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Synthetic biology is an interdisciplinary science that involves using principles from disciplines such as engineering, molecular biology, cell biology, and systems biology. It involves remodeling existing organisms from nature or constructing completely new synthetic organisms for applications such as protein or enzyme production, bioremediation, value-added macromolecule production, and the addition of desirable traits to crops, to name a few.
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A resource dependent protein synthesis model for evaluating synthetic circuits.

Wolfgang Halter1, Jan Maximilian Montenbruck1, Zoltan A Tuza1

  • 1Institute for Systems Theory and Automatic Control, University of Stuttgart, Pfaffenwaldring 9, Stuttgart, Germany.

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|March 14, 2017
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Summary

We developed a novel protein synthesis model to simulate synthetic gene networks. This model analyzes resource limitations and dynamic mechanisms for improved synthetic biology designs.

Keywords:
Genetic regulatory networksHost-circuit interactionsNormally hyperbolic manifoldsResource dependenceSynthetic biology

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Area of Science:

  • Systems Biology
  • Synthetic Biology
  • Computational Biology

Background:

  • Designing synthetic gene networks requires accurate models of protein synthesis.
  • Existing models may not fully capture the impact of limited cellular resources.

Purpose of the Study:

  • To present a novel protein synthesis model for in silico design of synthetic gene networks.
  • To analyze the dynamic mechanisms of protein synthesis under resource constraints.

Main Methods:

  • The model is an extension of the Ribosome Flow Model.
  • It describes the movement of RNA polymerase and ribosomes on DNA and mRNA templates.
  • Convergence properties were analyzed using geometric considerations.

Main Results:

  • The model provides insights into the dynamic mechanisms of protein synthesis.
  • It successfully models resource limitations and molecular traffic.
  • The model can evaluate synthetic gene circuit performance under varying loads.

Conclusions:

  • The novel protein synthesis model enhances the in silico design of synthetic gene networks.
  • It offers a valuable tool for understanding and predicting synthetic gene circuit behavior.
  • This approach aids in optimizing synthetic biology applications by accounting for resource limitations.