Sandbox 30: Difference between revisions

Papain is a 23.4 kDa, 212 residue cysteine endopeptidase originating from the fruit of ''Carica papaya'', where it is present in significant amounts along with three other cysteine proteases, chymopapain, glycyl endopeptidase, and caricain<ref name="9PAP PDB">[http://www.pdb.org/pdb/explore/explore.do?structureId=9PAP] 9PAP PDB</ref><ref name="sigma">[http://www.sigmaaldrich.com/life-science/metabolomics/enzyme-explorer/analytical-enzymes/papain.html] Sigma Aldrich</ref><ref name="worthington">[http://www.worthington-biochem.com/pap/default.html] Worthington Biochemical Corporation</ref>.  Its action was first described by G.C. Roy in 1873.  It was studied intensively from the 1950s to the 1960s, during which time it became the second enzyme ever to have its structure determined by x-ray crystallography.  Finally, high resolution structural analysis in the 1980s allowed an accurate description of the enzyme's active site<ref name="worthington" />.  As an enzyme, papain displays very wide hydrolase activity, serving as a general amidase and esterase in addition to its protease activity.  As a protease, papain can hydrolyze bonds of basic amino acids, leucine, and glycine.  It shows preference for residues preceded by a large hydrophobic residue, but will not cleave if valine is present on the carboxyl side of a potential cleavage site.  In addition to being a very non-specific enzyme, papain is also unusually heat resistant, with maximal activity occurring at a temperature of 65° C.  These properties have led to use of papain in a large variety areas.  One of these areas is biological research, where papain is utilized in cell isolation.  It is also useful in immunological techniques because of its ability to cleave the connection between the crystallizable fragment domain and the immunoglobulin domain of antibodies<ref name="sigma" />.  Papain has also found use as an inflammation control agent, a digestive aid, and even a meat tenderizer<ref>[http://www.webmd.com/vitamins-supplements/ingredientmono-69-PAPAIN.aspx?activeIngredientId=69&activeIngredientName=PAPAIN] WebMD</ref>.

The secondary structure of papain consists of 7 <scene name='Sandbox_30/Papain_secondary_helices/3'>α helices</scene>, 17 <scene name='Sandbox_30/Papain_secondary_sheets/3'>β strands</scene>, all of which are antiparallel, and a large amount (about 50% of total residues) of <scene name='Sandbox_30/Papain_secondary_orf/4'>ordered non-repetitive structures</scene>.  The <scene name='Sandbox_30/Papain_rainbow/3'>rainbow coloration view</scene>, which goes from blue (amino terminus) to red (carboxyl terminus) is useful for tracing the order of these structures through the chain.  These secondary structures form as a result of favorable hydrogen bonding interactions within the polypeptide backbone.  Meanwhile, secondary structures are kept in place by hydrophobic interactions and hydrogen bonds between sidechains of adjacent structures.  For example, the <scene name='Sandbox_30/Papain_secondary_helices_1/1'>first helix</scene> (residues 25-42) is maintained as a result of <scene name='Sandbox_30/Papain_secondary_helices_hbond/3'>hydrogen bonds</scene> between backbone carbonyl atoms and the hydrogen on the amide nitrogen four residues away.  However, <scene name='Sandbox_30/Papain_secondary_heliceshbond2/1'>no hydrogen bonds</scene> are present between this helix and the rest of the protein, suggesting that this helix is coordinated entirely by hydrophobic interactions, which is reasonable given its place in the center of the enzyme.  As expected, the helix contains many <scene name='Sandbox_30/Papain_secondary_helix1_phobic/1'>hydrophobic residues</scene> (red residues are hydrophilic).  The tertiary structure of papain is also maintained by three <scene name='Sandbox_30/Papain_disulfides/3'>disulfide bonds</scene>, which connect <scene name='Sandbox_30/Papain_disulfides_22-63/1'>Cys-22 to Cys63</scene>,