Question

A peptide sequence was fragmented using two different methods (enzymatic and or chemical) to generate the following sequences:

Method 1:

VMKGPPAK

CDLR

MNMK

Method 2:

KCDLR

VM

KGPPAKM

NM

a. Determind the sequence of the peptide.

b. Which enzyme or chemical was used to generate the fragments in method 1?

c. What type of motif or secondary structure would you expect to form in this particular peptide sequence?

Answer 1

Ans. #a. Overlap the peptide fragments obtained from method 1 over the peptides from method 2 based on common sequence as shown in figure.

#b. Note that the peptide bond is cleaved at the C-terminal of lysine (K) residues.

Trypsin hydrolyzes the peptide bond at C-terminal of amino acids with basic side chains. So, the enzyme used in method 1 is trypsin.

#c. Note that the peptide has two proline residues and one glycine residue. Both proline and glycine destabilizes a-helix. So, the given peptide is most likely NOT to attain a-helix conformation.

Presence of P and H residues helps the peptide chain take bends and greater extent of rotations (dihedral angles) around the peptide bonds. The conditions favor the formation of b-chain (two or more b-chains associated together are called b-sheet).

Therefore, the peptide is most likely to a b-chain.