Adding modifications to end terminus of peptides


I am working on the structure determination of peptides that have a C terminus amide modification. How can I edit the chain sequence to incorporate the modification?

Thank you.

Surabh KT

Hi Surabh,

Although we currently do not fully support modified amino acids in V3 there is a way around it. It requires a few manual modifications by generating Chem Comp in ChemBuild (ChemBuild - Software for the biomolecular NMR community CCPN). Depending on what you are aiming to do this might be sufficient.

First you need to import a compound into chemBuild in pdb format. What works well for me is to generate the pdb in ATB server ( from a smile string.

You can, if you need to, update names of atom sets (for instance Alanine HB1 HB2 HB3 is written as HB% from NEF nomenclature to pseudoatoms (QB) used by Cyana).

Give the compound three letter name and Ccpn code (GNX for instance).

When you are ready to export your compound from ChemBuild go to Export > Ccpn Xml and in the resulting window you need to type the name of your compound (for instance GNX) without any extensions, ChemBuild creates a folder (called GNX) in which the actual xml file is saved (it will contain the gnx code in its name). This file has a very specific and long name, which should be left unchanged.

In Analysis V3 I create a peptide chain (chain A) and use Alanine in the sequence position where I want my modified residue.

To import the new residue, go to Macro > Run Ccpn Macros > ChainFromChemComp, select the chem comp file you created, use previously chosen Ccpn code (GNX) as a “Residue 3 Letter Code” and tick “Add Non Stereo-Specific Atom”, you can also change “Residue Number” to reflect your final position in the peptide. This will create chain B.

In the next step create nmrChains from chain A and then from chain B. Delete the unwanted alanine from nmrChain A. In nmrChain B you should have a single nmrResidue GNX, edit it and change nmrChain from B to A. This should give nmrChain A with all your residues and atoms in correct positions and nmrAtoms you can use in assignments. You can now delete chain B is you want.

The problem with this approach is that the residues are not “covalently linked” in the project, so the backbone assignment module would not work, however this solution is ok for assigning peaks. The next issue is that when exporting to NEF file, chain information is stored in the molecular system saveframe, which has to be modified manually (the unwanted alanine replaced with correct modified residue (GNX in this case) and then chain B deleted).

I do admit it is quite involved and streamlining this process is on our TO DO list (but its hard to predict timeframe).

Please let me know if you have any questions.

Best wishes,

Hi Eliza,

Thank you for the response. I’ll try this out.

Surabh KT