Difference between revisions of "Team:Nanjing-China/Modeling"

Our project uses Bacillus subtilis as the bioreactor to deal with heavy metals: Au, Pb and U. B. subtilis is not the bacteria used the most widely in iGEM competition, so we want to acquire thorough understanding of it through modeling part.

In the modeling part, we have built three models: Growth, Transcription-Translation and Bioabsorption. In the first part, we worked out growth curves of B. subtilis‘s vegetative state and spore state, using Logistic model. In the second part, we compared the efficiency of three different promoters we use: Pveg, Ptas and Pcot and try to find which one has the highest efficiency. In the third part, we used GolB-Au as an example to shed light on the optimal concentration of metal ions and the time for binding proteins’ saturation.

Through modeling, we know B. subtilis better and find optimal experimental conditions. Besides, we can also find out whether our wet lab results conform to the modeling results.

Here comes our modeling.

Based on a set of differential equations describing the kinetics of absorptive protein absorbing specific ions, the model is designed to predict the efficiency and affinity of the binding process. Given a certain initial concentration of absorptive protein, the model calculates the time necessary for a certain proportion of absorptive protein to be occupied, simulating the efficiency of the heavy ion-capturing process.

Assuming that three types of absorptive protein are not interfered by each other and possess similar characteristics, we can simulate the gold ion-capturing process to make a basic prediction of the other two.

Since the initial concentration of gold ion injected into the system is typically very large compared to the initial concentration of GolB, we consider that the concentration of gold ion is unchanged.

In the solution,

In this equation,

    [Au-GolB](0)=0；

    [Au-GolB](∞)=[GolB] (0), assume that GolB binding sites can be fully saturated given enough time, as ka1[Au]>> .

With the parameters determined from the experiments, the model is then instantiated and used to predict the time period necessary for the binding sites to be saturated.

As is shown on the graph, with higher concentration of gold ion, the ion-capturing process tends to be quicker. Whereas, the final balance is supposed to be similar. Besides, around 3 hours is enough for GolB protein binding sites to be saturated. This result helps us find out the optimal concentration of Au and the time for GolB’s saturation during experiments.

The modeling results of Pb(II) and UO22+ capturing process of absorptive proteins are showed below. Similar to gold ion capturing, the main trend of the whole process is that higher ion concentration leads to a faster absorption process. Since the different types of protein possess different characteristics and interactions with corresponding ions, the time needed to build a balance varies. (PbR: about 1h; UBP: about 35min) Interestingly, with a lower concentration of UO22+, the final complex concentration seems higher, which we assume results from the decrease of competitive inhibition.

https://2014.igem.org/Team:INSA-Lyon/Modeling

http://www.mathworks.nl/products/matlab

http://www.ncbi.nlm.nih.gov/Structure/mmdb

1. Wei Wei, Tianze Zhu, et al, Engineering a gold-specific regulon for cell-based visual detection andrecovery of gold, Chem. Sci., 2012, 3, 1780–1784

2. Lu Zhou, Mike Bosscher, et al, A protein engineered to bind uranyl selectively and with femtomolar affinity, Nature Chem., 2014,3:236-241

3. Wei Wei, Xiangzhi Liu, et al, Simple Whole-Cell Biodetection and Bioremediation of Heavy Metals Based on an Engineered Lead-Specific Operon, Environmental Science & Technology,2014,6,3363-3371