Bio Development

Modeling

In the first section, the related proteins of each enzyme are searched by using SWISS-MODEL, and then searched for the organisms of each protein. The proteins are finally performed protein-ligand docking to calculate the binding affinity of each protein. For the binding affinity, the more negative number shows the better binding affinity.

The table 1 shows the result of xylanase-cellulose docking. The first one which ranked 0 is the docking result between original xylanase and cellulose, and their binding affinity shows -5.8. While the protein with PDB ID of 5hxv has the best rank in this simulation, it has the binding affinity of -10.6. This protein 5hxv is a eukaryotic protein which classified to hydrolase, its sequence identity which compared to the original protein sequence is 52.247%. From rank 79 to 98, the binding affinity is not shown due to the docking error during the docking simulation in AutoDock. Furthermore, according to the table 1, the proteins those ranked in top 3 are produced from eukaryotes. The number of eukaryotic protein in the top 10 proteins is 6.

The table 2 shows the result of glucanase-cellulose docking. The 3O5S protein which ranked 78 is the docking result between original glucanase and cellulose, and their binding affinity shows -5.7. While the protein with PDB ID of 2vy0 and 3wdy has the best rank in this simulation, they have the binding affinity of -9.7. Protein 2vy0 is a prokaryotic protein, its sequence identity which compared to the original protein sequence is 26.316%; while protein 3wdy is a eukaryotic protein, its sequence identity which compared to the original protein sequence is 18.023%; and both of them are classified to hydrolase. From rank 80 to 81, the binding affinity is not shown due to the docking error during the docking simulation in AutoDock. Furthermore, according to the table 1, the number of eukaryotic protein in the top 10 proteins is 4.

Table 3 shows the result of lipase-triacylglycerol docking. The 1LGY lipase which ranked 109 is the docking result between original lipase and triacylglycerol, and their binding affinity shows -4.4. While the lipase with PDB ID of 1AQL, 2YIJ and 4K6K has the best rank in the lipase-triacylglycerol docking with score of -6.5, and its sequence identity which compared to the original lipase amino acid sequence is about 14~24%. Among these top 3, lipase 4K6K is produced by a eukaryotic organism called Moesziomyces antarcticus which classified to yeast. Since our project is using yeast as our enzyme secreting organism, this 4K6K protein might perform better in the deinking system. Furthermore, according to the table 3, the number of eukaryotic protein in the top 10 proteins is 8.

For the purpose of confirming the effectiveness of top rank protein, we had visualized the protein-ligand docking situation by using protein 2vg9 as the test object. Figure 1 shows that the cellulose molecule is completely surrounded by xylanase 2vg9 molecule, and the whole binding situation is looked like the cellulose molecule is fit to the shape of xylanase 2vg9 molecule. This phenomenon means that the binding between this enzyme and ligand is very ideal. In figure 2, the binding situation of protein which lowly ranked is relatively worse than highly ranked protein, because we observed that the cellulose is just bind on aside of protein, the efficiency of reaction between this protein and ligand might be not in good condition.

Therefore, according to the results, we can confirm that the high rank proteins are more suitable to be used in the enzymatic deinking process, and we can also increase the prospect of success in the experiment by using the high rank proteins instead of original protein which produced from Bacillus subtilis. In the future, this computer simulation results will be used as a reference for the sequence design in the wet lab.

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