Add missing terminal cappings#

Adding terminal cappings to peptides and proteins.

Capping the termini of peptides and proteins can be important for ensuring charge neutrality, stability, or for matching biological conditions. Terminal cappings are often required in molecular modeling, particularly when working with small peptides or fragments.

Added in version 1.0.0.

How this function works#

API documentation

Follow this link for a detailed description of the input arguments, raised errors, and returned objects: molsysmt.build.add_missing_terminal_cappings().

The function molsysmt.build.add_missing_terminal_cappings() adds chemical groups to the N-terminus, the C-terminus, or both. These groups can be neutral or charged depending on the chosen capping residues. By default, it completes the terminal atoms without introducing caps, resulting in charged termini. Alternatively, you can specify capping groups such as ACE for the N-terminus or NME for the C-terminus to neutralize the ends.

Let’s illustrate how this function works with a simple tripeptide example:

import molsysmt as msm

molsys = msm.build.build_peptide('AlaValPro', to_form='molsysmt.MolSys')

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

index	id	name	type	n atoms	molecule type	entity name
0	1	ALA	amino acid	10	peptide	peptide 0
1	2	VAL	amino acid	16	peptide	peptide 0
2	3	PRO	amino acid	14	peptide	peptide 0

As shown, the termini of the peptide are currently uncapped. We now add the atoms required to complete the terminal amino acids without capping groups. This produces a charged version of the peptide.

molsys_charged = msm.build.add_missing_terminal_cappings(molsys, N_terminal=None, C_terminal=None)

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

index	id	name	type	n atoms	molecule type	entity name
0	1	ALA	amino acid	12	peptide	peptide 0
1	2	VAL	amino acid	16	peptide	peptide 0
2	3	PRO	amino acid	15	peptide	peptide 0

Let’s confirm that the terminal groups carry charges under these conditions.

msm.physchem.get_charge(molsys_charged, element='group')

Magnitude	[0.0 0.0 0.0]
Units	elementary_charge

To neutralize the terminal charges, we can cap the N-terminus with an acetyl group (ACE) and the C-terminus with a N-methyl amide (NME).

molsys_uncharged = msm.build.add_missing_terminal_cappings(molsys, N_terminal='ACE', C_terminal='NME')

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

index	id	name	type	n atoms	molecule type	entity name
0	0	ACE	terminal capping	6	peptide	peptide 0
1	1	ALA	amino acid	10	peptide	peptide 0
2	2	VAL	amino acid	16	peptide	peptide 0
3	3	PRO	amino acid	14	peptide	peptide 0
4	4	NME	terminal capping	6	peptide	peptide 0

We check the charges again to confirm that the peptide is now neutral.

msm.physchem.get_charge(molsys_uncharged, element='group')

Magnitude	[0.0 0.0 0.0 0.0 0.0]
Units	elementary_charge