acknowledgments

J.H.A.M. and I.F.V. acknowledge the financial support from project FONDECYT No. 1140618. R.R. acknowledges support from a doctoral fellowship CONICYT-PCHA/Folio 21130949. We thank Prof. Angel Martínez, from Centro de Investigaciones Biológicas (CIB), Madrid, Spain, for his help in the revision and valuable comments on the first draft of the manuscript. 

Supplementary material

214_2016_1828_MOESM1_ESM.docx (1.2 mb)
Supplementary material 1 (DOCX 1232 kb)

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Copyright information

© Springer-Verlag Berlin Heidelberg 2016

Authors and Affiliations

  • Rodrigo Recabarren
    • 1
  • Isabel Fuenzalida-Valdivia
    • 1
  • Jans Alzate-Morales
    • 1
  1. 1.Centro de Bioinformática y Simulación Molecular, Facultad de IngenieríaUniversidad de TalcaTalcaChile

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