b Now check each peptide for sequence busters amino acids a

(b) 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 texst).

(c) 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).

(a) CRAGNRKIVLETY

(b) SEDNFGAPKSILW

(c) QKASVEMAVRNSG

Solution

For question part a and b there is no table of AA propensities. So I am answering option c.

a. CRAGNRKIVLETY

CYS-ARG-ALA-GLY-ASN-ARG-LYS-ILE-VAL-LEU-GLU-THR-TYR

This sequence has Arginine and lysine adjacent base residues, which would destabilise an alpha helix, so it is more likely to form a beta strand.

b. SEDNFGAPKSILW

SER-GLU-ASP-ASN-PHE-GLY-ALA-PRO-LYS-SER-ILE-LEU-TRP

This sequence has Gly and Pro base residues which are alpha helix breakers but inhibits beta strands, So, it is the least likely to form beta strand.

c. QKASVEMAVRNSG

GLU-LYS-ALA-SER-VAL-GLU-MET-ALA-VAL-ARG-ASN-SER-GLY

It has three charged residues Lys, Glu, Arg. So, it is most likely to form an alpha helix.