Proteases are often described simply as enzymes that break peptides down. That description misses useful detail: the position of a cut, the resulting fragments and the evidence for the event all matter. A cleavage claim should identify a reaction, not merely attach the word unstable to a molecule.
Identify the bond being cleaved
NC-IUBMB uses peptidase for an enzyme that hydrolyses peptide bonds, with protease as a synonymous general term. Endopeptidases act within a polypeptide chain; exopeptidases act near its ends. The distinction describes where the enzyme acts, rather than a universal rate of breakdown.NC-IUBMB — Enzymes acting on peptide bonds (opens in a new tab)
| Type | Conceptual location |
|---|---|
| Internal cleavage | A peptide bond within the chain |
| Terminal cleavage | A peptide bond near an accessible chain end |
A reported cut changes the identity of the intact chain being followed. It does not mean that every residue has instantly become a free amino acid. Read the identified products, if supplied, before describing how extensively the material was broken down.
Read positions relative to the cut
Cleavage-site notation places P1 immediately before the cut and P1′ immediately after it when the substrate is written from N-terminus to C-terminus. P2 and P2′ are the next residues outward. These labels describe positions relative to a chosen bond, not fixed residue numbers for the whole molecule.NC-IUBMB — Enzymes acting on peptide bonds (opens in a new tab)
Take the invented sequence Ala–Gly–Lys–Ser–Val and an explicitly proposed cut between Lys and Ser. In that illustration, Lys is P1, Ser is P1′, Gly is P2 and Val is P2′. Lys also happens to be residue 3 in the full sequence. P1 and residue 3 therefore refer to the same residue using different numbering systems.
If the proposed cut moves, the P labels move with it. Keep the complete sequence numbering alongside the local cleavage notation when comparing diagrams, especially when papers use fragments of different lengths.
A sequence preference is not a universal guarantee
Peptidase specificity can depend on residues around the bond and on substrate conformation. A single preferred residue is therefore an incomplete description of substrate recognition. The nomenclature guidance explicitly recognises this complexity.NC-IUBMB — Enzymes acting on peptide bonds (opens in a new tab)
A database pattern can be useful for asking where cleavage might occur, but an untested sequence match remains a prediction. Conversely, failing to find one familiar motif does not establish resistance to every protease. Those conclusions would require evidence covering the relevant enzymes and conditions.
Distinguish observed sites from inferred ones
MEROPS records substrate and cleavage information and explains its evidence annotations. Its substrate legend distinguishes physiological, non-physiological and synthetic substrates, and identifies evidence types such as mass spectrometry and N-terminal sequencing. Those distinctions help a reader understand what an entry represents.EMBL-EBI MEROPS — Specificity and substrate features (opens in a new tab)EMBL-EBI MEROPS — Substrate evidence key (opens in a new tab)
A cleavage observed with a synthetic test substrate is evidence for that experiment. It should not silently become proof that an intact biological precursor is cut in the same way in a living system. Follow the original reference for the substrate and experimental context.
Likewise, disappearance of an intact-peptide signal and identification of a specific fragment are different observations. If the study reports only the first, avoid supplying an unmeasured fragment or naming a responsible enzyme on its behalf.
Describe cleavage without overextending it
- Name the enzyme and substrate form where established.
- Locate the bond using sequence numbering and local site notation.
- Distinguish a measured product from a proposed product.
- Keep the experimental setting and time separate from storage or clinical claims.
A precise statement about one supported cleavage event is more useful than saying a peptide is generally fragile. It tells a reader what changed, where it changed and what evidence supports the explanation. Detailed stability measurements can then address how quickly and under which conditions that event matters.
Sources and further detail
- NC-IUBMB — Enzymes acting on peptide bonds (opens in a new tab)
Nomenclature preamble defining peptidases, terminal/internal cleavage and substrate-position notation.
- EMBL-EBI MEROPS — Specificity and substrate features (opens in a new tab)
Database documentation on observed cleavage sites, specificity representations and substrate evidence.
- EMBL-EBI MEROPS — Substrate evidence key (opens in a new tab)
The table legend distinguishes physiological, non-physiological and synthetic substrates and evidence codes. No calpain-specific rate is inferred.
Sources checked 19 September 2026. Worked examples are illustrative unless a supplied report is explicitly identified. This article has not undergone independent scientific peer review.