In Silico Mutagenesis#

Introducing point mutations in memory, rebuilding side chains, and evaluating structural shifts.

Rational protein engineering frequently requires evaluating the impact of single or multiple amino acid substitutions. In silico mutagenesis requires updating topological chemical identity, generating realistic side-chain rotamers, and relaxing potential steric clashes with neighboring residues.

In this recipe, we perform an in-memory mutation on T4 Lysozyme using molsysmt.build.mutate(), rebuild missing side-chain atoms, and compare the mutant with the wild type.

Added in version 1.0.0.

Loading Wild Type#

We load the high-resolution T4 Lysozyme structure and inspect the target residue (Lysine 19, group index 18):

import molsysmt as msm

# Load wild-type T4 Lysozyme
molsys_wt = msm.convert(msm.systems['T4 lysozyme L99A']['181l.h5msm'], to_form='molsysmt.MolSys')
molsys_wt = msm.extract(molsys_wt, selection='molecule_type=="protein"')

# Inspect target residue before mutation
names, ids = msm.get(molsys_wt, element='group', selection=18, name=True, id=True)
print(f"Target residue: {names[0]} {ids[0]}")

Target residue: LYS 19

Point Mutation#

We mutate Lysine 19 to an Alanine (ALA) using molsysmt.build.mutate(). MolSysMT updates residue chemistry, atom topology, and removes orphaned side-chain atoms:

# Mutate Lys19 to Ala
molsys_mut = msm.build.mutate(molsys_wt, mutations={18: 'ALA'}, keys='group_index')

# Inspect mutated residue
mut_names, mut_ids = msm.get(molsys_mut, element='group', selection=18, name=True, id=True)
print(f"Mutated residue: {mut_names[0]} {mut_ids[0]}")
print(f"Wild-type atoms: {msm.get(molsys_wt, n_atoms=True)}, Mutant atoms: {msm.get(molsys_mut, n_atoms=True)}")

Mutated residue: ALA 19
Wild-type atoms: 1289, Mutant atoms: 1285

Side Chain Reconstruction#

We rebuild missing heavy atoms and restore hydrogen protonation states at physiological pH:

# Complete missing heavy atoms
molsys_mut = msm.build.add_missing_heavy_atoms(molsys_mut)

# Protonate at pH 7.4
molsys_mut = msm.build.add_missing_hydrogens(molsys_mut, pH=7.4)

msm.info(molsys_mut)
form n_atoms n_groups n_components n_chains n_molecules n_entities n_proteins n_structures
molsysmt.MolSys 2590 162 1 1 1 1 1 1

Structural Superposition#

We superimpose the mutant structure onto the wild type to evaluate backbone alignment and confirm structural fidelity:

# Align mutant onto wild-type C-alpha backbone
molsys_mut_aligned = msm.structure.least_rmsd_fit(
    molsys_mut,
    selection_fit='atom_name=="CA"',
    reference_molecular_system=molsys_wt,
    reference_selection_fit='atom_name=="CA"'
)

# Compute residual RMSD
rmsd_val = msm.structure.get_rmsd(
    molsys_mut_aligned,
    selection='atom_name=="CA"',
    reference_molecular_system=molsys_wt,
    reference_selection='atom_name=="CA"'
)
print(f"Backbone C-alpha RMSD between WT and L19A mutant: {rmsd_val[0]:.4f} nm")

Backbone C-alpha RMSD between WT and L19A mutant: 0.0000 nanometer nm

Viewing Mutant Structure#

We visualize the repaired mutant structure in 3D:

msm.view(molsys_mut)

See also