Path B - Module 34: Comparison & Superposition#

How does your engineered mutant differ from the wild-type PETase? To quantify the structural change, you cannot just look at the coordinates. You need to Align both structures in space and measure the RMSD (Root Mean Square Deviation).

import molsysmt as msm
from molsysmt import systems

# Load the original PETase (Wild-type)
wt_petase = msm.convert('pdb:6EQE', to_form='molsysmt.MolSys', selection='molecule_type=="protein"')

# Load your mutant PETase (from a previous module state or a file)
mutant_petase = msm.copy(wt_petase)
# Simulate a mutation shift (dummy translation for the example)
msm.structure.translate(mutant_petase, selection='group_index==[10:50]', vector='0.2 nm')

1. The Need for Alignment#

If you calculate the RMSD without alignment, any small rotation or translation of the protein will result in a huge error value.

# RMSD without alignment (likely very high)
raw_rmsd = msm.structure.get_rmsd(mutant_petase, reference_molecular_system=wt_petase)
print(f"Raw RMSD: {raw_rmsd}")

2. Least-RMSD Fit#

The function least_rmsd_align() moves the target system to match the reference as closely as possible, minimizing the distance between their atoms.

# Align the mutant to the wild-type and get the final RMSD
opt_rmsd = msm.structure.least_rmsd_align(mutant_petase, reference_molecular_system=wt_petase)

print(f"Optimized RMSD after alignment: {opt_rmsd}")

3. Visual Superposition#

Visualizing both structures together allows you to identify where exactly the engineering caused the largest structural shifts.

msm.view([wt_petase, mutant_petase])

🏆 Path B Challenge: The Structural Auditor#

  1. Calculate the RMSD of the Active Site residues only (160, 206, 237).

  2. Is the active site more stable than the rest of the protein?

  3. Use msm.structure.least_rmsd_fit() to permanently update the coordinates of your mutant to be aligned with the wild-type.

Structural similarity is the first proof of concept. In Module 35, we will identify the most important Modes of Motion in your enzyme using PCA.