Sandbox chameleon

General question

To determine the extent to which non-local factors influence the formation of secondary structural elements

Methodology

Design the longest possible sequence that can fold into an alpha-helix when inserted into one place in a protein sequence and a beta-sheet when inserted into another

Two key references to read on this ones on a Chameleon peptide^[1] and an analysis of Helix-to-Strand Transition Between Peptides with Identical Sequences^[2].

Seeing is believing

Display this IgG-Binding domain in i.e. going from Blue---Red from N--->C terminal. To simplify things entire chain is colored . Displaying the structure mutated structure, where 5 amino acids, in this region , are change to the Chameleon sequence, i.e. AWTVEKAFKTF i.e. going from: TTYKLILNGKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEK TTYKLILNGKTLKGETTTEAVDAWTVEKAFKTFANDNGVDGEWTYDDATKTFTVTEK

If a similar change from the Wild-Type to 5 amino acids, in the region are changed to the Chameleon sequence, i.e. going from:

TTYKLILNGKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEK

TTYKLILNGKTLKGETTTEAVDAATAEKVFKQYANDNGVDGAWTVEKAFKTFTVTEK