The following peptide sequence is a fragment within a globul

__The following peptide sequence is a fragment within a globular protein: Pro Ala Tyr Lys Met Ser Glu His Ala Ser Arg Leu Gly ... a. What secondary structure do you expect this fragment to form within the context of the protein? b. Approximately how long do you think this fragment would be? c. What is the net charge of this region of the protein in water at pH 8? d. How would a mutation that resulted in a change of the His to a Pro affect the structure of this fragment?

Solution

a. Mostly the peptide contain Hydrophilic amino acids with significant charge on it. So it can form intra chain hydrogen interactions and produce alfa helix

b. Each amino acid length in alfa helix is 1.5 A. Then the total amino acids in the peptide is 13. Then the total length of this peptide is =13 x 1.5 A = 19.5 Angstrom units

c. At pH 8, the peptide portion contain overall charge of positive. That is approximately +2. Three positive charges at Lys, Arg and His, one Negative charge at end Gly. So overall charge is +2

d. Histidine is neutal aminoacid, and it is well stabilizes alfa helix. when it replaced by Proline, a nutral amino acid destabilize the alfa helix