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Adding spectrum type 2D HSQC-TOCSY

Author aneleya
Registered 

#1 | Posted: 23 Feb 2016 11:28 
Hi,

I would like to add new spectrum type for 2D [1H, 113Cd] HSQC-TOCSY, could you please help with writing of experimental procedure?
I am not sure about how to write correct all the steps and hops...

Thank you,

Jelena

Author Admin
Admin 

#2 | Posted: 23 Feb 2016 16:54 | Edited by: Admin 
Hi Jelena
As far as I understand this is an HSQC based on Cadmium instead of the more common 13C, and there is an additional TOCSY transfer, and only two dimensions are recorded. I'm not an expert for these kind of exeriments but have you tried something like this:
Screenshot
I have forwarded the request to Fred who certainly has a better answer than this one ;-)
Regards
Rochus

Author aneleya
Registered 

#3 | Posted: 23 Feb 2016 17:48 
Hi Rochus,

yes I tried that, but now the problem is when I go to peak new system it doesn't offer me any spins (just "?") and if I put manually that this is amide H (or HB) and Cd correlation he records the new spin system put doesn't show it in the spectra as a peak.

Best,
Jelena

Author rkeller
Registered 

#4 | Posted: 23 Feb 2016 18:04 
Hi Jelena
Ok; for spin inference to work of course there must be residue types available including all isotopes visible in the experiments. If you use the default template, only amino acids are represented (especially in the generic residue type used for backbone assignment). For each new "NMR domain" someone needs to adjust the templates. I'm not aware someone using Cd NMR experiments up to now. Maybe Fred knows someone.
Regards
Rochus

Author damberger
Registered 

#5 | Posted: 24 Feb 2016 10:00 
HI Jelena, you are breaking new ground as far as I know. If you create ResidueTypes which include the Cd atom you will be able to see TOCSY transfers from the 1H coupled to Cd to other 1H atoms in the spinsystem. How many bonds separate the Cd from the 1H it is coupled to? In the SpectrumType proposed by Rochus, it is only one bond. If you expect also couplings of longer range like 2 bonds for example you will need to change hops in step 2 to 2. You will not be able to see couplings from this Cd to other residues (for example if you have a Cd coordinated by the sidechains of multiple residues). In this case it might be possible to represent the contacts by creating Spinlinks from the Cd to 1H atoms in other SpinSystems. Rochus, is this possible? I.e. creating SpinLinks between Cd and 1H atoms? Could one design a SpectrumType which combined steps with hops = -1 to represent Cd->1H 'NOESY' steps and steps with 1H->1H hops=3 (repeat) to represent the TOCSY transfers?

Author aneleya
Registered 

#6 | Posted: 24 Feb 2016 11:41 
Hi Fred,

for this experiment I use little bit modified Bruker pulse program hsqcetgpml. Therefore, I see Cd correlations to Hb, Ha and amide protons of a Cysteine or Histidine residue.(Cd ions in my case bind to S of a Cysteine side chain or one of the N of a aromatic ring of a Histidine side chain).
So I see up to 5 bonds correlations.

Author Renuka
Registered 

#7 | Posted: 12 Sep 2016 13:20 
Hello,
I wish to add a BEST_HNCO spectrum to synchroscope with a 2D HSQC spectrum but I am unable to see any spectrum at all in the strip with HNCO. Moreover,whenever i am loading my spectrum,the original spectrum doesn't show the CO dimension.
Please help me solve this.

Thankyou,

Renuka

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