Proteolytic cleavage

Proteolytic cleavage is basically the process of breaking the peptide bonds between amino acids in proteins. This process is carried out by enzymes called peptidases, proteases or proteolytic cleavage enzymes.

Proteins often undergo proteolytic processing by specific proteolytic enzymes (proteases/peptidases) before final maturation of the protein. Proteins can also be cleaved as a result of intracellular processing of, for example, misfolded proteins. Another example of proteolytic processing of proteins is secretory proteins or proteins targeted to organelles, which have their signal peptide removed by specific signal peptidases before release to the extracellular environment or specific organelle.

Mentioned below, is a few processes where proteolytic enzymes act on a protein substrate.

• N-terminal methionine residues are often removed after translation.
• Signal peptides or targeting sequences are removed during translocation through a membrane.
• Viral proteins that were translated from a monocistronic mRNA are cleaved.
• Proteins or peptides can be cleaved and used as nutrients.
• Precursor proteins are often processed to yield the mature protein.

Proteolytic cleavage of proteins has shown its importance in laboratory experiments where it is often useful to work with specific peptide fragments instead of entire proteins.

Proteases also have commercial applications. As an example, proteases can be used as detergents for cleavage of proteinaceous stains in clothing.

The general nomenclature of cleavage site positions of the substrate were formulated by Schecter and Berger, 1967-68 [Schechter and Berger, 1967], [Schechter and Berger, 1968]. They designate the cleavage site between P1-P1', incrementing the numbering in the N-terminal direction of the cleaved peptide bond (P2, P3, P4, etc..). On the carboxyl side of the cleavage site numbering are likewise incremented (P1', P2', P3' etc. ). This is visualized in figure 4.1.

Proteases often have a specific recognition site where the peptide bond is cleaved. As an example, trypsin only cleaves at lysine or arginine residues, but it does not matter (with a few exeptions) which amino acid is located in position P1'(carboxyterminal of the cleavage site). Another example is, trombin which cleaves if an arginine is found in position P1 but not if at the same time an D or E is found in position P1'. See figure 4.2.

Bioinformatics approaches are used to identify potential peptidase cleavage sites. By scanning the amino acid sequence for patterns which match the corresponding cleavage site for the protease, fragments can be found. When identifying cleaved fragments it is of some importance to know a calculated molecular weight and isoelectric point.

Other useful resources

The Peptidase Database: http://merops.sanger.ac.uk/