Stereospecific assignment in V2

Analysis Version 2
1

We are trying to assign the side chains of a protein in a way that is non-stereospecific. If we pick one peak to be Cgamma 1 for valine and another to be Cgamma 2 for the same residue, it swaps the assignment of these two peaks when we move to a different plane. It goes like that for side-chain resonances with close chemical shift values & similar naming conventions (e.g., Leucine). Any trick to fix that in CcPnmr V2? Thanks

2

Hi,

two points:

  1. If you are doing non-steroespecific assignment you should be using the CGa/b nomenclature rather than CG1/2. CG1/2 is for stereospecific assignments.
  2. V2 has the convention that Cga and Cgb are always in a particular order - either Cga is always the lower chemical shift and Cgb the higher or the other other way round (I can’t remember which, but you should be able to work it out easily enough). So that is why it may be switching things around when you add the second assignment. I’m afraid that is not something that can be changed. I guess if you make sure you always assign the higher/lower ppm value which will be designated as a first, then you can stop the switching. But given that the assignment is non-stereospecific it shouldn’t matter which way round they are, anyway. But it can certainly be a bit disconcerting to see the swap if you are not expecting it. In V3 it is up to you which is which.

Vicky

3

Thank you, Vicky. Your input is greatly appreciated and provides what I need to know.

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