Peptide Nmr Assignment

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1.  Peptide Structure NMR Problem

For an introduction to using NMR to analyze the structure of the peptide, start here.

Amino acid sequence of the peptide:

K1  T2  L3  T4  L5  E6  A7  A8  L9  R10  N11  A12  W13  L14  R15  E16  V17  G18  L19  K20

NMR spectra:

a)  One-dimensional NMR spectrum of the peptide (500 MHz)

1-D NMR spectrum

b)  2-D TOCSY spectrum.

Each cross peak indicates a pair of 1H nuclei located within the same amino acids.  In general, strong peaks indicate 1H nuclei separated by 2 or 3 bonds; weaker peaks indicate 1H nuclei separated by > 3 bonds.

full_view tocsy
tocsy_section1.pdf
tocsy_section2.pdf
tocsy_section3.pdf
tocsy_section4.pdf
tocsy_section5.pdf
tocsy_section6.pdf

c)  2-D NOE spectrum,  80 msec mixing time.

In the 80 msec mixing time spectrum, each cross peak indicates a pair of 1H nuclei separated by less than about 4.5 angstroms, and not necessarily located within the same amino acid. Strong cross peaks indicate 1H nuclei separated by < 3 angstroms; weak cross peaks indicate pairs of protons separated by approximately < 4.5 angstroms.

full view noesy
noe section1.pdf
noe section2.pdf
noe section3.pdf
noe section4.pdf
noe section5.pdf
noe section6.pdf
noe section7.pdf
noe section8.pdf
noe section9.pdf

d)  2-D NOE spectrum, 400 msec mixing time.

In the 400 msec mixing time spectrum, the NOE effect extends to a longer range, by means of spin-diffusion. Strong cross peaks indicate 1H nuclei separated by approximately < 3.5 Å; weak cross peaks indicate pairs of protons separated by approximately < 6 Å.

noe (400ms) section1.pdf
noe (400ms) section2.pdf
noe (400ms) section3.pdf
noe (400ms) section4.pdf
noe (400ms) section5.pdf
noe (400ms) section6.pdf
noe (400ms) section7.pdf
noe (400ms) section8.pdf
noe (400ms) section9.pdf

e)  2-D COSY spectrum.

Each cross peak indicates a pair of 1H nuclei located within the same amino acids separated by 2 or 3 bonds.

 cosy section1.pdf
 cosy section2.pdf
 cosy section3.pdf
 cosy section4.pdf
 cosy section5.pdf

f)  A "PDB" coordinate file for the peptide is provided here. These coordinates are essentially a "random coil" starting structure, and can be refined using the information provided in the NMR spectra and X-PLOR (or other programs) to determine the actual structure of the peptide.

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2.  Useful things for the peptide NMR problem

Typical proton NMR chemical shifts for amino acids
Typical NMR chemical shifts for proteins:  H-1, C-13 & N-15 nuclei
Identifying amino acids in protein NMR spectra
Distances and torsion angles in regular secondary structures
More distances in regular secondary structure
Typical NOE cross peaks in a helix
Typical NOE cross peaks in a beta strand
Typical NOE cross peaks in a beta sheet
Naming of atoms in isoleucine and tryptophan
Naming of atoms in histidine
Using "Sparky" to evaluate volumes of peaks in 2-D spectra

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