NMR for a 30-residue peptide

[bimo]

Dear all,

Is that possible to do structure determination of a 30-residue peptide
using 500 MHz NMR?

I have a 30-residue linear peptide with three Gly and two AHx
(aminohexanoic acid) groups at the center of the peptide. I read some
papers from people who use 500 MHz NMR to determine the structure of
up to 20-residue peptides, but not a 30-residue peptide.

Many thanks.

Bimo

--
Bimo A Tejo, Ph.D
Department of Chemistry
Faculty of Science
Universiti Putra Malaysia
43400 UPM Serdang, Malaysia.
Tel: +60-3-8946-7488 (office) | +60-3-8946-6790 (lab)
Fax: +60-3-8943-5380

[Steve]

It all depends on the quality of the spectra - if yours are good, then it should be relatively staightforward, unless anyone knows any different?

[Hydrazin]

I have solved the structure of a alpha-helical peptide, containing 27 residues, bound to micelles. I had to cut of six amino acids (from 33) because of overlap. CD spectroscopy helped to give some hints about secondary structure formation.

But, it all depends on the spectra quality. I think for a non membrane bound peptide noesy/tocsy spectra and even cosy should look very nice. If the work is very important, partially 15N labelling might be helpfull.

[Vivekanandan Subramanian]

Hi Bimo,

You can run 1D 1H-NMR spectra at 5 different temperatures starting from 288 K until 308 K (if your peptide is stable) and see at what temperature you see good dispersion in the amide proton region (~ between 6.8 to 12 ppm). Select the optimal temperature/pH to see good dispersion in the amide proton region. Do TOCSY and NOESY at two different temperatures (say, 300 K and 303 K). This will help you during your peak assignment in NOESY when there is any overlapping residues present in the spectrum. I have done assignment and structure for 42 amino acid peptide and 65 amino acid protein structure (unlabelled) using 500 MHz Bruker spectrometer. If your peptide has beta-sheet conformation your job becomes relatively easy as you will have good dispersion in the amide region of the spectrum. Alpha helical peptide comes in a very narrow region and you will see lot of overlapping residues. But performing NOESY and TOCSY and two to three different temperatures can alleviate this problem to certain extent.

- Vivekanandan Subramanian

[krishnarjuna]

Hi,

you can do NMR for 30 residue peptide on 500 MHz. Many people use 500 MHz for proteins itself. So you can proceed with 500 MHz. You need higher field only for better resolution and sensitivity. Good Luck.

cheers, krishna

[krishnarjuna]

Originally Posted by bimo

Dear all,

Is that possible to do structure determination of a 30-residue peptide
using 500 MHz NMR?

I have a 30-residue linear peptide with three Gly and two AHx
(aminohexanoic acid) groups at the center of the peptide. I read some
papers from people who use 500 MHz NMR to determine the structure of
up to 20-residue peptides, but not a 30-residue peptide.

Many thanks.

Bimo

--
Bimo A Tejo, Ph.D
Department of Chemistry
Faculty of Science
Universiti Putra Malaysia
43400 UPM Serdang, Malaysia.
Tel: +60-3-8946-7488 (office) | +60-3-8946-6790 (lab)
Fax: +60-3-8943-5380

Hi,

I did solved structure of 26 residue helical peptide and data was acquired on 700 MHz and also 500 MHz spectrometers (read this paper: Theoretical and in vitro studies of a C-terminal peptide from PGKC of Leishmania
mexicana mexicana). It depends on the spectral quality and spectral quality is depends on concentration of the sample and structure of the peptide. Higher field meagnets are better resolution and otherwise 500 MHz spectrometer is more than sufficient for 30 mer peptide.

Good Luck