I am trying to build a custom poly peptide that is ~50 amino acids in length, and it will ideally have a charge of ~+4 at pH 7. I can get the positively charged attributes from incorporating a few arginine and lysine residues, but what should the rest of the peptide be composed of? I want to be sure that the peptide wont adopt any distinct secondary/tertiary/quartenary structure.
You should read some of the reviews on antimicrobial peptide structures, as they're usually cationic and sometimes around 50 amino acids. There is one structural class that's characterised by not possessing distinct secondary structure, as you desire.
The short version is, incorporate lots of glycine, as that is not conducive to secondary structure formation due to its large freedom of movement due to no side chain, as well as proline, which lacks the amide proton required for hydrogen bonding.
That should be the basis of your unstructured peptide. Avoid alanine, as it is quite prominent in alpha helix formation.
If you look at the AAIndex, you will find the percentages of each residue that are found in each type of secondary structure.
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