The peptide sequence is the most important aspect when it comes to biological activity of the peptide. The amino acid composition as well as the sequence also have a direct impact on the products of synthesis and purification as well as the solubility of that particular peptide. For any peptide project to be viable, it has to be easy to synthesize and reduce on the costs and increase the convenience of using it for different applications. Below are a few tips worth considering whenever you are dealing with peptide synthesis and purification-:
The sequence length
To reduce the cost, minimize impurities and increase the overall yield, restrict the length of the sequence to between 10 and 15 residues. As is always the case, the purity of the synthesized peptide will decrease with an increase in length.
Reduce prone to oxidation
Peptides with multiple Trp, Met or Cys residues are more prone to oxidation and other side reactions which may have a negative impact on the overall solubility and purity of the peptide. To reduce such instances of oxidation, these residues should be avoided or used minimally or they should be replaced with other suitable alternatives.
Amino acid composition
Most people overlook the overall composition of amino acid during peptide synthesis, and this is usually a big mistake. The overall composition of amino acid with have a great bearing on the final solubility, purification and synthesis of the peptide. It is recommended that the hydrophobic amino acid should not exceed 50% and there must be at least one charged residue for every group of five amino acids in the sequence.
Amino acid in the N-terminus
N-terminal glutamine should be avoided in the sequence because it may cyclize and this may lead to pyroglutamation if the conditions are acidic. If the N-terminal glutamine must be in the sequence, then an acetyl group must be added to the amino group or a suitable pyroglutamate must be used.