Peptide Knowledge Center

How to design peptide sequence

The sequence, length and amino acid composition of the peptide affect whether the peptide can be assembled correctly and whether it can be purified. These factors also determine the solubility of the final peptide product. The following points should be considered when designing peptides:

1. Design of peptide sequence

The biological activity of most peptides is derived from the N-terminus, C-terminus, or middle portion of natural proteins. But for a variety of reasons, these natural sequences sometimes need to be modified. Even for relatively short sequences, there are some essential and unnecessary amino acid residues, but the importance of these residues is not easy to determine. We usually make some modifications to these non-essential amino acid residues: substitution of amino acid residues (solubility, stability, etc.); Chemical modification (stability, structural function studies); Ligand antigen, etc. For some sequences from the middle of the protein, it is sometimes necessary to block the n-terminal or C-terminal with acetylation and amide to avoid introducing charges that are not present in the natural sequence.


2. Length of the peptide

As the length of the peptide increases, the length of the crude peptide is usually reduced. Peptides with less than 15 amino acid residues in length are relatively easy to synthesize.

3. Solubility

The amino acid composition of peptides is an important aspect of peptide design that is often overlooked. The composition of amino acids greatly affects the solubility of peptides. Peptides containing a high proportion of hydrophobic residues have limited or no solubility in aqueous solutions, such as leucine, valine, isoleucine, methionine, phenylalanine, and tryptophan. These peptides are then difficult to experiment with, and they are also difficult to purify. We recommend keeping the proportion of hydrophobic amino acids in the peptide below 50%, and at least one charged residue for every five residues. At physiological pH, aspartate, glutamate, lysine, and arginine all have charged side chains.

4. Difficult amino acids

peptides containing multiple cysteine, methionine, or tryptophan are difficult to obtain high purity, because the side chains of these amino acids are easily oxidized or side reactions occur. If possible, the peptide should contain as few of these residues as possible. Usually we can use norleucine instead of methionine and serine instead of cysteine. If there are many peptides derived from natural proteins or Overlapping peptides that need to be synthesized, changes can be made at the starting point of each peptide to achieve a better balance between hydrophilic and hydrophobic residues.

5. Secondary structure

The last thing we need to consider when designing peptides is the formation of beta folds. During the synthesis process, as the peptide chain lengthens, the β-fold structure results in a very large number of missing sequences in the final product. Choosing not to contain more consecutive sequences of valine, isoleucine, tyrosine, phenylalanine, tryptophan, leucine, glutamine, and threonine can avoid this problem. If a sequence containing consecutive residues cannot be avoided, we can insert a glycine or proline into every three residues, replace glutamine with asparagine, or replace threonine with serine.

In the end

The custom peptide synthesis business of Omizzur Biotech includes: pharmaceutical peptides, clinical peptides, staple peptides, starch peptides, transmembrane peptides, various antimicrobial peptides, cosmetic peptides, various acid modified peptides, various amine compounds.And more product information is available at