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The field of synthetic biology relies heavily on mathematical models to simulate and predict the process of biological systems. Our team established two models simulating the process of sweeteners binding on T1R2-T1R3 receptor and the process of sweeteners signal transduction in GPCR pathway. After that we designed and improved our biological systems based on the simulation results.

We developed our models for the following four main purposes:

1. Simulate different sweeteners how to bind on receptors.

2. Build a structural model to provide us with a solution for retrofitting and designing Gα.

3. The establishment of the GPCR signal transduction model gives us a better understanding of the sweetness signal in our system.

4. Simulate the relationship between sweetness signal and RFP fluorescence intensity and define the relationship between sweetness and fluorescence intensity.

Our structural model used the method of homology modeling on the SWISS MODEL server and then used AutoDock for molecular docking. The GPCR model was established by the reaction kinetics equation (RKE) of each signal transduction process. We used MATLAB to solve the ordinary differential equations (ODEs). Finally, we obtained the relationship between sweetener concentration and fluorescence intensity of our biological system.

System Overview

Our goal is to detect the sweetness of the sweeteners by retrofitting the GPCR signal transduction pathway in yeast (Cen.PK-1C).

The structure of TIR2-T1R3 (Picture from：Molecular mechanism of sweetness sensation)

In order to make the signal more accurate and reliable, we established T1R2-T1R3 receptor structure model and took aspartame, glycyrrhizic acid, stevioside and so on with its docking. And we got the binding sites of different sweeteners with T1R2-T1R3 receptor.

The design of sugar hunter

As you can see, this is a simple line model for our biological systems. We can divide it into four modules: the T1R2-T1R3 receptor module, the nucleotide exchange reaction module, the MAPK kinase module, and the RFP expression module.