Team:BIT-China/Model

BIT-CHINA

Modeling

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The field of synthetic biology relies heavily on mathematical models that help simulate and predict the process of biological systems. Our team established two models to simulate the process of sweeteners binding to the receptor T1R2/T1R3 and the process of sweeteners signal transduction in mating pheromone pathway. Then improve our biological systems based on the simulation results.

The T1R2/T1R3 structure was built using SWISS-MODEL, then docking with the small molecule by AutoDock Vina. The signal transduction model is established by reaction kinetics equations (RKE) and MATLAB to solve the ordinary differential equations (ODEs).

We developed our models based on three main purposes:

1. Determine the binding pattern between sweeteners and T1R2/T1R3.

2. Establish the GPCR signal transduction model for signal measurement.

3. Simulate the relationship between sweetness and red fluorescence intensity of mRFP, which was employed as a reporter.

Overview of system

Our goal is to detect the sweetness of the sweetener based on retrofitting the mating pheromone response pathway in Saccharomyces Cerevisiae (CENPK2-1C).

Fig. 1 Each domain of the T1R2/T1R3 heterodimer

Initially，to make the signal input more accurate and reliable, we simulated the model of T1R2/T1R3 receptor's structure (Fig. 1), and choose some classic sweeteners docking with T1R2/T1R3.

Fig. 2 A simplified model of the α pheromone pathway with T1R2/T1R3

Next, the GPCR signal transduction model was established for signal measurement. Based on yeast MAPK signal pathway (Fig. 2), we made simple model for our biological systems. This pathway was divided into four modules: the activation of T1R2/T1R3 receptor, the activaion of G-protein cycle, the MAPK cascade, and the expression of RFP. We used ODEs to describe the changes in the concentration of protein involving in signal transmit process.

More details are shown next page.

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