Question

It is possible to make some predictions about protein secondary structure based on the primary sequence. Consider the following amino acid sequence:

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28

Ile-Ala-His-Thr-Tyr-Gly-Pro-Phe-Glu-Ala-Ala-Met-Cys-Lys-Trp-Glu-Ala-Gln-Pro-Asp-Gly-Met-Glu-Cys-Ala-Phe-His-Arg

A) Where might Beta-Turns occur?

B) Where might intrachain disulfide cross-linkages be formed?

C) Assuming that this sequence is part of a larger globular protein, what is the probable location (exterior or interior of the protein) of the amino acid residues:

Asp Ile Thr Ala Gln Lys

Explain your reasoning.

Answer 1

A. Beta turns are linked with Prolines having the cyclic structure which are present at 7^th and 19^th position. These cyclic structures are good in term of bends inside the protein structure.

B. Disulfide cross linking found at cysteines residues which are present at 13^th and 24^th position. Cysteine residues have thiol groups which help in bond formation.

C. Polar amino acid locate them self at the outside location and Non-Polar amino acid will locate themselves at inside of the protein structure. Polar amino acids are Asp, Gln, and Lys, Non Polar amino acids are Ala and Ile. “Thr” have the intermediate polarity which can be found at the either side.