What is a peptide? Peptide bonds and sequences explained

What a peptide is

A peptide is a chain of amino acids joined by peptide bonds. Each amino acid has an amino group, a carboxyl group and a side chain; twenty standard amino acids, which differ only in their side chains, make up most natural peptides and proteins. The order of the amino acids in the chain, called the sequence, defines the peptide.

GHK, for example, is the three amino acids glycine, histidine and lysine joined in that order. Change the order or one amino acid and the result is a different peptide, with a different name, formula and mass.

How a peptide bond forms

A peptide bond is an amide bond between the carboxyl group of one amino acid and the amino group of the next. Forming it releases one molecule of water, so it is a condensation reaction; adding the water back breaks the bond again, which is hydrolysis. Because the C–N bond has partial double-bond character, the atoms around it lie in one plane and do not rotate freely, which shapes how peptide chains fold.

Every peptide bond removes one water molecule, so the molecular weight of a peptide is the sum of its amino acids minus about 18.02 for each bond. KPV (lysine, proline, valine) shows this: 146.19 + 115.13 + 117.15 = 378.47, and 378.47 − 2 × 18.02 = 342.43, the molecular weight on its compound profile.

In the laboratory, peptides are made by forming these bonds one amino acid at a time, usually by solid-phase peptide synthesis, and are then purified by HPLC and freeze-dried.

Dipeptides, oligopeptides, polypeptides and proteins

Peptides are named by the number of amino acids in the chain. The boundaries are conventions rather than fixed rules, and textbooks draw them in slightly different places.

What separates a protein from a long peptide is mostly structure: a protein folds into a stable three-dimensional shape, often from several chains, while most short peptides have no fixed fold.

How to read a peptide sequence

Sequences are written from the N-terminus, the end with the free amino group, to the C-terminus, the end with the free carboxyl group, in three-letter codes such as Gly-His-Lys or one-letter codes such as GHK.

Prefixes and suffixes show the end groups: H- is a free amino end and Ac- an acetylated one; -OH is a free acid and -NH2 an amide. SNAP-8 is written Ac-EEMQRRAD-NH2: eight amino acids with an acetyl group at the N-terminus and an amide at the C-terminus. Other notations mark D-amino acids, cyclic peptides and disulfide bridges between two cysteines.

Bonds and parts that are not in the sequence

Not every link in a peptide-like molecule is a standard peptide bond. Glutathione (γ-L-glutamyl-L-cysteinylglycine) is joined through the side-chain carboxyl group of glutamic acid rather than its main-chain carboxyl, a γ-glutamyl bond, so it is a tripeptide by composition but not a standard one.

Other parts of a material appear in its formula but not in its sequence. In GHK-Cu, copper(II) is bound to the tripeptide GHK. Synthetic peptides are usually supplied as salts, such as acetate or trifluoroacetate, and these counter-ions add weight without being part of the chain. Such details change the molecular formula and weight, so compare them on the compound profile and the certificate of analysis.

Checks when you compare peptide materials

The sequence and its end groups define a peptide. When you compare two materials, check:

• The full sequence, including end groups, not only the name: two materials with the same name can differ at the ends.
• The molecular formula and weight against the sequence: an acetyl group adds about 42, and an amide end weighs about 1 less than a free acid.
• The mass spectrum, which confirms the mass of the chain, and the HPLC purity, which shows how much of the signal is in the main peak.
• The form supplied: peptides change faster in solution than as a dry solid, through hydrolysis of peptide bonds and reactions such as oxidation and deamidation, which is one reason they are supplied lyophilized.