Path D - Module 22: Structural Auditing (Diagnostics)#

Potassium channels are tetramers: four identical chains that form a central pore. If your starting model is missing one chain or if the selectivity filter is incomplete, your simulation will be biophysically invalid.

In this module, you will perform a high-level audit of a Membrane-Embedded Ion Channel.

import molsysmt as msm
from molsysmt import systems

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

1. Auditing the Tetramer Hierarchy#

Let’s check if the symmetry is correct. How many protein chains are in our model?

n_chains = msm.get(molsys, selection='molecule_type=="protein"', n_chains=True)
print(f"The channel has {n_chains} chains. Is it a tetramer? {n_chains == 4}")

2. Identifying Broken Loops#

Many membrane proteins have missing loops because they are highly flexible. Let’s audit the sequence gaps.

missing_res = msm.build.get_missing_residues(molsys)
print(f"Structural gaps detected: {missing_res}")

3. Presence of Lipids#

Does your crystal structure already have lipid molecules or detergents attached?

has_lipids = msm.contains(molsys, 'molecule_type=="lipid"')
print(f"Are there any lipids in the original file? {has_lipids}")

🏆 Path D Challenge: The Nano-Inspector#

  1. Load the PDB ID 1VVII (Villin, for a quick small-protein check).

  2. Use msm.build.get_non_standard_residues() to see if there are any metal ions in the pocket.

  3. Check for Missing Heavy Atoms in the catalytic triad residues (if applicable).

  4. Audit if the system has Periodic Boundary Conditions defined in the PDB header using msm.pbc.has_pbc().

Your diagnostic is finished. In Module 23, we will Repair the selectivity filter and add the necessary hydrogens for electrostatic analysis.