Modeling
Modeling allows us to better interpret and understand our experiment. We used modeling to better understand how our proteins are binding to PFAS and their binding strengths.
Docking
We used Autodock 4 to simulate the interactions between our proteins and ligands.We took enzyme models off of Protein Data Bank and PFAS models off of PubChem to use for our simulations. Docking was performed for two proteins and two forms of PFAS
- haloacid dehalogenase(1aq6) with perfluorooctanoic acid (PFOA)
- haloacid dehalogenase(1aq6) with perfluorooctanesulfonic acid (PFOS)
- fluoroacetate dehalogenase(3r40) with perfluorooctanoic acid (PFOA)
- fluoroacetate dehalogenase(3r40) with perfluorooctanesulfonic acid (PFOS)
Using Autodock 4, we find the optimal conformation to have the highest interactions between the enzyme and PFAS. From there, we took our docking results into Protein Data Bank’s Protein-Ligand Interaction Profiler to analyze the interactions between our enzymes and the PFAS.
Haloacid Dehalogenase and Perfluorooctanoic Acid
(1aq6 and PFOA optimal configuration and bonds)
Haloacid Dehalogenase and Perfluorooctanesulfonic Acid
(1aq6 and PFOS optimal configuration and bonds)
Fluoroacetate Dehalogenase and Perfluorooctanic Acid
(3r40 and PFOA optimal configuration and bonds)
Fluoroacetate Dehalogenase and Perfluorooctanesulfonic Acid
(3r40 and PFOS optimal configuration and bonds)
Table Summary
| Protein and Ligand | 1aq6 and PFOA | 1aq6 and PFOS | 3r40 and PFOA | 3r40 and PFOS |
|---|---|---|---|---|
| Binding Energy | -5.8 | -4.85 | -8.32 | -8.26 |
| Ligand Efficiency | -0.23 | -0.17 | -0.33 | -0.28 |
| Inhibition Constant | 56.45 µM | 277.97 µM | 796.96 nM | 880.27 nM |
| Intermolecular Energy | -8.18 | -7.54 | -10.71 | -10.95 |
| Internal Energy | -0.72 | -1.81 | 0.07 | -1.89 |
| Torsional Energy | 2.39 | 2.68 | 2.93 | 2.68 |
| Unbound Energy | -0.72 | -1.81 | 0.07 | -1.89 |
| Cluster RMSD | 0.0 | 0.0 | 0.0 | 0.0 |
| Reference RMSD | 50.35 | 63.02 | 37.5 | 38.04 |
These binding sites in all four combinations all consist of hydrogen bonds, halogen bonds, and salt bridges(except for haloacid dehalogenase and perfluorooctanesulfonic acid). These types of bonds all contribute to oxidative reactions, which we are trying to achieve with these enzymes to break down PFAS.
The data is not particularly promising since the binding energy is on the lower side, with pretty high inhibition constants and reference RMSD values. However, they should still be quite viable. The binding energy for haloacid dehalogenase is lower than optimal, however, because there is not much free energy, we know that there is strong binding affinity. The larger torsional energy also indicates that the PFAS will not easily change conformations, indicating that the protein-ligand complex would not change easily. The large inhibition constant also means that the enzyme activity is likely not to be disrupted, which allows for PFAS to continuously be broken down. The low cluster RMSD also indicates that it is an effective binding site. The reference RMSD is particularly high, but this is because we docked without predetermining an active site, which resulted in this high value.