Path B - Module 39: Physicochemical Properties#

To finalize your industrial design, you need scientific numbers that quantify the “pocket” of your enzyme. How much surface area is the plastic substrate losing when it enters the catalytic cleft?

In this module, you will learn to use Buried Area and other physical descriptors to prove the efficiency of your engineered PETase.

import molsysmt as msm
from molsysmt import systems

# Load our solvated complex
petase = msm.convert('pdb:6EQE', to_form='molsysmt.MolSys', selection='molecule_type=="protein"')
bhet = msm.convert('C1=CC(=CC=C1C(=O)OCCO)C(=O)OCCO', from_form='string:smiles', to_form='molsysmt.MolSys')
molsys = msm.merge([petase, bhet])

1. Global Charge and Mass#

Check if your His-tag and your mutations changed the total charge of the enzyme, which could affect its solubility in the bioreactor.

total_charge = msm.physchem.get_charge(molsys, selection='molecule_type=="protein"')
total_mass = msm.physchem.get_mass(molsys, selection='molecule_type=="protein"')

print(f"Engineered Enzyme Charge: {total_charge}")
print(f"Engineered Enzyme Mass: {total_mass}")

2. Interface Analysis: Buried Area#

A good biocatalyst should have a high buried area for its substrate, meaning the substrate is well-protected and oriented within the active site.

# Calculate the surface area that is buried upon complexation
buried = msm.physchem.get_area_buried(molsys, selection='molecule_type=="protein"', 
                                      selection_2='molecule_type=="small molecule"')

print(f"Lost surface area (Buried Area): {buried}")

# Calculate the fraction of the plastic monomer that is hidden inside the enzyme
fraction = msm.physchem.get_buried_fraction(molsys, selection='molecule_type=="small molecule"', 
                                            selection_2='molecule_type=="protein"')

print(f"Percentage of BHET inside the pocket: {fraction*100:.1f}%")

🏁 END OF PHASE 4: DATA ANALYST#

Congratulations! You have completed the biophysical characterization of your industrial enzyme. You have:

  1. Measured catalytic distances.

  2. Mapped the binding pocket neighbors.

  3. Visualized interaction matrices.

  4. Assessed stability via RG and PCA.

  5. Verified the secondary structure fold.

  6. Quantified H-bond networks and Buried Surface Area.

Now that your characterization is solid, we move to Phase 5: The Physics Lab, where we will simulate the enzyme’s behavior under industrial conditions.