Understanding 3D NMR HNCA Spectra: Identifying Peak Data and Arranging in Order

[Allday]

hey bio people,

Im a physics student, but I am taking a class in biophysics with hopes to work in the space that the two disciplines share. Anybody do 3D NMR here...

I'm looking at slices in the N direction of a 3D HNCA spectrum of a short protein (so the amide hydrogen and alpha carbon correlations) and there are two peaks in each slice. to me this represents the data from 4 residues because 4 N slices with data indicate at least 4 amide groups. logical? the next step is to arrange them in order, but I think I can do that if i know the number of residues I am dealing with and 4 is what I am thinking. confirmation or correction would be helpfull,

thanks

 

[Mike H]

First, you really should know how many residues you have in your protein and what they are (although it sounds like you have more a short peptide sequence than some ridiculously huge 300 residue protein). That should be information you are either informed of or are able to get by sequencing. I work in a protein NMR lab, we always extensively characterize our proteins in terms of sequence and size before doing assignments. Of course, there are some people who think you should be able to do peptide NMR without such information, I consider them a bit messed up in the head...

Anyway, figuring that the four N slices are adequately dispersed (e.g., not dealing with 112.3 ppm, 112.4 ppm, 112.5 ppm, and 112.6 ppm or something as bad), you can probably presume that you have four different amides. That there are two peaks in each slice has to do with the HNCA experiment - the magnetization can transfer one bond to the adjacent CA or through two bonds to the preceding CA.

I'm not sure what you're talking about in terms of arranging the slices in order, though. They show up where they show up in the spectrum, you don't go shuffling your slices around since they are attached to an amide N chemical shift.

 

[Moonbear]

You'll probably get more help from the chemists than the biologists on an NMR question. Either way, I'm moving it over to the "other sciences" homework forum which is for both biology and chemistry homework type questions.