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Endopeptidases are enzymes that catalyze the hydrolysis of internal peptide bonds and exopeptidases are the enzymes which catalyze the hydrolysis of N- or C-terminal residues.

Endopeptidases and exopeptidases are collectively called peptidases. Polypeptides can be fragmented using a variety of endopeptidases like Trypsin, Elastase, Thermolysin etc.

The sequence of the peptide given above is:

Asn-Met-Thr-Gln-Gly-Arg-Cys-Lys-Pro-Val-Asn-Thr-Phe-Val-His-Glu-Pro-Leu-Val-Asp-Val-Gln-Asn-Val-Cys-Phe-Lys-Glu

Trypsin cleaves peptide bonds on the carboxyl terminus (on the C side) of the positively charged residues Lysine (Lys) and Arginine (Arg), only if the following residue is not Proline (Pro).

By using trypsin, following 3 fragments are obtained.

3. Glu

Chymotrypsin cleaves peptide bonds on the carboxyl terminus (on the C side) of the bulky hydrophobic residues i.e., Phenylalanine (Phe), Tryptophan (Trp) and Tyrosine (Tyr), only if the following residue is not Proline (Pro).

By using chymotrypsin following 3 fragments are obtained.

1. Asn-Met-Thr-Gln-Gly-Arg-Cys-Lys-Pro-Val-Asn-Thr-Phe
2. Val-His-Glu-Pro-Leu-Val-Asp-Val-Gln-Asn-Val-Cys-Phe
3. Lys-Glu

Elastase cleaves peptide bonds on the carboxyl terminus (on the C side) of the small neutral residues i.e., Alanine (Ala), Glycine (Gly), Serine (Ser) and Valine (Val) only if the following residue is not Proline (Pro).

By using chymotrypsin, following 5 fragments are obtained.

1. Asn-Met-Thr-Gln-Gly
2. Arg-Cys-Lys-Pro-Val
3. Asp-Val
4. Gln-Asn-Val
5. Cys-Phe-Lys-Glu

Thermolysin cleaves the peptide bonds on the amino terminus (on the N side) of residues Isoleucine (Ile), Methionine (Met), Phenylalanine (Phe), Tryptophan (Trp), Tyrosine (Tyr), Valine (Val), only if the preceding residue is not Proline (Pro) and occasionally cleaves the residues Alanine (Ala), Asparagine (Asp), Histidine (His) and Threonine (Thr).

By using Thermolysin, following 9 fragments are obtained.

1. Asn
2. Met-Thr-Gln-Gly-Arg-Cys-Lys-Pro-Val-Asn-Thr
3. Phe
4. Val
5. His-Glu-Pro-Leu
6. Val-Asp
7. Val-Gln-Asn
8. Val-Cys
9. Phe-Lys-Glu

Pepsin cleaves the peptide bonds on the amino terminus (on the N side) of residues leucine (Leu), Phenylalanine (Phe), Tryptophan (Trp), and Tyrosine (Tyr), only if the preceding residue is not Proline (Pro) but it can cleave at other residues also as it is quite non-specific.

By using Pepsin, following 3 fragments are obtained but we can get more 3 as it is highly non-specific.

1. Asn-Met-Thr-Gln-Gly-Arg-Cys-Lys-Pro-Val-Asn-Thr
2. Phe-Val-His-Glu-Pro-Leu-Val-Asp-Val-Gln-Asn-Val-Cys
3. Phe-Lys-Glu

It cleaves peptide bonds on the carboxyl terminus (on the C side) of Glutamic acid (Glu). By usingendopeptidase V8following 2 fragments are obtained.

1. Asn-Met-Thr-Gln-Gly-Arg-Cys-Lys-Pro-Val-Asn-Thr-Phe-Val-His-Glu
2. Pro-Leu-Val-Asp-Val-Gln-Asn-Val-Cys-Phe-Lys-Glu

Thus, Thermolysin would produce most fragments and endopeptidase V8 would produce the fewest fragments.