Question

Consider the hypothetical serine protease below, which shows the specificity pockets. The S1 pocket has a glutamic acid in the bottom, the S2 pocket is small and hydrophobic, and the S1\' pocket is deep and hydrophobic. Suggest a 3 amino acid sequence that this protease would cleave and indicate between which sites the peptide bond would be broken.

Answer 1

Concepts and reason

Enzymes are the biological catalysts that enhance the rate of biological reactions by lowering the activation energy required for the reaction to take place without being itself consumed in the reaction. A French chemist, Anselme Payen first discovered the enzyme, diastase in the year, 1833. The word enzyme was first used by Wilhelm Kuhne in the year, 1877.

Fundamentals

Enzymes are mostly proteins by nature and are known to catalyze more than 5,000 biochemical reactions. The enzymes act on the substrate and convert it into product. The active site of the enzyme interacts with the substrate to form an enzyme substrate complex. Serine proteases are the enzymes that act on the peptide bonds between the proteins. Some examples of serine proteases include Chymotrypsin, trypsin, elastase, etc.

The given hypothetical structure is:

The given hypothetical structure contains the pockets S₁, S₂, and S1’. The S1 pocket has glutamic acid at its bottom. The S1’ is deep and hydrophobic that can accommodate bulky side chains. The S2 pocket is small and hydrophobic. Therefore, the sequence that the protease would cleave is Glycine-Lysine-Phenylalanine (Gly-Lys-Phe).

The cleavage takes place between the amino acid end and the carboxyl end of an amino acid sequence. The given sequence has amino acid end at the Si and carboxyl end at the S1’. Therefore, the cleavage occurs between S1 and S1’.

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