How to assign minor population peaks (arising from proline isomerisation)

Analysis Version 3
1

Hello,

I have quite a few residues that have two peaks in my HSQC due to proline isomerisation (its an IDP). For now, I have assigned them both to the same residue (the second peak I did manually) and had to merge them, however I’d like a way to denote which is the minor peak - I can see it being confusing down the line to have them called the same thing. Is there any way to do that, or a better way to assign the second peak?

Thanks,
Jaz

2

To me the correct answer is you have 2 chains A and B or CIS and TRANS [chains don’t have to be single letters!] and most peaks (ie the ones which show no chemical shift difference) are assigned to both, then where the chemical shifts are different the separated peaks will be assigned to the specific chain for the isomer…

regards
Gary

Dr Gary S Thompson NMR Facility Manager
CCPN CoI & Working Group Member
Wellcome Trust Biomolecular NMR Facility
School of Biosciences, Division of Natural Sciences
University of Kent, Canterbury, Kent, England, CT2 7NZ

:phone::01227 82 7117
:email:: g.s.thompson@kent.ac.uk
orchid: ORCID

3

And if you want to put Gary’s suggestion (which I would also recommend) into practice, then you can create a new NmrChain based on your first one (double-click New NmrChain in the sidebar, and then select Clone from NmrChain). You should probably also create a matching Molecular Chain. You can do right-click on the first Chain and then Clone.

Screenshot 2025-03-14 at 10.38.20
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What you’ll then need to do is duplicate all the peak assignments. You should be able to do that with the following macro (make sure you replace A and B with whatever you have as your Chains are called):

for pk in project.peaks:
    if len(pk.assignments) > 0:
        for dim in pk.spectrum.dimensionIndices:
            nalist = []
            axCde = pk.spectrum.axisCodes[dim]
            for na in pk.assignmentsByDimensions[dim]:
                nalist.append(na.pid)
                newNaPid = na.pid.replace('A', 'B')
                newNa = get(newNaPid)
                nalist.append(newNaPid)
            pk.assignDimension(axCde, nalist)

This will duplicate all the peak assignments and then everything will be assigned to both NmrChains. You’ll then just need to go through the peaks which are are distinct between the two and remove the relevant assignment. Probably done most easily with the Peak Assigner.

It’s probably helpful to have your peak labels set to something like ‘short’ rather than ‘minimal’ so that you see the Chain name as part of the assignment in your spectra.

Hope this helps,

Vicky

4

Thank you both, seems like a good way to do it. I gave it a go with the macro and I think it worked.
Thanks! Jaz

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