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Data Processing to Probe the Cellular Hydrogen Peroxide Landscape

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Computational Methods for Estimating the Kinetic Parameters of Biological Systems

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2385))

Abstract

Hydrogen peroxide (H2O2) regulates signaling pathways by modulating the activity of redox-sensitive proteins denominated redox switches. The magnitude of the transient variations in localized H2O2 pools during signaling events and how these variations impact redox switches present in the cell remain elusive. A canonical model with two chemical reactions comprising the oxidation/reduction cycle of a redox switch is described. The model is dimensionless with respect to the redox switch concentration. Thus, the time-series data required to apply the equations deduced is the percentage of oxidation of a redox switch, avoiding the application of absolute concentrations that are often difficult to measure experimentally. Here, we describe detailed protocols for the processing of experimental data with the canonical model to probe the absolute concentrations of H2O2 found in the vicinity of redox switches and probes, as well as the kinetic parameters that describe the reduction and oxidation of redox switches. The protocols are an analytical tool that helps to depict the cellular hydrogen peroxide signaling landscape, giving new insights on H2O2 signaling mechanisms, and hold the potential to be a framework for a future redox kinetomics analytical platform.

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Acknowledgments

This research was financed by Fundação para a Ciência e a Tecnologia (FCT) through projects UIDB/00100/2020 (CQE) and UIDB/04138/2020 (IMED).

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Authors and Affiliations

  1. Departamento de Química e Bioquímica and Centro de Química Estrutural, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal

    Fernando Antunes

  2. Departamento de Microbiologia e Imunologia and iMED.ULisboa, Faculdade de Farmácia, Universidade de Lisboa, Lisbon, Portugal

    Paula Brito

Authors
  1. Fernando Antunes
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  2. Paula Brito
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Correspondence to Fernando Antunes .

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Editors and Affiliations

  1. Insilico Medicine Hong Kong Ltd, Pak Shek Kok, Hong Kong

    Quentin Vanhaelen

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Antunes, F., Brito, P. (2022). Data Processing to Probe the Cellular Hydrogen Peroxide Landscape. In: Vanhaelen, Q. (eds) Computational Methods for Estimating the Kinetic Parameters of Biological Systems. Methods in Molecular Biology, vol 2385. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1767-0_8

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  • DOI: https://doi.org/10.1007/978-1-0716-1767-0_8

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1766-3

  • Online ISBN: 978-1-0716-1767-0

  • eBook Packages: Springer Protocols

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