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A Simple Protein Synthesis Model for the PURE System Operation

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Abstract

The encapsulation of transcription–translation (TX–TL) cell-free machinery inside lipid vesicles (liposomes) is a key element in synthetic cell technology. The PURE system is a TX–TL kit composed of well-characterized parts, whose concentrations are fine tunable, which works according to a modular architecture. For these reasons, the PURE system perfectly fulfils the requirements of synthetic biology and is widely used for constructing synthetic cells. In this work, we present a simplified mathematical model to simulate the PURE system operations. Based on Michaelis–Menten kinetics and differential equations, the model describes protein synthesis dynamics by using 9 chemical species, 6 reactions and 16 kinetic parameters. The model correctly predicts the time course for messenger RNA and protein production and allows quantitative predictions. By means of this model, it is possible to foresee how the PURE system species affect the mechanism of proteins synthesis and therefore help in understanding scenarios where the concentration of the PURE system components has been modified purposely or as a result of stochastic fluctuations (for example after random encapsulation inside vesicles). The model also makes the determination of response coefficients for all species involved in the TX–TL mechanism possible and allows for scrutiny on how chemical energy is consumed by the three PURE system modules (transcription, translation and aminoacylation).

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Acknowledgments

We are grateful to Pier Luigi Luisi for his guidance in the field of synthetic cells and for useful comments on the manuscript. The modeling work has been started within the PRIN2008 (2008FY7RJ4) Synthetic Cells project and further expanded thanks to networking initiatives such EU-COST Actions CM0703 (Systems Chemistry) and CM1304 (Emergence and Evolution of Complex Chemical Systems). We thank Margherita Caputo (Univ. Bari) and Francesca D’Angelo (Roma Tre Univ.) for their involvement in the initial phase of the work.

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Authors and Affiliations

  1. Chemistry Department, University of Bari, Via Orabona 4, Bari, Italy

    Fabio Mavelli

  2. Biology Department, University of Pisa, Via Derna 1, Pisa, Italy

    Roberto Marangoni

  3. CNR - Institute of Biophysics, Via G. Moruzzi 1, Pisa, Italy

    Roberto Marangoni

  4. Science Department, Roma Tre University, Viale G. Marconi 446, Rome, Italy

    Pasquale Stano

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  1. Fabio Mavelli
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Correspondence to Pasquale Stano.

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Mavelli, F., Marangoni, R. & Stano, P. A Simple Protein Synthesis Model for the PURE System Operation. Bull Math Biol 77, 1185–1212 (2015). https://doi.org/10.1007/s11538-015-0082-8

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