Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Article
  • Published:

Rational design of functional and tunable oscillating enzymatic networks

Nature Chemistry volume 7, pages 160–165 (2015)Cite this article

Subjects

Abstract

Life is sustained by complex systems operating far from equilibrium and consisting of a multitude of enzymatic reaction networks. The operating principles of biology's regulatory networks are known, but the in vitro assembly of out-of-equilibrium enzymatic reaction networks has proved challenging, limiting the development of synthetic systems showing autonomous behaviour. Here, we present a strategy for the rational design of programmable functional reaction networks that exhibit dynamic behaviour. We demonstrate that a network built around autoactivation and delayed negative feedback of the enzyme trypsin is capable of producing sustained oscillating concentrations of active trypsin for over 65 h. Other functions, such as amplification, analog-to-digital conversion and periodic control over equilibrium systems, are obtained by linking multiple network modules in microfluidic flow reactors. The methodology developed here provides a general framework to construct dissipative, tunable and robust (bio)chemical reaction networks.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Rational design and experimental assembly of a flow-based enzymatic oscillator.
Figure 2: Characterization of the flow-based enzymatic oscillator.
Figure 3: Tunability and robustness of the enzymatic oscillator.
Figure 4: Coupling of oscillations in trypsin concentration to a variety of chemical and physical processes in systems of two reactors.

Similar content being viewed by others

References

  1. Bray, D. Protein molecules as computational elements in living cells. Nature 376, 307–312 (1995).

    Article  CAS  Google Scholar 

  2. Koshland, D. E., Goldbeter, A. & Stock, J. B. Amplification and adaptation in regulatory and sensory systems. Science 217, 220–225 (1982).

    Article  CAS  Google Scholar 

  3. Kholodenko, B. N. Cell-signalling dynamics in time and space. Nature Rev. Mol. Cell Biol. 7, 165–176 (2006).

    Article  CAS  Google Scholar 

  4. Ferrell, J. E., Tsai, T. Y. & Yang, C. Q. O. Modeling the cell cycle: why do certain circuits oscillate? Cell 144, 874–885 (2011).

    Article  CAS  Google Scholar 

  5. Yashin, V. V. & Balazs, A. C. Pattern formation and shape changes in self-oscillating polymer gels. Science 314, 798–801 (2006).

    Article  CAS  Google Scholar 

  6. Stuart, M. A. C. et al. Emerging applications of stimuli-responsive polymer materials. Nature Mater. 9, 101–113 (2011).

    Article  Google Scholar 

  7. Debnath, S., Roy, S. & Ulijn, R. V. Peptide nanofibers with dynamic instability through nonequilibrium biocatalytic assembly. J. Am. Chem. Soc. 135, 16789–16792 (2013).

    Article  CAS  Google Scholar 

  8. Elowitz, M. B. & Leibler, S. A synthetic oscillatory network of transcriptional regulators. Nature 403, 335–338 (2000).

    Article  CAS  Google Scholar 

  9. Hasty, J., McMillen, D. & Collins, J. J. Engineered gene circuits. Nature 420, 224–230 (2002).

    Article  CAS  Google Scholar 

  10. Kim, J. & Winfree, E. Synthetic in vitro transcriptional oscillators. Mol. Syst. Biol. 7, 465 (2011).

    Article  Google Scholar 

  11. Franco, E. et al. Timing molecular motion and production with a synthetic transcriptional clock. Proc. Natl Acad. Sci. USA 108, 784–793 (2011).

    Article  Google Scholar 

  12. Chirieleison, S. M., Allen, P. B., Simpson, Z. B., Ellington, A. D. & Chen, X. Pattern transformation with DNA circuits. Nature Chem. 5, 1000–1005 (2013).

    Article  CAS  Google Scholar 

  13. Fujii, T. & Rondelez, Y. Predator–prey molecular ecosystems. ACS Nano 7, 27–34 (2013).

    Article  CAS  Google Scholar 

  14. Montagne, K., Plasson, R., Sakai, Y., Fujii, T. & Rondelez, Y. Programming an in vitro DNA oscillator using a molecular networking strategy. Mol. Syst. Biol. 7, 466 (2011).

    Article  Google Scholar 

  15. Epstein, I. R. & Showalter, K. Nonlinear chemical dynamics: oscillations, patterns, and chaos. J. Phys. Chem. 100, 13132–13147 (1996).

    Article  CAS  Google Scholar 

  16. Horváth, J., Szalai, I. & De Kepper, P. An experimental design method leading to chemical Turing patterns. Science 324, 772–775 (2009).

    Article  Google Scholar 

  17. De Kepper, P., Epstein, I. R. & Kustin, K. A. Systematically designed homogeneous oscillating reaction: the arsenite-iodate-chlorite system. J. Am. Chem. Soc. 103, 2133–2134 (1981).

    Article  CAS  Google Scholar 

  18. Taylor, A. F., Tinsley, M. R., Wang, F., Huang, Z. & Showalter, K. Dynamical quorum sensing and synchronization in large populations of chemical oscillators. Science 323, 614–617 (2009).

    Article  CAS  Google Scholar 

  19. Yoshida, R., Takahashi, T., Yamaguchi, T. & Ichijo, H. Self-oscillating gel. J. Am. Chem. Soc. 118, 5134–5135 (1996).

    Article  CAS  Google Scholar 

  20. Boekhoven, J. et al. Catalytic control over supramolecular gel formation. Nature Chem. 5, 433–437 (2013).

    Article  CAS  Google Scholar 

  21. Boekhoven, J. et al. Dissipative self-assembly of a molecular gelator by using a chemical fuel. Angew. Chem. Int. Ed. 49, 4825–4828 (2010).

    Article  CAS  Google Scholar 

  22. Carnall, J. M. A. et al. Mechanosensitive self-replication driven by self-organization. Science 327, 1502–1506 (2010).

    Article  CAS  Google Scholar 

  23. He, X. et al. Synthetic homeostatic materials with chemo-mechano-chemical self-regulation. Nature 487, 214–218 (2012).

    Article  CAS  Google Scholar 

  24. Gerdts, C. J., Sharoyan, D. E. & Ismagilov, R. F. A synthetic reaction network: chemical amplification using nonequilibrium autocatalytic reactions coupled in time. J. Am. Chem. Soc. 126, 6327–6331 (2004).

    Article  CAS  Google Scholar 

  25. Warren, S. C., Guney-Altay, O. & Grzybowski, B. A. Responsive and nonequilibrium nanomaterials. J. Phys. Chem. Lett. 3, 2103–2111 (2012).

    Article  CAS  Google Scholar 

  26. Goodwin, B. C. Oscillatory behavior in enzymatic control processes. Adv. Enzyme Regul. 3, 425–438 (1965).

    Article  CAS  Google Scholar 

  27. Novak, B. & Tyson, J. J. Design principles of biochemical oscillators. Nature Rev. Mol. Cell Biol. 9, 981–991 (2008).

    Article  CAS  Google Scholar 

  28. Kurin-Csörgei, K., Epstein, I. R. & Orbán, M. Systematic design of chemical oscillators using complexation and precipitation equilibria. Nature 433, 139–142 (2005).

    Article  Google Scholar 

  29. Boissonade, J. & De Kepper, P. Transitions from bistability to limit cycle oscillations. Theoretical analysis and experimental evidence in an open chemical system. J. Phys. Chem. 84, 501–506 (1980).

    Article  CAS  Google Scholar 

  30. Aubel, D. & Fussenegger, M. Watch the clock—engineering biological systems to be on time. Curr. Opin. Genet. Dev. 20, 634–643 (2010).

    Article  CAS  Google Scholar 

  31. Abita, J-P., Delaage, M. & Lazdunsk, M. Mechanism of activation of trypsinogen—role of 4 N-terminal aspartyl residues. Eur. J. Biochem. 8, 314–324 (1969).

    Article  CAS  Google Scholar 

  32. Seely, J. H. & Benoiton, N. L. Effect of N-methylation and chain length on kinetic constants of trypsin substrates epsilon-N-methyllysine and homolysine derivatives as substrates. Can. J. Biochem. Cell B 48, 1122–1131 (1970).

    CAS  Google Scholar 

  33. Barkai, N. & Leibler, S. Robustness in simple biochemical networks. Nature 387, 913–917 (1997).

    Article  CAS  Google Scholar 

  34. Lucasius, C. B. & Kateman, G. Understanding and using genetic algorithms—Part 1. Concepts, properties and context. Chemometr. Intell. Lab. Sys. 19, 1–33 (1993).

    Article  CAS  Google Scholar 

  35. Priftis, D. & Tirrell, M. Phase behavior and complex coacervation of aqueous polypeptide solutions. Soft Matter 8, 9396–9405 (2012).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

The authors thank H. Adams for help with peptide synthesis. This work was supported by the European Research Council (ERC, advanced grant 246812 Intercom, to W.T.S.H.), the Netherlands Organization for Scientific Research (NWO, VICI grant 700.10.44, to W.T.S.H.), a Marie Curie Intra-European Fellowship (grant 300519, to S.N.S.) and funding from the Dutch Ministry of Education, Culture and Science (Gravity programme 024.001.035).

Author information

Author notes

  1. Sergey N. Semenov and Albert S. Y. Wong: These authors contributed equally to this work

Authors and Affiliations

  1. Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, Nijmegen, 6525 AJ, The Netherlands

    Sergey N. Semenov, Albert S. Y. Wong, R. Martijn van der Made, Sjoerd G. J. Postma, Joost Groen & Wilhelm T. S. Huck

  2. Institute for Complex Molecular Systems, Eindhoven University of Technology, Den Dolech 2, Eindhoven, 5600 MB, The Netherlands.

    Hendrik W. H. van Roekel & Tom F. A. de Greef

Authors
  1. Sergey N. Semenov
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Albert S. Y. Wong
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. R. Martijn van der Made
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Sjoerd G. J. Postma
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Joost Groen
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Hendrik W. H. van Roekel
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Tom F. A. de Greef
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Wilhelm T. S. Huck
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

W.T.S.H. supervised the research. S.N.S., A.S.Y.W. and W.T.S.H. planned the project and designed experiments. S.N.S. designed the oscillating network, and synthesized and optimized all compounds. S.N.S., A.S.Y.W., S.G.J.P. and J.G. performed experiments and analysed data. S.N.S., A.S.Y.W. and R.M.M. built and refined the model and wrote the required scripts for analysis. A.S.Y.W., R.M.M., H.W.H.R. and T.F.A.G. performed computational simulations. S.N.S., A.S.Y.W., S.G.J.P., T.F.A.G., and W.T.S.H. wrote the manuscript.

Corresponding author

Correspondence to Wilhelm T. S. Huck.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary information

Supplementary information (PDF 3720 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Semenov, S., Wong, A., van der Made, R. et al. Rational design of functional and tunable oscillating enzymatic networks. Nature Chem 7, 160–165 (2015). https://doi.org/10.1038/nchem.2142

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nchem.2142

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing