Sandbox 36

From Proteopedia

Papain

Introduction

Papain is a sulfhydryl protease derived from the papaya fruit. Papain has many varied and important commercial uses. It is often used as a meat tenderizer because it can hydrolyze the peptide bonds of collagen, elastin, and actomyosin. It is also used in contact lens solution to remove protein deposits on the lenses. Papain also has many medical uses and is used to treat pain, swelling, and fluid retention following trauma and surgery. More commonly, papain is used as a digestive supplement.

Structure

Papain consists of a single polypeptide chain of 212 amino acid residues. As with all proteins, folding to form secondary and tertiary structures is largely determined by the interactions of the to exclude water. 55 of these residues form 7 and 45 residues form 17 strands. Besides these structures, the secondary structure of papain is irregular. The protein's tertiary structure consists of two domains divided by a cleft in which the active site resides.

Catalytic Diad

The is located in the cleft between the two domains. The active site contains a made up of Cysteine-25 and Histidine-159. Aspartate-158 also plays a role in catalysis but it is not considered part of the diad. Papain's active site can accommodate seven amino acids of a substrate. When the peptide is cleaved, the first four resides reside on the amino side of the peptide bond while the other three reside on the carboxyl side. Papain prefers to cleave at: (hydrophobic)-(Arg or Lys)- cleaves here -(not Val). Hydrophobic is Ala, Val, Leu, Ile, Phe, Trp, or Tyr.

Catalytic Inhibitors

Stefin B is acts as competitive inhibitor to cysteine proteases that binds tightly but reversibly to the papain active site. Stefin inhibitors are characterized by M_r of about 11,000, no disulfphie bonds and no associated carbohydrates.

In Stefin B, the Gly9 residue along with two hairpin loops form a "wedge" complementary to the active site groove of papain. This wedge makes extensive and tight interactions with papain and a total of 128 intermolecular atom-atom interactions occur. Met6-Pro11, Gln53-Asn59, Gln101-His104 and Tyr124-Phe125 are all segments on the wedge that all have some interaction to the enzyme though not always direct. Fruther Met7, Ser8, Val55, Ala56 and Tyr124 of the inhibitor are involved contact with the enzyme. All residues from the base and both sides of the active site cleft are involved in the complex with the inhibtor (Trp 177, Ser21, Cys63, CYm25). Additionally there are many solvent mediated plar interactions between stefin and papain.