Peptides possess characteristic backbones formed by chains of amino acids. Additional amino acid structures attached at sidechains of one or more of the peptide amino acid residues create branched peptides, also known as isopeptides (named after isopeptide bond, which is an amide bond that is not present on the main chain of the molecule).
Let us review a number of ways a branched peptide can be created, based on specific moieties where amino acid sidechains are extended.
Amino Group Branching
One of the most popular ways to create a branched peptide is through amino group isopeptide bonding, primarily the epsilon-amino group of Lysine residues.
In the figure 1 you can see two separate linear peptide sequences, conveyed with N, or amine, termini on the left, and C, or carboxyl, termini on the right. The Lysine residue where we want to branch is printed in red.
In the figure 2 the notation of the Lysine residue in red has been expanded to detailed organic structure. A hydrogen substituent of the Lysine sidechain amino group has gone away where the second peptide chain is attached through amide bond; the “-OH” of the Thr residue of the second sequence has also gone away in the process of bond formation.
As you can see, the secondary sequence attaches by the carboxyl end. When writing peptide sequences linearly, attachments to amino acid sidechains are indicated in parenthesis to the right of the corresponding amino acids. The branched peptide shown in figure 2 can be written linearly as follows:
Please note that the importance of conveying the proximity of the sidechain Thr residue to the Lys residue overrides the convention of writing amino acid sequences in the direction from N to C termini. As such amino group branched subsequences in linear notation are written in the direction opposite to the direction of the sequences they attach to.
The same branched peptide may be written in one-letter amino acid code as follows:
Hydroxyl Group Branching
Similar to Lysine branched peptides, isopeptide branches can be created at amino acids containing sidechain hydroxyl moiety. This method is primarily applicable to Serine and Threonine branched peptides. An example of the latter you can see in the following figure (the Thr residue is expanded in red).
As with amino group branching, hydroxyl group branching produces subsequences with attachment point at the carboxyl end. The peptide from the figure 3, in one-letter code linear notation, can be written as follows:
Carboxyl Group Branching
Conversely to the previously discussed two types of branching, branching at sidechain carboxyl functional group containing amino acids (Aspartic Acid and Glutamic Acid) features subsequences that are attached by the amino end. Figure 4 shows an example of a peptide branched at the Aspartic Acid residue (expanded in red).
Please note that in linear notation carboxyl group branched subsequences point in the same direction as the sequences they are branching from (which is normally from left to right, from amino terminal to carboxyl terminal).
The peptide from figure 4 is written as follows in three-letter code:
The same peptide in one-letter code would look like the following:
The peptide calculator tool on this website understands all three methods of creating branched peptides discussed in the article.