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| {{Template:Oberholser_Sandbox_Reservation}} | | {{Template:Oberholser_Sandbox_Reservation}} |
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| | <Structure load='1AKE' size='500' frame='true' align='right' caption='Adenylate Kinase' scene='Matt's Beautiful Protein' /> |
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| ='''Papain'''= | | The <scene name='Sandbox_37/Matt_adenylate_kinase_37/1'>Adenylate Kinase</scene> protein is shown here with alpha helices (cyan) and beta sheets (green) surrounding the non-hydrolysable substrate analogue (orange). |
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| ==Introduction==
| | The <scene name='Sandbox_37/Matt_helix_beta_colored/1'>Secondary Structure</scene> of the protein is shown here with alpha helices (green) and beta sheets (blue) highlighted appropriately. |
| [[Image:Papaya.jpg | right| thumb| ''Carica papaya'']]
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| <scene name='Sandbox_37/Main_scene/1'>Papain</scene> is a cysteine protease that is stable and active under a wide range of conditions. The enzyme present in the leaves, latex, roots, and fruit of the papaya plant (''Carica papaya'').<ref>http://www.britannica.com/EBchecked/topic/441803/papain</ref> The papain proteins are synthesized as inactive precursors that become active within two minutes of the plant being wounded and the latex is expelled.<ref>http://www.worthington-biochem.com/pap/default.html</ref> The latex is dried and then purified to extract the active papain enzme. The enzyme was first studied and isolated in the 1960's. It has a 23.4kDa theoretical molecular weight and works at an optimum pH of 6-7 and optimum temperature of 60-70 degrees Celsius. | |
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| ==Structure==
| | The <scene name='Sandbox_37/Matt_hydrogen_bonds_good/1'>Hydrogen Bonds</scene> of chain A of the protein are highlighted in orange here. |
| <StructureSection load='9PAP' size='400' align='left' caption='Papain (9PAP)' scene=''></StructureSection>
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| Papain's three-dimensional structure is at 1.65 Angstrom resolution. It consists of one polypepetide chain that is made up of 212 amino acids residues. There are three <scene name='Sandbox_37/Papain_disulfide_bonds/1'>disulfide bonds</scene> present in the enzyme that maintains the protein's structure. Papain consists of 25% alpha helices and 21% beta sheets within its <scene name='Sandbox_37/Papain_beta-alpha/1'>secondary structure</scene>. Alpha helices are shown in red and beta sheets are shown in green. The enzyme's structure has a mixture of <scene name='Sandbox_37/Papain_hydrophobic/7'>hydrophobic residues</scene> shown in yellow and hydrophilic residues shown in purple. This corresponds to the protein's <scene name='Sandbox_37/Papain_polar/1'>polar residues</scene> shown in orange and nonpolar residues shown in green. Papain is naturally found with many <scene name='Sandbox_37/Ligand/3'>ligands</scene>. The majority are methanol molecules because the crystallization medium is 62% (w/w) methanol in water and only 29 out of 224 solvent molecules can be regarded with any certainty as methanol molecules.<ref>http://www.pdb.org/pdb/explore.do?structureId=9PAP</ref> Here, the enzyme's sulfhydryl group can also be seen which is necessary for the activity of the enzyme. <scene name='Sandbox_37/Papain_van_der_waals/1'>Van der Waals interactions</scene> and <scene name='Sandbox_37/Papain_hydrogen_bonds/1'>hydrogen bonds</scene> between the ligands and protein maintain the structural domains of papain. Water molecules are depicted as pink spheres.Twenty-one water molecules are located in contact areas between adjacent papain molecules.
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| ==Mechanism==
| | The <scene name='Sandbox_37/Matt_hydrophobic_good/1'>Hydrophobic Interactions</scene> are shown here in red. |
| [[Image:Papain mechanism.jpg | right| thumb| Mechanism of papain catalysis]]
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| Papain cleaves peptide bonds of basic amino acids, leucine, or glycine. It also hydrolyzes esters and amides.<ref>http://www.sigmaaldrich.com/life-science/metabolomics/enzyme-explorer/analytical-enzymes/papain.html</ref> Its mechanism of breaking peptide bonds takes place in its <scene name='Sandbox_37/Papain_active_site/1'>active site</scene>. The active site is in a cleft formed by the two distinct structural domains of the protein. The active site contains a catalytic diad of residues cysteine-25 and histidine-159. The asparagine-175 residue helps with orientation during catalysis. The catalytic diad is similar to the catalytic triad seen in most serine proteases. His-159 deprotonates cys-25, then cys-25 attacks the carbonyl of the peptide as a nucleophile. A water molecule then deacylates the enzyme and releases the peptide.
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| ==Inhibition==
| | The <scene name='Sandbox_37/Matt_hydrophilic_good/1'>Hydrophilic Interactions</scene> are shown here in black. |
| <Structure load='1pop' size='400' frame='true' align='right' caption='Papain with leupeptin inhibitor (1POP)' scene='' />
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| One inhibitor of papain is leupeptin. The carbonyl carbon of this <scene name='Sandbox_37/Papain_inhibitor/3'>inhibitor</scene> is covalently bound by the Cys-25 sulphur atom of papain and is tetrahedrally coordinated. The carbonyl oxygen atom of the inhibitor faces the oxyanion hole and makes hydrogen bond contacts with Gln-19 and Cys-25.<ref>http://www.pdb.org/pdb/explore/remediatedSequence.do?structureId=1POP¶ms.chainEntityStrategyStr=all</ref> The <scene name='Sandbox_37/Papain_inhibitor_van_der_waals/2'>van der Waals interactions</scene> and
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| <scene name='Sandbox_37/Papain_inhibitor_hydrogen_bond/1'>hydrogen bonds</scene> between papain and leupeptin keep the active site closed and the residues (shown in brown) can no longer catalyze.
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| ==Function== | | The <scene name='Sandbox_37/Matt_solvent/1'>Solvent</scene> , which is water, is shown here in red. Water's primary location is on the outer parts of the protein, or the hydrophilic regions. |
| Papain is used as a powdered meat tenderizer because of its ability to break down tough meat fibers. It can also be used as a treatment for jellyfish and bee stings because it can break down the protein toxins in the venom.<ref>http://en.wikipedia.org/wiki/Papain</ref> Papain can also digest immunoglobulins (antibodies) by breaking the two Fab fragments from the Fc fragment. This prevents the immunoglobulin's ability to promote agglutination.
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| [[Image:Ramachandran plot.JPG| right| thumb| Ramachandran plot of papain amino acid residues]]
| | The side chains that interact with the <scene name='Sandbox_37/Matt_ligand/1'>ligand</scene> are shown here in crimson. The interactions occur with the hydrophobic side chains. The rest of the protein is faded blue. |
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| ==References== | | The <scene name='Sandbox_37/Matt_catalytic_residues/1'>catalytic residues</scene> of this protein are shown here in lime green. |
| <references /> | |
