Structural Biochemistry/Proteins/Cutting Enzymes

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General Information[edit]

Some enzymes in the body are used to cleave or cut the peptide bonds in the polypeptides that make up proteins. These enzymes mostly operate by hydrolyzing the carboxy-terminal of the targeted amino acids. Specific enzymes target specific amino acids based on their physical or chemical properties such as polarity or hydrophilicity. This ability to shorten the polypeptides helps in sequencing proteins in Edman degradation. Since it is found that after utilizing Edman degradation sixty times the efficiency will decrease by 2%. By cleaving the polypeptides into shorter bonds it allows Edman degradation to keep an efficiency of 100%.

Enzymatic Cleavage[edit]

The following are enzymatic cleavages that mainly cleave at the carboxyl side of a residue. The only exception is the carboxypeptidase A by which will cleave at the amino side of a c-terminal amino acid.

Enzymatic Cleavage Cleavage Site
Trypsin Cleavage the peptide bonds at the carboxyl end of lysine and arginine residues. The exception to this is that lysine will not be cleaved if it is followed by a proline because proline transform the amine from primary amine to a secondary amine. Trypsin will only have hydrolysis with primary amines.
Clostripain Cleavage at the carboxyl side of arginine residues
Chymotrypsin Cleavage at the carboxyl side of tyrosine, tryptophan, phenylalanine, leucine, and methionine
Carboxypeptidase A Amino side of C-terminal amino acid EXCEPT for arginine, lysine, and proline
Staphyloccocal protease Cutting at the carboxyl side of aspartate and glutamate residue (for glutamate, certain conditions are applied)
Thrombin The carboxyl side of arginine


Cleavage at the carboxyl side of alanine and glycine

Chemical Cleavage[edit]

Some chemicals can be used to detect the presence of certain amino acids in the polypeptide. Some examples are following:

Enzymatic Cleavage Cleavage Site
Cyanobromide Cleavage at carboxyl side of methionine residues.
O-Iodosobenzoate Cutting at carboxyl side of tryptophan residues
Hydroxylamine Cutting at asparagine-glycine bonds
2-Nitro-5-thiocyanobenzoate Cleavage at the amino side of cysteine residues

In addition, Edman degradation technique can be used to determine the amino terminal of the polypeptide. Phenyl isothiocyanate reacts with the uncharged amino group to form phenylthiocarbamoyl derivative. Under mildly acidic condition, the cyclic derivative contained the N-terminal amino acid (phenylthiohydantoin (PTH)-amino acid)was released and therefore the identity was determined through chromatographic procedures. This technique can be used to determine the sequence of a short polypeptide by repeating the same reaction and yielding another PTH-amino acid complex, which can again be identified by chromatography.