BioNMR - αH(i,i+1) NOEs in helical peptide, can this be present continuously...

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αH(i,i+1) NOEs in helical peptide, can this be present continuously...

Hi,

I have observed some interesting NOEs for my peptide (5 kDa) in my 2D NOESY spectrum recorded at 900 MHz. I see NOEs that forms an α-helical pattern between 12-24 residues and N&C-terminus of my peptide is unstructured and does not have any secondary structure. The interesting part is, apart from seeing helical NOE patterns, such as αN(i,i+3)and αβ(i,i+3) for the residues between 12 & 24, I see in the alpha proton chemical shift regions of my 2D NOESY spectrum, a continuous αH(i,i+1) NOEs for the residues where I have helical secondary structural region (12-24 aa). That is, I see NOE patterns like 12Hα -13Hα, 13Hα to 14Hα, 14Hα-15Hα, 15Hα to 16Hα, 17Hα-18Hα, 19Hα to 20 Hα and so on until 24th residue. In general, I have never seen in any literature reported this type of NOE patterns for the α-helical peptide. The mixing time that I used for my NOE is 300 ms. Did any of you have observed this type of Hα(i)-Hα(i+1) NOEs for α-helical regions of peptide? I would appreciate your answers and thanks a lot.
- Vivek

alpha- alpha NOE

Hi,

If you are observing alpha-alpha NOEs continuously it must be beta sheet structure. In alpha helix you should observe continuous NH-NH NOEs. If both are present then your molecule must be existing in two conformations.

cheers, krishna.

how do the ha to ha noe's compare to the hn to hn Noe's for the same residues.

300ms is pretty long for a 5kda peptide - it wouldn't be surprising to see spin diffusion errors.