Path B - Module 25: Solvation & Ion Engineering#

PETase enzymes in industrial reactors operate in specific saline conditions. To accurately predict the stability of your mutant enzyme, you need to simulate it in a realistic aqueous environment.

In this module, you will learn to solvate your PETase and add ions to mimic the ionic strength of an industrial buffer.

import molsysmt as msm
from molsysmt import systems

# 1. Load the PETase protein core
petase = msm.convert('pdb:6EQE', to_form='molsysmt.MolSys', selection='molecule_type=="protein"')
msm.build.add_missing_heavy_atoms(petase)

# 2. Bring back the 6xHis-Tag we designed in the previous module
his_tag = msm.build.build_peptide('HHHHHH')

1. Merging the Enzyme and the Tag#

Before putting them in water, we merge the enzyme and its tag into a single molecular system.

system = msm.merge([petase, his_tag])

print(f"Total atoms in the system: {msm.get(system, element='system', n_atoms=True)}")
msm.info(system, element='molecule')

2. High-Clearance Solvation#

For stability studies, we often need a larger water box to avoid the protein interacting with its own periodic images.

# Solvate with 1.5 nm of clearance and a cubic box
solvated_system = msm.build.solvate(system, box_shape='cubic', clearance='1.5 nm')

print(f"System solvated. Total molecules: {msm.get(solvated_system, element='system', n_molecules=True)}")

3. Industrial Ionic Strength#

Let’s set the salt concentration to 100 mM of NaCl, a typical value for enzymatic assays.

# Solvate and add salt to reach 0.1 M
final_system = msm.build.solvate(system, box_shape='cubic', clearance='1.2 nm', 
                           ionic_strength='100 mM', neutralization='neutralize')

msm.info(final_system, element='entity')

🏆 Path B Challenge: The Buffer Master#

  1. Create a pure Water Box of 5x5x5 nm using msm.build.make_water_box().

  2. Use msm.get() to calculate the Density of your water box (Mass/Volume).

  3. Add Magnesium Chloride (MgCl2) to your PETase system instead of NaCl, at a concentration of 50 mM.

  4. Verify the number of Magnesium ions added using msm.get(..., n_ions=True) or msm.info().

Your industrial biocatalyst is now in its working environment. In Module 26, we will perform some Attribute Engineering to clean up the names of our new components.