Building Complex Dimers#

Harvesting, aligning, and merging monomers from disparate PDB structures into a complete complex.

Biological assemblies deposited in the Protein Data Bank often present incomplete asymmetric units, missing loops, or alternate conformations split across different chains. For instance, PDB entry 1BRS contains three Barnase-Barstar heterodimers in the asymmetric unit, but individual chains vary in resolution and sequence completeness.

In this recipe, we demonstrate how to harvest high-quality Barnase and Barstar monomers, align them onto the canonical binding orientation using sequence-aware structural alignment, merge them into a single molecular system, and repair missing heavy atoms and hydrogens.

Added in version 1.0.0.

Harvesting Monomers#

We begin by loading the multi-chain assembly from PDB entry 1BRS. We strip crystallographic waters and ions to retain purely the protein chains, then extract Barnase (chain B), the best-resolved Barstar monomer (chain F), and the reference bound Barstar partner (chain E):

import molsysmt as msm

# Load the multi-chain assembly and strip solvent/ions
molsys = msm.convert('pdb_id:1BRS')
molsys = msm.extract(molsys, selection="molecule_type=='protein'")

# Inspect the protein chains available in the asymmetric unit
print(msm.get(molsys, element='chain', name=True, n_atoms=True))

# Extract individual monomer chains
barnase = msm.extract(molsys, selection="chain_name=='B'")
barstar_ref = msm.extract(molsys, selection="chain_name=='E'")  # Reference binding pose
barstar_best = msm.extract(molsys, selection="chain_name=='F'") # High-resolution monomer

print(f"Barnase B atoms: {msm.get(barnase, n_atoms=True)}")
print(f"Barstar F atoms: {msm.get(barstar_best, n_atoms=True)}")

[['A', 'B', 'C', 'D', 'E', 'F'], [864, 878, 839, 693, 665, 699]]

Barnase B atoms: 878
Barstar F atoms: 699

Viewing Monomers#

We visualize the harvested Barnase monomer prior to superposition:

msm.view(barnase)

Structural Alignment#

To place the high-resolution Barstar monomer (barstar_best) into the functional binding pocket of Barnase, we align its C-alpha backbone onto the bound reference chain (barstar_ref) using molsysmt.structure.least_rmsd_align():

# Align Barstar F onto the bound coordinates of Barstar E
barstar_aligned = msm.structure.least_rmsd_align(
    barstar_best,
    selection='atom_name=="CA"',
    reference_molecular_system=barstar_ref
)

print("Barstar F coordinates successfully superimposed onto chain E reference pose.")

Barstar F coordinates successfully superimposed onto chain E reference pose.

Viewing Alignment#

We can inspect both monomers in 3D space to verify that Barstar is correctly oriented relative to Barnase:

msm.view([barnase, barstar_aligned])

Merging Monomers#

Now that both monomers reside in their relative spatial coordinates, we merge them into a single molecular system with molsysmt.basic.merge():

# Merge Barnase and aligned Barstar into a unified dimer
dimer = msm.merge([barnase, barstar_aligned])
msm.info(dimer)

form	n_atoms	n_groups	n_components	n_chains	n_molecules	n_entities	n_proteins	n_structures
molsysmt.MolSys	1577	199	2	2	2	2	2	1

Chemical Curation#

We complete missing heavy atoms and add hydrogen atoms at physiological pH (7.4):

# Repair missing heavy atoms and protonate at physiological pH
dimer = msm.build.add_missing_heavy_atoms(dimer)
dimer = msm.build.add_missing_hydrogens(dimer, pH=7.4)

print(f"Curated Dimer contains {msm.get(dimer, n_atoms=True)} atoms.")

Curated Dimer contains 3159 atoms.

Viewing Dimer#

We visualize the fully assembled and curated Barnase-Barstar complex:

msm.view(dimer)

Summary#

We have successfully assembled a clean, complete, and repaired Barnase-Barstar heterodimer from separate experimental chains.

# Print final summary metrics
n_atoms, n_groups, n_chains = msm.get(dimer, n_atoms=True, n_groups=True, n_chains=True)
print(f"Constructed Dimer: {n_atoms} atoms across {n_groups} residues in {n_chains} chains.")

Constructed Dimer: 3159 atoms across 199 residues in 2 chains.