Team:NTHU Taiwan/Model
Simulation
We use the software, "AutoDock4" and "Amber", to confirm that both PFOA and PFOS will bind to the active site of Fac-dex (Fluoroacetate Dehelogenase).
| Software | Description |
| AutoDock4 |
This software is used for calculating where the ligand has the lowest potential energy. This method is called "Docking". The principle of docking is that we set up a 3D coordinate box and give each atom of enzyme a location and charge. In this box, we use computer to calculate where the potential energy between enzyme and ligand is the lowest. In general, the lowest-energyed location should be at enzyme active site. |
| Amber |
This software is used for studying the physical movements of atoms and molecules. This method is called "Molecular Dynamics simulation(MD)". By using the software, we can predict if the ligand is able to stay in active site for a period. In addition, more real conditions, such as temperature and ion concentration, can be involved in the simulation. The conditions of all the simulation using by this software are: at 25℃, 1 atm, in LB medium. |
Result:
AutoDock：
| View the result with WebGL. | View the result with images. |
We use the software, "AutoDock", to confirm if the compound have the lowest potential energy at the activity site, and use the software, "Chimera", to export the result.
Choose a result that you want to view:
| PFOA | PFOS | Fluoroacetic Acid |
The molecules displayed are the activity site of fac-dex(Aspartic acid(Asp) and Histidine(His)) and the targets(fluoroacetic acid, PFOA, PFOS).
Docking for fluoroacetic acid:
Get a close look to the activety site:
The distance between these molecules is 2.85A
Docking for PFOA:
Get a close look to the activety site:
The distance between these molecules is 4.64A
Docking for PFOS:
Get a close look to the activety site:
The distance between these molecules is 3.68A
The molecules displayed are the activity site of fac-dex(Aspartic acid(Asp) and Histidine(His)) and the targets(fluoroacetic acid, PFOA, PFOS).
After calculation, computer displayed the position that holds the lowest energy of three ligands, fluoroacetic acid (the origin ligand), PFOA, and PFOS. First, we compared our two interesting ligands (PFOA&PFOS) with the fluoroacetic acid and we can find out that they use similar way to get into the enzyme. Second, we compared the positions of ligands and the active sites, and we observed that both our ligands are closed to the active sites. Based on these results, we can strongly suggest that our ligand can enter the active site of enzyme.
Amber：
Please visit the page Amber Result to see the result.
