Peptide Nomenclature: Sequences, Analogs, Fragments and Salts

Research peptide names look arbitrary until you know the conventions. Almost every element of a name — brackets, number ranges, suffixes, salt designations — encodes something specific about the molecule. This is a practical guide to reading them.

Sequences: one- and three-letter codes

Amino acids have both a three-letter code (Gly, Ala, Lys) and a one-letter code (G, A, K). Sequences are written N-terminus to C-terminus, left to right, which is also the direction of biosynthesis. So the tripeptide KPV is Lys-Pro-Val: lysine, proline, valine.

Direction matters. Lys-Pro-Val and Val-Pro-Lys are different molecules with the same composition. When a paper gives a sequence without stating direction, N-to-C is the assumption.

Bracket notation for substitutions

Square brackets before a parent name list modifications to it. Read [Nle&sup4;,D-Phe&sup7;]-α-MSH as: the alpha-MSH sequence, with norleucine substituted at position 4 and D-phenylalanine at position 7. Sawyer and colleagues introduced exactly this analog, measuring a large increase in potency and resistance to enzymatic degradation in the frog skin melanophore bioassay (PNAS, 1980; PMID 6777774).

The two most common modification types:

• D-amino acids. Naturally occurring residues are L-form. Substituting the D-enantiomer at a protease cleavage site slows degradation, because proteases are stereospecific. A D- prefix always signals this.
• Non-proteinogenic residues. Norleucine (Nle), aminoisobutyric acid (Aib), ornithine (Orn) and others do not appear in the standard twenty. Aib in particular is used to block DPP-4 cleavage in incretin analogs.

Fragments: number ranges

A range in parentheses denotes a contiguous piece of a longer parent sequence. ACTH(4-10) is residues 4 through 10 of adrenocorticotropic hormone. hGH(176-191) is the C-terminal fragment of human growth hormone marketed as AOD-9604. GRF(1-29) is the first 29 residues of growth hormone-releasing factor — the molecule usually sold as sermorelin, though the primary literature indexes it under the fragment notation rather than the trade name.

That mismatch between literature naming and commercial naming is a recurring obstacle when searching for source material. If a compound name returns little, try the fragment notation.

Terminal modifications

The C-terminus is normally a free carboxylic acid. An -NH₂ or -amide suffix means it has been amidated, which mimics many native hormones and improves stability. GRF(1-29)NH₂ is the amidated form.

N-terminal acetylation (Ac-) similarly caps the free amine. Both changes remove a charged terminus and alter both stability and receptor interaction.

DAC and acylation

Some names encode a half-life strategy rather than a sequence change. DAC stands for Drug Affinity Complex — a maleimide group that forms a covalent bond with cysteine-34 of serum albumin, giving a much longer circulating half-life. This is why “CJC-1295 with DAC” and “CJC-1295 without DAC” are pharmacokinetically different despite sharing a core sequence; the latter is essentially modified GRF(1-29). Jetté and colleagues characterised the conjugation chemistry and its effect in rats (Endocrinology, 2005; PMID 15817669).

Fatty-acid acylation achieves a similar end non-covalently, using a lipid chain that binds albumin reversibly.

Salt forms and why they affect your calculations

Peptides with basic residues are usually isolated as salts. TFA (trifluoroacetate) is the default from reversed-phase purification. Acetate is used where TFA would interfere with an assay, since TFA is cytotoxic at sufficient concentration in cell culture.

The counter-ion contributes mass. Together with residual water, this is why net peptide content is typically 70–90% of vial weight, and why gravimetric concentration calculations need that figure rather than the nominal label weight.

Quick reference

• [Xⁿ] — substitution at position n
• D- — D-enantiomer, protease resistance
• (n-m) — fragment, residues n through m
• -NH₂ — amidated C-terminus
• Ac- — acetylated N-terminus
• DAC — albumin-binding conjugate
• TFA / acetate — salt form

Browse the research peptide catalogue, or read our guide to reading a certificate of analysis.

All products referenced are supplied for laboratory research use only and are not approved for human consumption, clinical, or veterinary use.