Team:SCUT-China/Modeling/Results

Analysis

To prove the accuracy of kinetic equations of the related domains, we stacked the related equations according to the sequence of DEBS 1. When establishing the kinetic model of domain, we got into trouble. According to the analysis of reaction mechanism and kinetic equation we show before, the initial value of the kinetic equations on second AT domain depends on the concentration of DEBS 1, that is, the result of the kinetic equations on Module 2 are not affected by the result of previous domains.

However, if we have a further simplified model in which the second AT domain is ignored, the whole kinetic model stacked will be affected by the whole DEBS 1, including Loading, Module 1, Module 2.

Therefore, we establish two kinetic models stacked, and compare them with each other. Then we compare them with the kinetic model of the whole DEBS 1.
The kinetic data we have found:

The sequence of DEBS 1 + TE is AT, ACP, KS, AT, KR, ACP, KS, AT, KR, ACP, TE.

The sequence of the first kinetic model is AT, ACP, KS, AT, KR, ACP, KS, KR, ACP, TE (the second AT domain ignored).
The model stacked :

The sequence of the second kinetic model is AT, ACP, KS, AT, KR, ACP, TE(Module 2 ignored).
The model stacked :

Then we compare Model 1 with Model 2.

Analysis: According to the graph, we can conclude that two models have relatively large differences( The difference of Subtraction Model has a range of -0.10~0.06 μM and the difference of Division Model has a range of 0.65~1.05 ). This difference may result from the concentration difference of module 1 products and the extended units. When the concentration of the extended units more than that is needed to participate in the reactions, the concentration of Module 1 products is critical. At this time, it is suitable to choose Model 2. On the contrary, it is suitable to choose Model 1.

The third model:(the kinetic model of the whole DEBS 1)

Three models

Compared with model 1 :

Compared with model 2 :

Analysis: According to the graph, we can There are relatively large differences between Model 3 and two models showed before. The initial rates of two models are relatively quicker than Model 3 and the concentration is more a half too.

In comparison of three models, we draw a conclusion that the simulation of DEBS1 catalyzed reactions is not accurate.

The possible reason are:
(1) Determination of kinetic constants is in specific environment. The constants provided from literature are not companied with the related data of environment. Therefore, we have no evidence to select the constants.
(2) In modeling work, we just simply mathematically stacked the kinetic equations. The model is too ideal. However, the model of the whole DEBS 1 is suitable to reality. So it is common of large differences.
(3) According to the related literature, reactions may occur on some linkers between two domains. We predict that we should consider the kinetic mechanism of reactions occurring on linkers. But this time, we have ignored it.

Future Work

In the future, we will go on optimizing the models. We will have further research about kinetic constants by reviewing literature or determination of experiment. In addition, we will add the factor of environment to the models and improve their rationality. We will also have further research about kinetic mechanism of linkers.

Reference:

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