Using the table of AA propensities from the book rate of the

Using the table of AA propensities from the book, rate of the following peptides for its likelihood to be found in either an alpha-helix or a beta-sheet, by adding up the values for each amino acid in each conformation. Now, check each peptide for \"sequence busters\" amino acids and groups of amino acids that are hardly ever found in helices or sheets (these are listed in the texts). Pick the one sequence most likely to be in a helix and the one most likely to be in a sheet and justify your choice based on your work above in (a) and (b). CRAGNRKIVLETY SEDNFGAPKSILW QKASVEMAVRNSG

Solution

ANS:

Given Peptide Sequence:

(A) CRAGNRKIVLETY
(B) SEDNFGAPKSILW
(C) QKASVEMAVRNSG

Peptide A has an adjacent basic residues R, K (Arg and Lys), which would destabilize an helix so it is more likely to be a beta strand.
Peptide B contains Gly and Pro, both of which are helix-breaking amino acids. The presence of Gly and Pro can inhibits the formation of strand; due to this nature peptide B is least likely to form a strand.

In Peptide C 3 charged amino acid residues (Lys, Glu, and Arg) are present. These residues are aligned on one face of the helix, so it is most likely to be form an -helix.

a. ANS:

(A) CRAGNRKIVLETY Peptide Sequence can present in beta strand.
(B) SEDNFGAPKSILW Peptide Sequence can present in beta strand.
(C) QKASVEMAVRNSG Peptide Sequence can present in -helix.

b. ANS:

Sequence buster (stops):

In the peptide A, had an adjacent basic residues (Arg and Lys), it destabilizes the Alfa helix.

In the peptide B, Gly and Pro are present; both are helix-breaking amino acids.

In the peptide C, there are no sequence busters.

c. ANS:

Peptide A is more likely to be present in a beta sheet.

Peptide B is more likely to be present in a beta sheet.

Peptide C is present in helix form.