Path B - Module 37: Hydrogen Bonds & Salt Bridges#

Thermostability is not just about covalent bonds like disulfide bridges. It is also about a dense network of Non-Covalent Interactions. Every additional Hydrogen Bond in the protein core adds a few degrees of melting temperature.

In this module, you will learn to identify these stabilizing wires in your PETase enzyme using MolSysMT.

import molsysmt as msm
from molsysmt import systems

# Load our engineered complex (Ensure it has hydrogens!)
petase = msm.convert('pdb:6EQE', to_form='molsysmt.MolSys', selection='molecule_type=="protein"')
msm.build.add_missing_hydrogens(petase, pH=8.0)

bhet = msm.convert('C1=CC(=CC=C1C(=O)OCCO)C(=O)OCCO', from_form='string:smiles', to_form='molsysmt.MolSys')
msm.build.add_missing_hydrogens(bhet)

molsys = msm.merge([petase, bhet])

1. Detecting Stabilizing H-Bonds#

Let’s find all Hydrogen Bonds within the PETase. A well-designed industrial enzyme should maximize these interactions in flexible loops.

# Find internal H-bonds of the protein
hbonds = msm.hbonds.get_hbonds(molsys, selection='molecule_type=="protein"')

print(f"The PETase contains {len(hbonds)} internal hydrogen bonds.")

2. Salt Bridges and Charge Stability#

Salt bridges are very strong electrostatic interactions. In industrial conditions (high temperature), they are critical to keep the enzyme from unfolding.

# Find all salt bridges in the protein
salt_bridges = msm.structure.get_salt_bridges(molsys, selection='molecule_type=="protein"')

print(f"Found {len(salt_bridges)} salt bridges providing structural rigidity.")

3. Interface Interactions#

Does the plastic substrate (BHET) form any H-bonds with the enzyme? This is the “chemical key” for degradation.

# Find H-bonds between the BHET and the protein
inter_hbonds = msm.hbonds.get_hbonds(molsys, selection='molecule_type=="small molecule"', 
                                     selection_2='molecule_type=="protein"')

print(f"The plastic substrate forms {len(inter_hbonds)} hydrogen bonds with the active site.")

🏆 Path B Challenge: The Bonding Auditor#

  1. Identify which Residue ID in the protein forms the most H-bonds with the BHET substrate.

  2. Check if the Catalytic Serine (160) is acting as a Donor or an Acceptor in these interactions.

  3. Use msm.get_label() to generate a report of all residues participating in Salt Bridges.

Interactions define affinity. In Module 38, we will learn to use Advanced Algorithms to refine this analysis for industrial production.