Sandbox 38

Papain

spinqualitylabelsall models Structure of HMG-CoA reductase (PDB entry 1dq8) Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Introduction: Papain is a protease derived from the latex of the papaya fruit. The molecule consists of 212 amino acid residues that contribute to a single polypeptide chain. This chain, like all other proteins, contains a 3' Carbon and a 5' Nitrogen terminus. The red end of the protein indicates the 3' Carbon end, while the blue end indicates the 5' Nitrogen terminal. The varying colors in between are merely used to show the progression between the two terminals. The secondary structure of this molecule consists of 25% alpha helices, seen as pink "rockets", and 21% beta sheets, seen as orange "planks" . Traditionally, Papain has be used as a commercial meat tenderizer. This enzyme also has some medicinal uses, as it has be been used in wound debridement, and is ocassionally administered as a dietary supplement. This enzyme is able to aid in digestive problems, as it is able to break down food so it is easier to digest. Function: This hydrolytic enzyme is able to break peptide bonds through the deprotonation of Cys-25 by His-159, with the help of Aspartate-125, which stabilizes the Histadine ring in order for this deprotonation to take place. The Cys-25 residue is then able to perform a nucleophilic attack on the carbonyl carbon of the peptide backbone, freeing the amino terminal of the peptide, forming a covalent intermediate. Next, the enzyme is deacylated by water, and the carboxy-terminal portion of the peptide is released. Catalytic Mechanism General mechanism of papain catalysis. History: Papain was originally discovered during the colonial period in Congo. The native inhabitants discovered that wrapping their elephant meat in papaya leaves helped to tenderize the meat. While they did not know the direct cause, this was when the proteolytic enzyme was first discovered. The active binding site of this enzyme was first discovered by Drenth et al., through the crystallographic analysis of the enzymes structure. Composition of Papain: Papain consists primarily of carbon, nitrogen, sulfur, and oxygen. The composition of the enzyme can be view, as carbon is labled gray, oxygen red, nitrogen blue, and sulfur yellow. There are three disulfide bridges that contribute to the structure of Papain. These bonds are indicated by their yellow color, as they link particular cysteine residues. Throughout this enzyme, there are specific charged residues, indicating the most polar portions of the molecule. These charged residues can be visualized, as the cationic residues are blue in color, while the anionic residues are red. Partially charged residues are simply lighter in color. It is interesting to note that nearly all of these charged residues are located on the outer portion of the molecule in order to interact with the surrounding environment. Hydrophobicity and Hydrophilicity: These charged residues contribute to the overall hydrophobicity (water hating) and hydrophilicity (water loving) portions of the enzyme, as the hydrophobic and hydrophilic regions are a huge factor in determining protein folding. As mentioned before, the charged, hydrophilic, portions of the enzyme are primarily located on the out portion of the molecule. The polar amino acids are indicated by a purple color, while the hydrophobic residues are gray. ligands of Papain Hydrophobic Residues.