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