I have a HN HSQC spectrum from which I have been able to assign the chemical shifts of all the residues by comparing to literature spectra of similar samples. (its a small protein of size 52 residues)
I do not have other shift details such as for the backbone Carbons.
If you've assigned the shifts by analogy to other samples, you've already made the assumption that the structure is similar to those other samples. If it wasn't, the shifts would be in different places.
Matthew has quite the point... Also there is very little information about torsion angles in the HSQC. I guess you can also try to run it through TALOS+ and see if it accepts it...
@Mathew @Casper Thank you for your input....I compared the shifts to the samples (same protein prepared in other labs)....In principle we are expecting to get the same structure....the shifts are slightly different but comparable ....
I tried in TALOS+ it does not seem to accept only NH shifts....it fails to predict a secondary structure....
I will then try and label the sample with 13C and then proceed.
Thank you very much for your input.
When you say they are slightly different, how much are we talking - such changes are very common if the buffer and temperatures are slightly different? (Try looking at the histidines. These will indicate how similar the pH is)
@Casper de Lichtenberg differences of about ~0.05 to 0.008ppm in 1H and ~0.2ppm in Nitrogen
@Mathew Conroy, A CD spectrum cannot say which region of the protein is beta sheet and which region is helix and which region is coil.....I need to know 1 - 10 residues are helix/sheet, 10-20 are sheet....and so on.
Well that doesn't sound like alarmingly large changes...
Sure CD spectra are nice, but they only tell you what secondary structural elements your protein contain and to me it sounds like the idea is to identify residues that are part of these.
But of course if you just want to know whether your protein is folded, and that it has the right components... then sure, CD is faster and cheaper
@Casper....Our intention will be in the future to make NMR samples and study structural and functional roles of a protein using NMR....Hence a NMR spectra is always a must for us to understand the quality of the sample....Thank you very much for your input
In case you want to study structure, you have to label it with C13 as well, so I would just go ahead if the N15-HSQC looks good.
@Casper Thanks again..Yes I am aware of the requirements for the NMR structure calculation...Have performed it once earlier. Thank you for your time.
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