import molsysmt as msm

Mutate#

Mutate aminoacids in peptide or protein.

With the function molsysmt.build.mutate(), specific aminoacids of a peptide or a protein can be mutated. Let’s first of all build a short peptide to test how this function works.

molecular_system = msm.build.build_peptide('TyrGlyGlyPheMet')

msm.info(molecular_system, element='group')

index	id	name	type	n atoms	molecule type	entity name
0	1	TYR	amino acid	21	peptide	peptide 0
1	2	GLY	amino acid	7	peptide	peptide 0
2	3	GLY	amino acid	7	peptide	peptide 0
3	4	PHE	amino acid	20	peptide	peptide 0
4	5	MET	amino acid	17	peptide	peptide 0

Let’s now explore the different ways the function molsysmt.build.mutate() can be used. The input argument mutations accepts strings or lists of strings if the mutations are specified in the tradicional way: “old_residue_name-residue_id-new_residue_name”.

new_molecular_system = msm.build.mutate(molecular_system, mutations=["GLY-2-ALA", "GLY-3-LYS"], engine='PDBFixer')

Note

In the current version of MolSysMT, the function molsysmt.build.mutate works with the library PDBFixer behind doing the dirty job. There is no native algorithm to mutate aminoacids yet. So… do not forget to give credit to the PDBFixer developers if you are using this function.

msm.info(new_molecular_system, element='group')

index	id	name	type	n atoms	molecule type	entity name
0	1	TYR	amino acid	23	peptide	peptide 0
1	2	ALA	amino acid	10	peptide	peptide 0
2	3	LYS	amino acid	22	peptide	peptide 0
3	4	PHE	amino acid	20	peptide	peptide 0
4	5	MET	amino acid	18	peptide	peptide 0

In addition to a string or a list of strings, the input argument mutations accepts a dictionary where the keys can be the indices, ids or names of the residues to be mutated, and the corresponding values must be the new residue names. Let’s see some examples:

new_molecular_system = msm.build.mutate(molecular_system, mutations={1:'ALA', 2:'LYS'}, keys='group_index')

msm.convert(new_molecular_system, to_form='string:amino_acids_3')

'TyrAlaLysPheMet'

new_molecular_system = msm.build.mutate(molecular_system, mutations={2:'VAL', 3:'THR'}, keys='group_id')

msm.get(new_molecular_system, element='group', group_name=True)

['TYR', 'VAL', 'THR', 'PHE', 'MET']

Finally, the molsysmt.build.mutate() includes an option to select the region of the system where the mutations applies:

new_molecular_system = msm.build.mutate(molecular_system, mutations={'GLY':'ALA'}, keys='group_name', selection='group_id==[3,4,5]')

for group_id, group_name in msm.Iterator(new_molecular_system, element='group', group_id=True, group_name=True):
    print(group_id, group_name)

TYR
GLY
ALA
PHE
MET