Sandbox 38: Difference between revisions

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= '''Papain''' =
= '''Papain''' =


<StructureSection load='9PAP' size='500' side='right' caption=


== '''Function:''' ==
==Introduction==
[[Image:Papain_cartoon.png|200px|left|thumb|Cartoon Peak at Pepsin]]
 
DID YOU KNOW?
 
<scene name='Sandbox_35/Papain/1'>Papain</scene>. Meat tenderizer. Old time home remedy for insect, jellyfish, and stingray stings<ref>[http://www.ameriden.com/products/advanced-digestive-enzyme/] Ameridan International</ref>. Who would have thought that a sulfhydryl protease from the latex of the papaya fruit, ''Carica papaya'' and ''Vasconcellea cundinamarcensis'' would have such a practical application beyond proteopedia?


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.


== '''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.
This protease belongs to an extended family of aminopeptidases, dipeptidyl peptidases, endopeptidases, and other enzymes having both exo- and endo-peptidase activity. The inactivated zymogen with N-terminal propeptide regions - helping to stabilize against alkalinity and enabling proper folding - is activated through removal of the propeptide regions <ref>PMID: 7845226</ref><ref>PMID: 12188906</ref>.


== '''Composition of Papain:''' ==
<StructureSection load='9pap' size='500' side='right' caption='Structure of Papain (PDB entry [[9PAP]])' scene=''>
==Structure==
Its polypeptide chain consists of 212 amino acid residues folded to form a groove between its two domains containing the active site.
<scene name='Sandbox_35/Secondary_structure_papain/2'>secondary structure</scene>


Papain consists primarily of carbon, nitrogen, sulfur, and oxygen.  The composition of Papain can be viewed, as carbon is labled gray, oxygen red, nitrogen blue, and sulfur yellow. There are three 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 <scene name='Sandbox_38/Charge/3'>charged residues</scene> 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.
<scene name='Sandbox_35/2nd_struc_papain_beta/2'>beta sheets</scene>


== '''Hydrophobicity and Hydrophilicity:''' ==
<scene name='Sandbox_35/2nd_struc_papain_helix/2'>alpha helix</scene> <ref name="9PAP PDB">[http://www.pdb.org/pdb/explore/explore.do?structureId=9PAP]9PAP PDB</ref>


These charged residues contribute to the overall hydrophobicity (water hating) and hydrophilicity (water loving) portions of the enzyme, as the <scene name='Sandbox_38/Hydrophobic_and_polar_residues/2'>hydrophobic and hydrophilic regions</scene> 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.  <scene name='Sandbox_38/Papain_ligand_binding/1'>ligands of Papain</scene>
<scene name='Sandbox_35/Active_site_papain/3'>active site</scene> <ref>PMID: 8140097</ref>
<scene name='Sandbox_38/Hydrophobic_residues/1'>Hydrophobic Residues</scene>.
<scene name='Sandbox_35/Active_site_asp_158_papain/1'>TextToBeDisplayed</scene>
 
===Distribution of Residues===
<scene name='Sandbox_35/Papain_acid_and_basic_residues/1'>acidic and basic residues</scene>
 
<scene name='Sandbox_35/Hydrophobicity_papain/3'>polar and non-polar residue</scene>
 
<scene name='Sandbox_35/Papain_polar/1'>polar residues</scene>
 
<scene name='Sandbox_35/Nonpolar_papain/2'>non-polar residues</scene>
 
===Ligands interactions===
<scene name='Sandbox_35/Cathepsin_l_specific_inhibitor/2'>Cathepsin L specific inhibitor</scene>
Primarily hydrogen bonds with non-water and hydrophobic interactions
 
<scene name='Sandbox_35/Cathepsin_interaction/3'>interaction</scene>
</StructureSection>
</StructureSection>
==Catalytic Mechanism==
[[Image:Papainmech6.jpg|200px|left|thumb| General mechanism of papain catalysis<ref>[http://chemistry.umeche.maine.edu/CHY431/Peptidase10.html] University of Maine</ref>.]]
==References==
<references />
<ref group="xtra">PMID:8140097</ref>
http://www.pdb.org/pdb/explore/explore.do?structureId=2PAD
• Show the secondary structures.
• Compare the distribution of polar residues to that of nonpolar residues.
• Highlight the active site.
• If you can find a PDB file of the enzyme that contains a pseudo-substrate (may be inhibitor), highlight it.
• Show the contacts or attractions that are present between the pseudo-substrate and the protein, and if the enzyme has multiple subunits, show the contacts between the subunits.
• Identify any other ligands that are present in the structure and the types of contacts that are present between them and the protein
http://proteopedia.org/wiki/index.php/Sandbox_55#cite_note-18
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