Examine the following polypeptide sequence: 1-LeuValThrIleArgIleGlyGlyGlnLeuLysG

Question

Examine the following polypeptide sequence: 1-LeuValThrIleArgIleGlyGlyGlnLeuLysGluAlaLeuLeu-15

a) Based on this sequence, suggest a possible structural motif based on your knowledge of secondary structure and amino acid properties. Justify your answer. b) Comment on the overall stability of the motif. Justify your answer by listing 3 stabilizing and 2 destabilizing factors. c) Suppose you wanted to further stabilize this structural motif. What two amino acid residues would you change? What residue(s) would you replace them with? Explain your answer.

Explanation / Answer

1)

The given peptide sequence at physiological pH is:

(1)                 (5)                      (10)                   (15)

LeuValThrIleArgIleGlyGlyGlnLeuLysGluAlaLeuLeu

a) Based on this sequence, it is an (alpha) helix. The stabilizing factors are:  

b)

Hydrophobic interaction between the N and C terminal amino acids (Leu) is a stabilizing factor, because it is existed on the both sides of the peptide. Salt bride between the glutamine (9) and lysine (12) is another stabilizing factor.   Destabilizing factor is: it does not have Harper-Rose capping box structure, so there is no proper capping.     

c)

If I wanted to further stabilize this structural motif. The two amino acid residues I would like to change are N and C terminal Leu resides with Glutamine and lysine. These two resides act as perfect Harper-Rose capping box structure.

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