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Computational Simulations for Cyclizations Catalyzed by Plant Monoterpene Synthases

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Advances in Bioinformatics and Computational Biology (BSB 2020)

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Abstract

Metabolic pathways collectively define the biochemical repertory on an organism exposing the steps of its production. In silico metabolic pathways have been reconstructed using a wide range of computational methods. The reconstructed metabolic pathways can vary in some aspects, among which, in the context of this work, it is relevant to remark the data structure and granularity of biochemical details. Inferring chemical reactions using graph grammar rules is a method that exposes the initial, intermediates, and final products by modeling pathways over graphs and hypergraphs. Plant monoterpenes are volatile compounds with applications in industry, biotechnology, and medicine. They also play a vital ecological role. The last enzymatic reaction in the plant monoterpenes production chain is plentiful of possibilities due to the promiscuous nature of the terpene synthases (TPS), a case in which the application of inferring chemical reactions using graph grammar rules is suitable. In this work, we designed graph grammar rules that express cyclization reactions catalyzed by plant monoterpene synthases. As a result, it was generated a reachable chemical space of potential plant monoterpene blend, which can be computationally exploitable. In addition, these graph grammar rules were added to the 2Path, and a graphical interface was provided to aid the simulation code outlining.

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Notes

  1. 1.

    https://github.com/waldeyr/2PathTerpenes.

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Acknowledgments

This research was funded in part by CAPES through a sandwich scholarship to W.M.C.d.S. It was additionally supported in part by the Independent Research Fund Denmark, Natural Sciences, grant DFF-7014-00041. M.E.M.T.W. and M.B. has been continuously supported by productivity fellowship from CNPq.

Author information

Authors and Affiliations

  1. NEPBio - Federal Institute of Goiás, Formosa, Brazil

    Waldeyr Mendes Cordeiro da Silva & Daniela P. de Andrade

  2. University of Brasília, Brasília, DF, Brazil

    Waldeyr Mendes Cordeiro da Silva, Maria Emília M. T. Walter & Marcelo Brigido

  3. Department of Computer Science, Bioinformatics Group, Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany

    Waldeyr Mendes Cordeiro da Silva & Peter F. Stadler

  4. Department of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark

    Jakob L. Andersen & Peter F. Stadler

  5. German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany

    Peter F. Stadler

  6. Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria

    Christoph Flamm

  7. Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany

    Peter F. Stadler

  8. Santa Fe Institute, Santa Fe, USA

    Peter F. Stadler

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  1. Waldeyr Mendes Cordeiro da Silva
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Correspondence to Waldeyr Mendes Cordeiro da Silva .

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Editors and Affiliations

  1. University of São Paulo, São Paulo, Brazil

    João C. Setubal

  2. Instituto Federal de Goiás, Formosa, Goiás, Brazil

    Waldeyr Mendes Silva

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da Silva, W.M.C. et al. (2020). Computational Simulations for Cyclizations Catalyzed by Plant Monoterpene Synthases. In: Setubal, J.C., Silva, W.M. (eds) Advances in Bioinformatics and Computational Biology. BSB 2020. Lecture Notes in Computer Science(), vol 12558. Springer, Cham. https://doi.org/10.1007/978-3-030-65775-8_23

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  • DOI: https://doi.org/10.1007/978-3-030-65775-8_23

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