Skip to main content

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

Theoretical Chemistry Accounts volume 135, Article number: 71 (2016) Cite this article

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.

This is a preview of subscription content, access via your institution.

Access options

Buy single article

Instant access to the full article PDF.

USD 39.95

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Scheme 1
Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5

References

  1. Heitner C, Dimmel D, Schmidt J (2011) Lignin and lignans: advances in chemistry. CRC Press, Boca Raton, FL

    Google Scholar 

  2. Martínez ÁT et al (2010) Biodegradation of lignocellulosics: microbial, chemical, and enzymatic aspects of the fungal attack of lignin. Int Microbiol 8:195–204

    Google Scholar 

  3. Wong DWS (2009) Structure and action mechanism of ligninolytic enzymes. Appl Biochem Biotechnol 157:174–209

    Article  CAS  Google Scholar 

  4. Kirk TK, Farrell RL (1987) Enzymatic ‘combustion’: the microbial degradation of lignin. Annu Rev Microbiol 41:465–501

    Article  CAS  Google Scholar 

  5. Eriksson K-EL, Blanchette RA, Ander P (1990) Microbial and enzymatic degradation of wood and wood components. Springer, Berlin

    Book  Google Scholar 

  6. Kersten P, Cullen D (2007) Extracellular oxidative systems of the lignin-degrading Basidiomycete Phanerochaete chrysosporium. Fungal Genet Biol 44:77–87

    Article  CAS  Google Scholar 

  7. Tien M, Kirk TK (1983) Lignin-degrading enzyme from the hymenomycete Phanerochaete chrysosporium burds. Science 221:661–663

    Article  CAS  Google Scholar 

  8. Hammel KE et al (1993) Ligninolysis by a purified lignin peroxidase. J Biol Chem 268:12274–12281

    CAS  Google Scholar 

  9. Valli K, Wariishi H, Gold MH (1990) Oxidation of monomethoxylated aromatic compounds by lignin peroxidase: role of veratryl alcohol in lignin biodegradation. Biochemistry 29:8535–8539

    Article  CAS  Google Scholar 

  10. Banci L, Ciofi-Baffoni S, Tien M (1999) Lignin and Mn peroxidase-catalyzed oxidation of phenolic lignin oligomers. Biochemistry 38:3205–3210

    Article  CAS  Google Scholar 

  11. Glenn JK, Morgan MA, Mayfield MB, Kuwahara M, Gold MH (1983) An extracellular H2O2-requiring enzyme preparation involved in lignin biodegradation by the white rot basidiomycete Phanerochaete chrysosporium. Biochem Biophys Res Commun 114:1077–1083

    Article  CAS  Google Scholar 

  12. Chance B (1949) The reaction of catalase and cyanide. J Biol Chem 179:1299–1309

    CAS  Google Scholar 

  13. Niladevi KN (2009) In: Nigam PS, Pandey A (eds) Biotechnology for agro-industrial residues utilisation. Springer, Dordrecht, pp 397–414

    Chapter  Google Scholar 

  14. Novotný Č et al (2004) Ligninolytic fungi in bioremediation: extracellular enzyme production and degradation rate. Soil Biol Biochem 36:1545–1551

    Article  Google Scholar 

  15. Durán N, Esposito E (2000) Potential applications of oxidative enzymes and phenoloxidase-like compounds in wastewater and soil treatment: a review. Appl Catal B Environ 28:83–99

    Article  Google Scholar 

  16. Regalado C, García-Almendárez BE, Duarte-Vázquez MA (2004) Biotechnological applications of peroxidases. Phytochem Rev 3:243–256

    Article  CAS  Google Scholar 

  17. Choinowski T, Blodig W, Winterhalter KH, Piontek K (1999) The crystal structure of lignin peroxidase at 1.70 Å resolution reveals a hydroxy group on the Cβ of tryptophan 171: a novel radical site formed during the redox cycle1. J Mol Biol 286:809–827

    Article  CAS  Google Scholar 

  18. Piontek K, Glumoff T, Winterhalter K (1993) Low pH crystal structure of glycosylated lignin peroxidase from Phanerochaete chrysosporium at 2.5 Å resolution. FEBS Lett 315:119–124

    Article  CAS  Google Scholar 

  19. Edwards SL, Raag R, Wariishi H, Gold MH, Poulos TL (1993) Crystal structure of lignin peroxidase. Proc Natl Acad Sci USA 90:750–754

    Article  CAS  Google Scholar 

  20. Poulos TL, Edwards SL, Wariishi H, Gold MH (1993) Crystallographic refinement of lignin peroxidase at 2 A. J Biol Chem 268:4429–4440

    CAS  Google Scholar 

  21. Schoemaker HE, Lundell TK, Hatakka AI, Piontek K (1994) The oxidation of veratryl alcohol, dimeric lignin models and lignin by lignin peroxidase: the redox cycle revisited. FEMS Microbiol Rev 13:321–331

    Article  CAS  Google Scholar 

  22. Lundquist K, Kirk TK (1978) De novo synthesis and decomposition of veratryl alcohol by a lignindegrading basidiomycete. Phytochemistry 17:1676

    Article  CAS  Google Scholar 

  23. Francesca Gerini M, Roccatano D, Baciocchi E, Nola AD (2003) Molecular dynamics simulations of lignin peroxidase in solution. Biophys J 84:3883–3893

    Article  CAS  Google Scholar 

  24. Blodig W et al (1998) Autocatalytic formation of a hydroxy group at C beta of Trp171 in lignin peroxidase. Biochemistry 37:8832–8838

    Article  CAS  Google Scholar 

  25. Doyle WA, Blodig W, Veitch NC, Piontek K, Smith AT (1998) Two substrate interaction sites in lignin peroxidase revealed by site-directed mutagenesis. Biochemistry 37:15097–15105

    Article  CAS  Google Scholar 

  26. Timofeevski SL, Nie G, Reading NS, Aust SD (1999) Addition of veratryl alcohol oxidase activity to manganese peroxidase by site-directed mutagenesis. Biochem Biophys Res Commun 256:500–504

    Article  CAS  Google Scholar 

  27. Sollewijn-Gelpke MD, Lee J, Gold MH (2002) Lignin peroxidase oxidation of veratryl alcohol: effects of the mutants H82A, Q222A, W171A, and F267L†. Biochemistry 41:3498–3506

    Article  CAS  Google Scholar 

  28. Mester T et al (2001) Oxidation of a tetrameric nonphenolic lignin model compound by lignin peroxidase. J Biol Chem 276:22985–22990

    Article  CAS  Google Scholar 

  29. Harvey PJ, Schoemaker HE, Palmer JM (1986) Veratryl alcohol as a mediator and the role of radical cations in lignin biodegradation by Phanerochaete chrysosporium. FEBS Lett 195:242–246

    Article  CAS  Google Scholar 

  30. Goodwin DC, Aust SD, Grover TA (1995) Evidence for veratryl alcohol as a redox mediator in lignin peroxidase-catalyzed oxidation. Biochemistry 34:5060–5065

    Article  CAS  Google Scholar 

  31. Candeias LP, Harvey PJ (1995) Lifetime and reactivity of the veratryl alcohol radical cation. Implications for lignin peroxidase catalysis. J Biol Chem 270:16745–16748

    Article  CAS  Google Scholar 

  32. Baciocchi E, Bietti M, Francesca Gerini M, Lanzalunga O (2002) The mediation of veratryl alcohol in oxidations promoted by lignin peroxidase: the lifetime of veratryl alcohol radical cation. Biochem Biophys Res Commun 293:832–835

    Article  CAS  Google Scholar 

  33. Khindaria A, Yamazaki I, Aust SD (1996) Stabilization of the veratryl alcohol cation radical by lignin peroxidase. Biochemistry 35:6418–6424

    Article  CAS  Google Scholar 

  34. Khindaria A, Nie G, Aust SD (1997) Detection and characterization of the lignin peroxidase compound II-veratryl alcohol cation radical complex. Biochemistry 36:14181–14185

    Article  CAS  Google Scholar 

  35. Johjima T et al (1999) Direct interaction of lignin and lignin peroxidase from Phanerochaete chrysosporium. Proc Natl Acad Sci USA 96:1989–1994

    Article  CAS  Google Scholar 

  36. Baciocchi E, Fabbri C, Lanzalunga O (2003) Lignin peroxidase-catalyzed oxidation of nonphenolic trimeric lignin model compounds: fragmentation reactions in the intermediate radical cations. J Org Chem 68:9061–9069

    Article  CAS  Google Scholar 

  37. Hammel KE, Moen MA (1991) Depolymerization of a synthetic lignin in vitro by lignin peroxidase. Enzyme Microb Technol 13:15–18

    Article  CAS  Google Scholar 

  38. Paszczynski A, Crawford RL (1991) Degradation of azo compounds by ligninase from Phanerochaete chrysosporium: involvement of veratryl alcohol. Biochem Biophys Res Commun 178:1056–1063

    Article  CAS  Google Scholar 

  39. Chung N, Aust SD (1995) Veratryl alcohol-mediated indirect oxidation of phenol by lignin peroxidase. Arch Biochem Biophys 316:733–737

    Article  CAS  Google Scholar 

  40. Huang X et al (2003) The roles of veratryl alcohol and nonionic surfactant in the oxidation of phenolic compounds by lignin peroxidase. Biochem Biophys Res Commun 311:491–494

    Article  CAS  Google Scholar 

  41. Smith AT, Doyle WA (2006) Engineered peroxidases with veratryl alcohol oxidase activity. International Patent. WO/2006-114616, 2 Nov 2006

  42. Chen M et al (2011) Understanding lignin-degrading reactions of ligninolytic enzymes: binding affinity and interactional profile. PLoS One 6:e25647

    Article  CAS  Google Scholar 

  43. Miki Y et al (2013) Formation of a tyrosine adduct involved in lignin degradation by Trametopsis cervina lignin peroxidase: a novel peroxidase activation mechanism. Biochem J 452:575–584

    Article  CAS  Google Scholar 

  44. Miki Y, Ichinose H, Wariishi H (2010) Molecular characterization of lignin peroxidase from the white-rot basidiomycete Trametes cervina: a novel fungal peroxidase. FEMS Microbiol Lett 304:39–46

    Article  CAS  Google Scholar 

  45. Miki Y et al (2011) Crystallographic, kinetic, and spectroscopic study of the first ligninolytic peroxidase presenting a catalytic tyrosine. J Biol Chem 286:15525–15534

    Article  CAS  Google Scholar 

  46. Smith AT, Doyle WA, Dorlet P, Ivancich A (2009) Spectroscopic evidence for an engineered, catalytically active Trp radical that creates the unique reactivity of lignin peroxidase. Proc Natl Acad Sci 106:16084–16089

    Article  CAS  Google Scholar 

  47. Bernini C, Pogni R, Basosi R, Sinicropi A (2012) The nature of tryptophan radicals involved in the long-range electron transfer of lignin peroxidase and lignin peroxidase-like systems: insights from quantum mechanical/molecular mechanics simulations. Proteins Struct Funct Bioinform 80:1476–1483

    Article  CAS  Google Scholar 

  48. Piontek K, Smith AT, Blodig W (2001) Lignin peroxidase structure and function. Biochem Soc Trans 29:111–116

    Article  CAS  Google Scholar 

  49. Berman HM et al (2000) The protein data bank. Nucleic Acids Res 28:235–242

    Article  CAS  Google Scholar 

  50. Maestro (2014) Version 9.7, Schrödinger, LLC, New York, NY

  51. Sastry GM, Adzhigirey M, Day T, Annabhimoju R, Sherman W (2013) Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments. J Comput Aided Mol Des 27:221–234

    Article  Google Scholar 

  52. Schrödinger Suite 2014-1 Protein Preparation Wizard

  53. Blodig W, Smith AT, Doyle WA, Piontek K (2001) Crystal structures of pristine and oxidatively processed lignin peroxidase expressed in Escherichia coli and of the W171F variant that eliminates the redox active tryptophan 171. Implications for the reaction mechanism. J Mol Biol 305:851–861

    Article  CAS  Google Scholar 

  54. Olsson MHM, Søndergaard CR, Rostkowski M, Jensen JH (2011) PROPKA3: consistent treatment of internal and surface residues in empirical pKa predictions. J Chem Theory Comput 7:525–537

    Article  CAS  Google Scholar 

  55. Glide (2014) Version 6.2, Schrödinger, LLC, New York, NY

  56. Friesner RA et al (2004) Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J Med Chem 47:1739–1749

    Article  CAS  Google Scholar 

  57. Halgren TA et al (2004) Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening. J Med Chem 47:1750–1759

    Article  CAS  Google Scholar 

  58. Banks JL et al (2005) Integrated modeling program, applied chemical theory (IMPACT). J Comput Chem 26:1752–1780

    Article  CAS  Google Scholar 

  59. Desmond Molecular Dynamics System (2013) Version 3.4, D. E. Shaw Research, New York, NY

  60. Berendsen HJC, Postma JPM, van Gunsteren WF, Hermans J (1981) In: Pullman B (ed) Intermolecular forces. Springer, Dordrecht, pp 331–342

    Chapter  Google Scholar 

  61. Nosé S (1984) A unified formulation of the constant temperature molecular dynamics methods. J Chem Phys 81:511–519

    Article  Google Scholar 

  62. Martyna GJ, Tobias DJ, Klein ML (1994) Constant pressure molecular dynamics algorithms. J Chem Phys 101:4177–4189

    Article  CAS  Google Scholar 

  63. Essmann U et al (1995) A smooth particle mesh Ewald method. J Chem Phys 103:8577–8593

    Article  CAS  Google Scholar 

  64. Tuckerman M, Berne BJ, Martyna GJ (1992) Reversible multiple time scale molecular dynamics. J Chem Phys 97:1990–2001

    Article  CAS  Google Scholar 

  65. Prime (2014) Version 3.5, Schrödinger, LLC, New York, NY

  66. Jacobson MP et al (2004) A hierarchical approach to all-atom protein loop prediction. Proteins Struct Funct Bioinform 55:351–367

    Article  CAS  Google Scholar 

  67. Li J et al (2011) The VSGB 2.0 model: a next generation energy model for high resolution protein structure modeling. Proteins Struct Funct Bioinform 79:2794–2812

    Article  CAS  Google Scholar 

  68. Mulakala C, Viswanadhan VN (2013) Could MM–GBSA be accurate enough for calculation of absolute protein/ligand binding free energies? J Mol Graph Model 46:41–51

    Article  CAS  Google Scholar 

  69. Greenidge PA, Kramer C, Mozziconacci J-C, Wolf RM (2013) MM/GBSA binding energy prediction on the PDBbind data set: successes, failures, and directions for further improvement. J Chem Inf Model 53:201–209

    Article  CAS  Google Scholar 

  70. MacroModel (2014) Version 10.3, Schrödinger, LLC, New York, NY

  71. Shao J, Tanner SW, Thompson N, Cheatham TE (2007) Clustering molecular dynamics trajectories: 1. Characterizing the performance of different clustering algorithms. J Chem Theory Comput 3:2312–2334

    Article  CAS  Google Scholar 

  72. Lama D et al (2013) Rational optimization of conformational effects induced by hydrocarbon staples in peptides and their binding interfaces. Sci Rep 3:3451. doi:10.1038/srep03451

    Google Scholar 

  73. Hayes JM et al (2011) Kinetics, in silico docking, molecular dynamics, and MM–GBSA binding studies on prototype indirubins, KT5720, and staurosporine as phosphorylase kinase ATP-binding site inhibitors: the role of water molecules examined. Proteins 79:703–719

    Article  CAS  Google Scholar 

  74. Takashima S et al (2007) Correlation between cellulose binding and activity of cellulose-binding domain mutants of Humicola grisea cellobiohydrolase 1. FEBS Lett 581:5891–5896

    Article  CAS  Google Scholar 

  75. Linder M et al (1995) Identification of functionally important amino acids in the cellulose-binding domain of Trichoderma reesei cellobiohydrolase I. Protein Sci 4:1056–1064

    Article  CAS  Google Scholar 

Download references

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. 

Author information

Authors and Affiliations

  1. Centro de Bioinformática y Simulación Molecular, Facultad de Ingeniería, Universidad de Talca, 2 Norte 685, Casilla 721, Talca, Chile

    Rodrigo Recabarren, Isabel Fuenzalida-Valdivia & Jans Alzate-Morales

Authors
  1. Rodrigo Recabarren
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Isabel Fuenzalida-Valdivia
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Jans Alzate-Morales
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Jans Alzate-Morales.

Additional information

Published as part of the special collection of articles “CHITEL 2015 - Torino - Italy”.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (DOCX 1232 kb)

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Recabarren, R., Fuenzalida-Valdivia, I. & Alzate-Morales, J. Studying the binding mechanisms of veratryl alcohol to P. chrysosporium lignin peroxidase: insights from theoretical approaches. Theor Chem Acc 135, 71 (2016). https://doi.org/10.1007/s00214-016-1828-6

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s00214-016-1828-6

Keywords

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