N-Terminal Acetylation and C-Terminal Amidation
A peptide chain has two ends, and both are frequently modified. The changes are small in mass and large in consequence, and they are among the easiest things to get wrong when comparing a certificate against a sequence.
What each modification is
C-terminal amidation replaces the terminal carboxyl group with an amide. The written sequence gains a trailing NH2 and the molecule loses one negative charge. The mass difference from the free acid is roughly one dalton lower.
N-terminal acetylation caps the terminal amine with an acetyl group. The molecule loses one positive charge and gains 42 daltons.
Both occur naturally as post-translational modifications, and both are deliberately reproduced in synthesis when the target sequence carries them.
What capping changes
Removing a charged terminus alters the net charge, which shifts the isoelectric point and with it the pH at which the peptide is least soluble. Isoelectric point and pH-dependent solubility covers that relationship.
It also removes a recognition point. Aminopeptidases and carboxypeptidases act on free termini, and a capped terminus is not a substrate for them. This is the structural reason terminal modification appears so often in analog design, alongside the other alterations covered in peptide half-life and analog modifications.
Why the free acid is a different compound
An amidated peptide and its free-acid counterpart have the same residue sequence and differ by about one dalton. They are nonetheless different molecules with different charge, different chromatographic behaviour and different registry numbers.
The one-dalton gap is small enough that distinguishing them on a mass spectrum depends on resolution and on comparing like with like — monoisotopic against monoisotopic, average against average. Monoisotopic and average mass covers why that distinction matters at exactly this scale.
Sermorelin is the familiar example in this catalogue: GHRH(1-29) carries a C-terminal amide, and the free-acid form is a distinct compound. Sermorelin as the reference GHRH analog covers the sequence.
How they appear in nomenclature
Amidation is written as a trailing NH2 after the final residue. Acetylation is written as Ac- before the first. A sequence given without either notation is, by convention, the free acid with a free amine — though the convention is not universally observed, which is why the calculated mass on a certificate is more reliable than the way a name is written.
The heptapeptide commonly sold under a trade name illustrates both problems at once: it is acetylated, it is a fragment rather than the parent protein, and the trade name says neither. Thymosin beta-4 and the fragment covers that case, and peptide nomenclature covers the conventions generally.
All material is supplied for laboratory research use only. It is not a drug, not a supplement, and not for use in humans or animals.
