Pathway Modeling

  • Pablo Carbonell
Part of the Learning Materials in Biosciences book series (LMB)


Introducing an engineered metabolic pathway into the cell not only alters its equilibrium but also modifies its dynamics. Modeling the transient behavior of an engineered pathway using kinetic models can provide valuable insights in order to identify what are the rate-limiting steps and how are they interrelated with the flux exchanges of endogenous precursors in the cell. Moreover, understanding the dynamics of the metabolic pathway is a first step on robustness analysis, providing clues about points of intervention in the pathway for transcriptional (promoters, terminators) or translational (ribosome binding site) control by means of selection of genetic parts. In this chapter, you will learn some basic models for the main genetic parts that are involved in an engineered metabolic pathway and the tools for simulating their dynamic response.


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Further Reading

  1. Useful introductions to enzyme kinetics and the Michaelis-Menten model can be found in biochemistry textbooks:Google Scholar
  2. Berg, J.M., Tymoczko, J.L., Stryer, L.: Biochemistry. Freeman (2011)Google Scholar
  3. Nelson, D.L., Cox, M.M.: Lehninger Principles of Biochemistry. Freeman (2013)Google Scholar
  4. The following textbooks provide excellent and comprehensive introductions to the field of modeling and simulating pathway dynamics:Google Scholar
  5. Marchisio, M.A.: Introduction in Synthetic Biology: About Modeling, Computation, and Circuit Design. Springer (2018)Google Scholar
  6. Klipp, E., Liebermeister, W., Wierling, C., Kowald, A., Lehrach, H., Herwig, R.: Systems Biology: A Textbook. Wiley-Blackwell (2009)Google Scholar
  7. Wall, M.E.: Quantitative Biology: From Molecular to Cellular Systems. CRC Press (2013)Google Scholar
  8. Munsky, B., Hlavacek, W.S., Tsimring, L.S.: Quantitative Biology: Theory, Computational Methods, and Models. MIT Press (2018)Google Scholar

Copyright information

© Springer Nature Switzerland AG 2019

Authors and Affiliations

  • Pablo Carbonell
    • 1
  1. 1.Manchester Institute of BiotechnologyUniversity of ManchesterManchesterUK

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