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In silico analysis of Pycnoporus cinnabarinus laccase active site with toxic industrial dyes

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Abstract

Laccases belong to multicopper oxidases, a widespread class of enzymes implicated in many oxidative functions in various industrial oxidative processes like production of fine chemicals to bioremediation of contaminated soil and water. In order to understand the mechanisms of substrate binding and interaction between substrates and Pycnoporus cinnabarinus laccase, a homology model was generated. The resulted model was further validated and used for docking studies with toxic industrial dyes- acid blue 74, reactive black 5 and reactive blue 19. Interactions of chemical mediators with the laccase was also examined. The docking analysis showed that the active site always cannot accommodate the dye molecules, due to constricted nature of the active site pocket and steric hindrance of the residues whereas mediators are relatively small and can easily be accommodated into the active site pocket, which, thereafter leads to the productive binding. The binding properties of these compounds along with identification of critical active site residues can be used for further site-directed mutagenesis experiments in order to identify their role in activity and substrate specificity, ultimately leading to improved mutants for degradation of these toxic compounds.

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Abbreviations

ABTS:

2,2′-azino-bis(3-ethylbenzthiazoline-6-sulfonic acid)

PROSA:

Protein structure analysis

NAMD:

Nanoscale molecular dynamics

PDB:

Protein data bank

RMSD:

Root mean square deviation

CASTp:

Computed atlas of surface topography of proteins

GOLD:

Genetic optimization for ligand docking

MD:

Molecular dynamics

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Acknowledgments

Research in VV’s laboratory is supported by XI OBC plan grant of University of Hyderabad. The authors wish to thank Dr. A.K. Verma for his valuable suggestions.

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Authors and Affiliations

  1. Department of Bioinformatics, Institute of In silico Biology, Tirupati, 517501, India

    Nirmal K. Prasad & Swaraj Priyaranjan Kunal

  2. Department of Biotechnology and Bioinformatics Infrastructure Facility, University of Hyderabad, Hyderabad, 500046, India

    Vaibhav Vindal

  3. Mother Teresa College of Pharmacy, Ghatkesar, Hyderabad, 501301, India

    Siva Lakshmi Narayana & Srinivas M.

  4. Department of Biotechnology & Bioinformatics, Yogi Vemana University, Kadapa, 516 003, India

    Ramakrishna V.

Authors
  1. Nirmal K. Prasad
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  2. Vaibhav Vindal
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  3. Siva Lakshmi Narayana
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  4. Ramakrishna V.
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  5. Swaraj Priyaranjan Kunal
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Correspondence to Nirmal K. Prasad.

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Prasad, N.K., Vindal, V., Narayana, S.L. et al. In silico analysis of Pycnoporus cinnabarinus laccase active site with toxic industrial dyes. J Mol Model 18, 2013–2019 (2012). https://doi.org/10.1007/s00894-011-1215-0

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  • DOI: https://doi.org/10.1007/s00894-011-1215-0

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