Path D - Module 23: Structural Repair & Mutagenesis#

Membrane proteins are notoriously hard to model. Once you have audited your potassium channel, you need to fix its gaps and add hydrogens. This is especially important for the Selectivity Filter, where the electrostatic interaction with K+ ions is defined by the positions of the backbone Oxygen atoms.

In this module, you will learn to repair a membrane channel and perform a Mutation to simulate a gain-of-function variant.

import molsysmt as msm
from molsysmt import systems

# Load a channel system
molsys = msm.convert('pdb:1K4C', to_form='molsysmt.MolSys')

1. Reconstructing Gaps#

We use add_missing_heavy_atoms() to ensure that the selectivity filter residues (TVGYG) are complete.

# Repair the protein topology
msm.build.add_missing_heavy_atoms(molsys)

# Add hydrogens at pH 7.0
msm.build.add_missing_hydrogens(molsys, pH=7.0)

print(f"Channel repaired. Total atoms: {msm.get(molsys, element='system', n_atoms=True)}")

2. Mutating the Pore#

Let’s simulate a mutation in the pore that might change the selectivity. We will mutate a Valine in the filter to an Isoleucine.

# Identify Valine residues in the selectivity filter (e.g., ID 76)
val_indices = msm.select(molsys, selection='group_id==76', element='group')

# Mutate all four chains at once!
for idx in val_indices:
    msm.build.mutate(molsys, selection='group_index=='+str(idx), new_group_name='ILE')

print(f"Successfully performed {len(val_indices)} mutations to Isoleucine.")

🏆 Path D Challenge: The Nano-Surgeon#

  1. Find all Glycine residues in the protein.

  2. Mutate one of them in the hinge region (residue 99) to a Proline (PRO) to simulate a conformational lock.

  3. Use msm.info(element='group', selection='group_id==99') to verify the change.

  4. Check for Overlapping Molecules to ensure your new Proline doesn’t crash with the lipid environment.

The channel is now clean and modified! In Module 24, we will learn how to synthesize a custom lipid anchor or peptide ligand for our membrane study.