Team:OUC-China

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The last homologous protein

Analyzing the results of the quorum sensing experiment, it is found that when changing the concentration of IP, the GFP expression downstream of the SSRE promoter increased significantly(fig1), which means that the quorum sensing system present in Arabidopsis thaliana is not only present in yeast, but also in Aureobasidium melanogenum P16

Fig1. Adding different concentrations of IP, the SSRE promoter expression increase so that the quorum sensing system exits in Aureobasidium melanogenum P16.

Therefore, Aureobasidium melanogenum P16 contain a protein similar to the AtLPT4 protein definitely. Firstly, sequence align is utilized to find the similar sequence in Aureobasidium melanogenum P16 genome(table1)

It is shown that there are three sequences that are similar to AtPT4 protein. After that the 3D structure of these proteins are predicted by (PHYRE2) and structure align with AtLPT4 protein are done by pymol and RMSD values are calculated(table2).

The RMSD value between each two protein is calculated using pymol and the results are presented in the table2.

It can be seen that these proteins have a low degree of structural similarity with AtLPT4 in Arabidopsis and also have a low degree of overlap with each other(table2).

Fig2. A heatmap to present the RMSD of every two proteins.

To further verify that these three proteins have the function of the AtLPT4 protein, utilize autodock to analyze the interaction between these proteins and ATP(fig3 A-D).
Every protein can interact with ATP and the binding energy of them are almost similar. This is strong evidence that they are isoenzymes.

(Fig3A)The docking result of AtIPT4 protein

(Fig3B)The docking result of P16-1 protein

(Fig3C)The docking result of P16-2 protein

(Fig3D)The docking result of P16-3 protein

In order to further explore the relationship between these three proteins and ATP, the binding energy is calculated by molecular dynamics simulation (Table 3). Due to some unknown reasons, the results of P16-3 protein did not run out.

However, according to fig3, it is presented that the more violent fluctuation, the higher binding energy. Therefore it can be speculated that the binding energy of P16-3 is the highest one among the three proteins.

Prospect

Because of the limited time, it is not possible to proceed to the verification of the wet experiment. But after competition, our team hopes to continue to study the quorum sensing part, explore the relationship between these proteins, and optimize the circuit as much as possible