When you need peptides for custom synthesis, there are a lot of considerations you need to make during the designing process. These considerations will be responsible for the quality and compatibility with solvents and the integrity of your final synthesized peptides. Below is a look at the factors we consider as the most important when it comes to designing peptide synthesis:
The sequence length
You should be aware that the purity of the peptide will reduce with an increase in the sequence length. It implies that the longer the length of the sequence, the less pure the peptide will be. Be very careful with sequences that are comprised of more than 30 amino acids. This is because longer sequences will lead to a low number of amino acid couplings and this will have an impact on the solubility during the purification process.
The solubility of the peptide
The classification of amino acids is usually based on a hydropathy index. This index is dependent upon the hydrophilic and hydrophobic properties of the respective side chains. Exclusion or inclusion of hydrophilic and hydrophobic amino acids in the sequence will therefore affect the peptides ability to solubilize, purify and synthesize in an aqueous solution.
The stability of the peptide sequence
The other factor worth considering when designing a synthetic peptide is the peptide sequence stability. There are a number of approaches you can consider to improve peptide stability and these are designed to give you peptides with optimal solubility and higher peptide purity. It is also important to remember that the composition of amino acids present in the peptide sequence will have an impact on the overall stability and the following should be considered:
- For peptides with multiple Trp, Met or Cys amino acids, attaining high purity is difficult due to the possibilities of oxidation and side reactions
- Peptides with N-terminals are unstable and may easily cyclize when they come into contact with acidic cleavage conditions
- Asparagine has a protecting group that can’t be removed easily when it is at the N-terminal of the sequence.