Peptide Structure Determination by Different Methods

1. 27.8
Introduction to Peptide Structure
Determination

2. Primary Structure
The primary structure is the amino acid
sequence plus any disulfide links.

3. Classical Strategy (Sanger)
1. Determine what amino acids are present and
their molar ratios.
2. Cleave the peptide into smaller fragments,
and determine the amino acid composition of
these smaller fragments.
3. Identify the N-terminus and C-terminus in the
parent peptide and in each fragment.
4. Organize the information so that the
sequences of small fragments can be
overlapped to reveal the full sequence.

4. 27.9
Amino Acid Analysis

5. Amino Acid Analysis
Acid-hydrolysis of the peptide (6 M HCl, 24 hr)
gives a mixture of amino acids.
The mixture is separated by ion-exchange
chromatography, which depends on the
differences in pI among the various amino
acids.
Amino acids are detected using ninhydrin.
Automated method; requires only 10-5 to 10-7 g
of peptide.

6. 27.10
Partial Hydrolysis of Proteins

7. Partial Hydrolysis of Peptides and Proteins
Acid-hydrolysis of the peptide cleaves all of the
peptide bonds.
Cleaving some, but not all, of the peptide bonds
gives smaller fragments.
These smaller fragments are then separated
and the amino acids present in each fragment
determined.
Enzyme-catalyzed cleavage is the preferred
method for partial hydrolysis.

8. Carboxypeptidase
protein
H3NCHC
O
R
+
NHCHCO
O
R
–
C
O
Carboxypeptidase is a proteolytic enzyme
(catalyzes the hydrolysis of proteins).

9. Carboxypeptidase
protein
H3NCHC
O
R
+
NHCHCO
O
R
–
C
O
Carboxypeptidase is a proteolytic enzyme
(catalyzes the hydrolysis of proteins).
Carboxypeptidase is selective for cleaving
the peptide bond to the C-terminal amino acid.

10. Trypsin
Trypsin is selective for cleaving the peptide bond
to the carboxyl group of lysine or arginine.
NHCHC
O
R'
NHCHC
O
R"
NHCHC
O
R
lysine or arginine

11. Chymotrypsin
Chymotrypsin is selective for cleaving the peptide
bond to the carboxyl group of amino acids with
an aromatic side chain.
NHCHC
O
R'
NHCHC
O
R"
NHCHC
O
R
phenylalanine, tyrosine, tryptophan

12. 27.11
End Group Analysis

13. End Group Analysis
Amino sequence is ambiguous unless we know
whether to read it left-to-right or right-to-left.
We need to know what the N-terminal and C-
terminal amino acids are.
The C-terminal amino acid can be determined
by carboxypeptidase-catalyzed hydrolysis.
Several chemical methods have been
developed for identifying the N-terminus. They
depend on the fact that the amino N at the
terminus is more nucleophilic than any of the
amide nitrogens.

14. Sanger's Method
The key reagent in Sanger's method for
identifying the N-terminus is 1-fluoro-2,4-
dinitrobenzene.
1-Fluoro-2,4-dinitrobenzene is very reactive
toward nucleophilic aromatic substitution
(Section 23.5).
F
O2N
NO2

15. Sanger's Method
1-Fluoro-2,4-dinitrobenzene reacts with the
amino nitrogen of the N-terminal amino acid.
F
O2N
NO2
NHCH2C NHCHCO
CH3
NHCHC
CH2C6H5
H2NCHC
O O
O
O
CH(CH3)2
–
+

16. Sanger's Method
1-Fluoro-2,4-dinitrobenzene reacts with the
amino nitrogen of the N-terminal amino acid.
F
O2N
NO2
NHCH2C NHCHCO
CH3
NHCHC
CH2C6H5
H2NCHC
O O
O
O
CH(CH3)2
–
+
O2N
NO2
NHCH2C NHCHCO
CH3
NHCHC
CH2C6H5
NHCHC
O O
O
O
CH(CH3)2
–

17. Sanger's Method
Acid hydrolysis cleaves all of the peptide bonds
leaving a mixture of amino acids, only one of
which (the N-terminus) bears a 2,4-DNP group.
O2N
NO2
NHCH2C NHCHCO
CH3
NHCHC
CH2C6H5
NHCHC
O O
O
O
CH(CH3)2
–

18. Sanger's Method
Acid hydrolysis cleaves all of the peptide bonds
leaving a mixture of amino acids, only one of
which (the N-terminus) bears a 2,4-DNP group.
O2N
NO2
NHCH2C NHCHCO
CH3
NHCHC
CH2C6H5
NHCHC
O O
O
O
CH(CH3)2
–
H3O+
O
O2N
NO2
NHCHCOH
CH(CH3)2

19. Sanger's Method
Acid hydrolysis cleaves all of the peptide bonds
leaving a mixture of amino acids, only one of
which (the N-terminus) bears a 2,4-DNP group.
O2N
NO2
NHCH2C NHCHCO
CH3
NHCHC
CH2C6H5
NHCHC
O O
O
O
CH(CH3)2
–
H3O+
H3NCHCO–
CH3
+
H3NCH2CO–
O O
O
O2N
NO2
NHCHCOH
CH(CH3)2
+
O
H3NCHCO–
CH2C6H5
+
+ +
+

20. 27.12
Insulin

21. Insulin
Insulin is a polypeptide with 51 amino acids.
It has two chains, called the A chain (21 amino
acids) and the B chain (30 amino acids).
The following describes how the amino acid
sequence of the B chain was determined.

22. The B Chain of Bovine Insulin
Phenylalanine (F) is the N terminus.
Pepsin-catalyzed hydrolysis gave the four peptides:
FVNQHLCGSHL
VGAL
VCGERGF
YTPKA

23. The B Chain of Bovine Insulin
FVNQHLCGSHL
VGAL
VCGERGF
YTPKA

24. The B Chain of Bovine Insulin
Phenylalanine (F) is the N terminus.
Pepsin-catalyzed hydrolysis gave the four peptides:
FVNQHLCGSHL
VGAL
VCGERGF
YTPKA
Overlaps between the above peptide sequences were
found in four additional peptides:
SHLV
LVGA
ALT
TLVC

25. The B Chain of Bovine Insulin
FVNQHLCGSHL
SHLV
LVGA
VGAL
ALY
YLVC
VCGERGF
YTPKA

26. The B Chain of Bovine Insulin
Phenylalanine (F) is the N terminus.
Pepsin-catalyzed hydrolysis gave the four peptides:
FVNQHLCGSHL
VGAL
VCGERGF
YTPKA
Overlaps between the above peptide sequences were
found in four additional peptides:
SHLV
LVGA
ALT
TLVC
Trypsin-catalyzed hydrolysis gave GFFYTPK which
completes the sequence.

27. The B Chain of Bovine Insulin
FVNQHLCGSHL
SHLV
LVGA
VGAL
ALY
YLVC
VCGERGF
GFFYTPK
YTPKA

28. The B Chain of Bovine Insulin
FVNQHLCGSHL
SHLV
LVGA
VGAL
ALY
YLVC
VCGERGF
GFFYTPK
YTPKA
FVNQHLCGSHLVGALYLVCGERGFFYTPKA

29. Insulin
The sequence of the A chain was determined
using the same strategy.
Establishing the disulfide links between cysteine
residues completed the primary structure.

30. Primary Structure of Bovine Insulin
N terminus
of A chain
N terminus
of B chain
C terminus
of B chain
C terminus
of A chain
5
5
15
10
15
20
20
25
30
S S
10
S
S
S
S
F
F F
F
V N Q H L
C C
C
C
C
V
V
V
V
G
G
G
S
S
S
H L L
L
G A
A
A
C
L Y
Y
E
E L E
R
Y
Y
I Q
K P T
Q
N
N

31. 27.13
The Edman Degradation and
Automated Sequencing of
Peptides

32. Edman Degradation
1. Method for determining N-terminal amino
acid.
2. Can be done sequentially one residue at a
time on the same sample. Usually one can
determine the first 20 or so amino acids from
the N-terminus by this method.
3. 10-10 g of sample is sufficient.
4. Has been automated.

33. Edman Degradation
The key reagent in the Edman degradation is
phenyl isothiocyanate.
N C S

34. Edman Degradation
Phenyl isothiocyanate reacts with the amino
nitrogen of the N-terminal amino acid.
peptide
H3NCHC
O
R
+
NH
C6H5N C S +

35. Edman Degradation
peptide
H3NCHC
O
R
+
NH
C6H5N C S +
peptide
C6H5NHCNHCHC
O
R
NH
S

36. Edman Degradation
peptide
C6H5NHCNHCHC
O
R
NH
S
The product is a phenylthiocarbamoyl (PTC)
derivative.
The PTC derivative is then treated with HCl in
an anhydrous solvent. The N-terminal amino
acid is cleaved from the remainder of the
peptide.

37. Edman Degradation
peptide
C6H5NHCNHCHC
O
R
NH
S
HCl
peptide
H3N
+
+
C6H5NH C
S
C
N CH
R
O

38. Edman Degradation
C6H5NH C
S
C
N CH
R
O
The product is a thiazolone. Under the
conditions of its formation, the thiazolone
rearranges to a phenylthiohydantoin (PTH)
derivative.
peptide
H3N
+
+

39. Edman Degradation
C6H5NH C
S
C
N CH
R
O
C
C
N
HN CH
R
O
S
C6H5
The PTH derivative is
isolated and identified.
The remainder of the
peptide is subjected to
a second Edman
degradation.
peptide
H3N
+
+