{% extends "layout.html" %} {% block title %}Model{% endblock %} {% block lead %}Explain your model's assumptions, data, parameters, and results in a way that anyone could understand.{% endblock %} {% block page_content %}
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.
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
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
Haloacid Dehalogenase and Perfluorooctanesulfonic Acid
Fluoroacetate Dehalogenase and Perfluorooctanic Acid
Fluoroacetate Dehalogenase and Perfluorooctanesulfonic Acid
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 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.
Use modeling to gain insight into how your project works or should be implemented. Explain your model's assumptions, data, parameters, and results in a way that anyone could understand.
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Models and computer simulations provide a great way to describe the functioning and operation of BioBrick Parts and Devices. Synthetic biology is an engineering discipline and part of engineering is simulation and modeling to determine system behavior before building your design. Designing and simulating can be iterated many times in a computer before moving to the lab. This award is for teams who build a model of their system and use it to inform system design or simulate expected behavior before or in conjunction with experiments in the wetlab.
To compete for the Best Model prize, please describe your work on this page and also fill out the description on the judging form.
Please see the 2022 Awards Page for more information.
Mathematical models and computer simulations provide a great way to describe the function and operation of Parts and Devices. Synthetic Biology is an engineering discipline, and part of engineering is simulation and modeling to determine the behavior of your design before you build it. Designing and simulating can be iterated many times in a computer before moving to the lab.
Please note you can compete for both the Gold Medal criterion #3 and the Best Model prize with this page.