Path B - Module 36: Secondary Structure & Folds#

PETase belongs to the \(\alpha/\beta\) hydrolase family. It has a specific architecture of beta-sheets surrounded by alpha-helices. If your engineering (mutations) causes a loss of these structural elements, the enzyme will lose its activity.

In this module, you will learn to monitor the secondary structure profile of your industrial enzyme.

import molsysmt as msm
from molsysmt import systems

# Load your engineered PETase
petase = msm.convert('pdb:6EQE', to_form='molsysmt.MolSys', selection='molecule_type=="protein"')

1. Assigning the Hidrolase Fold#

Let’s identify the secondary structure of every residue in the enzyme using the integrated DSSP engine.

# Get the secondary structure assignments
ss = msm.get(petase, element='group', secondary_structure=True)

print(f"First 20 residues secondary structure:\n{ss[:20]}")

2. Monitoring Thermodynamic Stability#

Thermal stability is often linked to the preservation of the beta-sheet core. Let’s calculate the fraction of beta-sheets in our enzyme.

import numpy as np

unique, counts = np.unique(ss, return_counts=True)
stats = dict(zip(unique, counts))

total = sum(counts)
sheet_fraction = stats.get('Sheet', 0) / total

print(f"Beta-Sheet Content: {sheet_fraction*100:.1f}%")

🏆 Path B Challenge: The Structural Auditor#

  1. Calculate the secondary structure of your His-tag from Module 24. Does it have a defined structure or is it ‘Coil’?

  2. Compare the total number of Alpha-helices between the wild-type and your mutated PETase.

  3. Identify the Residue IDs that belong to the longest alpha-helix of the enzyme.

Folding is the prerequisite for function. In Module 37, we will look at the specific Hydrogen Bonds that stabilize these helices and sheets.