Subject: Re: Fw: [nmr_sparky] distance constraints in 13C-edited spectra
From: Betty Swanson
Date: Nov 23 7:42 PM

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DearMandar and Eiso,
I asked our NMR spectroscopist regarding the relatively weaker intensities of all cross-peaks in 13C-edited spectra (when compared with 15N-edited spectra). According to him the pulse sequence used was fine and he doesn’t know the cause of this problem. Anyway, thanks you both for your suggestions.
At present, I used CYANA/CANDID for generating the structures. The structures generated have secondary structural regions and folds consistent with the pattern of NOE connectivities. However, the phi-psi angles for several non-glycine residues lie in sterically unfavorable regions of the Ramachandran Plot. The same is observed even if phi-psi angle constraints obtained using the program PREDITOR are in are included. (The program PREDITOR uses as input chemical shifts. The phi-psi angle constraints generated by PREDITOR for non-glycine residues lie in sterically favorable regions of the Ramachandran plot). Do you’ll encounter these problems? If so what is the approach that has to be used to correct it?
Thanks,
Betty Swanson


Mandar T. Naik mandarn@... wrote:
Hi Betty
For Cyana to calibrateyour spectra differently, please leave the calibration line blank in CALC.cya. (see Cyana installation folder/demo/ auto/CALC. cya). Also please note Cyana doent account for spin diffusion, I hope the mixing times are not too long.
Best regards
-mandar

Dear SPARKY and CYANA users,

In SPARKY, for my protein the overall intensities of all cross peaks in the 13C-edited NOESY spectra are medium or weak. Hence, when I pool the peak lists from 15N-edited NOESY spectra and 13C-edited NOESY spectra and run CYANA, the upl file generated after cycle7 contains larger distance constraints (~5.5 angstrom) for specific cross peaks observed in the 13C-edited spectra. I expect constraints for those cross peaks to be short (less that 2.5 angstrom) because they correspond to long range daa connectivity in regions of protein corresponding to antiparallel betasheet.
Why does SPARKY display relatively weaker peak intensities for 13C-edited NOESY spectra when compared to 15N-edited NOESY spectra? Is this what you all generally observe? How do you all solve this problem? I think one method by which this problem can be solved is by calibrating peak heights separately for 15N-edited and 13C-edited spectra in CYANA. Can anybody tell me how to do that?

Thanks,

Betty Swanson




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