Modeling is a crucial activity in Synthetic Biology and Systems Biology, which can promote or even replace part of wet lab experiments. Similarly, our models this year not only promoted the progress of wet lab experiments, but also proved the feasibility of many regulatory systems in Vibrio natriegens theoretically, laying a foundation for future experimental verification. What's more, these models may provide another method solving problems of our project.

1. Modeling for the best CRISPRa construction

We systematically evaluated the fusion conformations of different activation domains (AD) and RNA polymerase proteins, hoping to screen out the most suitable AD. At the same time, we have selected the most suitable docking site and the best linker by modeling the linker of fusion protein;

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Fig 1. The docking results after Rdock, in which the green part is the 4LK1 protein C chain from PDB database, and the blue part is the V.n α protein predicted by SWISS-MODEL.

2. iFFL Strategy for Controlling Protein Expression

Incoherent feedforward loop(iFFL) is a regulatory pattern in which an activator X controls a target gene Z and also activates a repressor of that target gene, Y. We want to build an iFFL system in Vibrio natriegens, in order to achieve the goal that stabilized promoters incorporate additional elements to decouple gene expression from copy number;

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Figure 2.The schematic of the iFFL is shown. Copy number(X) influences both repressor(Y) and target gene(Z) expression. The repressor counteracts the effect on target gene expression.

3. Enzyme Kinetic of Naringenin Production

We applied enzyme kinetic model to explore the best expression combination of four enzymes and choose parts from SSR collection to optimize the production of naringenin;

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Figure 3.Naringenin synthesis pathway.


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