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In Silico Analysis of Class III Peroxidases: Hypothetical Structure, Ligand Binding Sites, Posttranslational Modifications, and Interaction with Substrates

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Plant Proteomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2139))

Abstract

Functional analyses of peroxidases are a major challenge. In silico analysis appears to be a powerful tool to overcome at least some of the problems that arose from (1) the numerous possible functions of peroxidases, (2) their low substrate specificity, and (3) the compensation of knockout mutants by other isoenzymes. Amino acid sequences and crystal structures of peroxidases were used for the prediction of tertiary structures, posttranslational modifications, ligand and substrate binding sites, and so on of uncharacterized peroxidases. This protocol presents tools and their applications for an in silico analysis of soluble and membrane-bound peroxidases, but it may be used for other proteins, too.

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Acknowledgments

This work was supported by a PhD student grant to K. R. from the Dr. Elisabeth Appuhn Foundation.

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Authors and Affiliations

  1. Oxidative Stress and Plant Proteomics Group, Institute for Plant Science and Microbiology, University of Hamburg, Hamburg, Germany

    Sabine Lüthje & Kalaivani Ramanathan

Authors
  1. Sabine Lüthje
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  2. Kalaivani Ramanathan
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Corresponding author

Correspondence to Sabine Lüthje .

Editor information

Editors and Affiliations

  1. Agroforestry and Plant Biochemistry, Proteomics and Systems Biology, Department of Biochemistry and Molecular Biology, University of Cordoba, Cordoba, Spain

    Jesus V. Jorrin-Novo

  2. Department of Organisms and Systems Biology, Institute of Biotechnology of Asturias, University of Oviedo, Oviedo, Asturias, Spain

    Luis Valledor

  3. Agroforestry and Plant Biochemistry, Proteomics and Systems Biology, Department of Biochemistry and Molecular Biology, University of Cordoba UCO-CeiA3, Cordoba, Cordoba, Spain

    Mari Angeles Castillejo

  4. Agroforestry and Plant Biochemistry, Proteomics and Systems Biology, Department of Biochemistry and Molecular Biology, University of Cordoba, Cordoba, Spain

    Maria-Dolores Rey

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Lüthje, S., Ramanathan, K. (2020). In Silico Analysis of Class III Peroxidases: Hypothetical Structure, Ligand Binding Sites, Posttranslational Modifications, and Interaction with Substrates. In: Jorrin-Novo, J., Valledor, L., Castillejo, M., Rey, MD. (eds) Plant Proteomics. Methods in Molecular Biology, vol 2139. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0528-8_24

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  • DOI: https://doi.org/10.1007/978-1-0716-0528-8_24

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-0527-1

  • Online ISBN: 978-1-0716-0528-8

  • eBook Packages: Springer Protocols

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