Sandbox 34: Difference between revisions

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=== Introduction ===

'''Papain''' is a [[cysteine protease]], also known as '''papaya proteinase I''', from the peptidase C1 family ~~with~~ E.C. 3.4.22.2. It functions as a hydrolase, endopeptidase, and thiol protease.<ref name="UniProt">http://www.uniprot.org/uniprot/P00784</ref> Its optimal activity values for pH lie between 6.0 and 7.0, and 65 °C as its optimal temperature for activity. Its pI values are 8.75 and 9.55. Papain is best visualized at a wavelength of 278 nm. <ref>http://www.sigmaaldrich.com/life-science/metabolomics/enzyme-explorer/analytical-enzymes/papain.html</ref> Naturally found in the latex of the papaya fruit, one of the most common uses of papain is as a meat tenderizer because of its ability to hydrolyze esters and amides.<ref>IUBMB Enzyme Nomenclature: www.chem.qmul.ac.uk/iubmb/enzyme/EC3/4/22/2.html</ref> Another common use is as a digestive aid. Papaya is commonly referenced as a preferred fruit for those suffering from gastroesophageal reflux disease due to its ability to help the the stomach with digestion of complex proteins.

'''Papain''' is a cysteine protease, also known as '''papaya proteinase I''', from the peptidase C1 family referenced as E.C. 3.4.22.2. It functions as a hydrolase, endopeptidase, and thiol protease.<ref name="UniProt">http://www.uniprot.org/uniprot/P00784</ref> Its optimal activity values for pH lie between 6.0 and 7.0, and 65 °C as its optimal temperature for activity. Its pI values are 8.75 and 9.55. Papain is best visualized at a wavelength of 278 nm. <ref>http://www.sigmaaldrich.com/life-science/metabolomics/enzyme-explorer/analytical-enzymes/papain.html</ref> Naturally found in the latex of the papaya fruit, one of the most common uses of papain is as a meat tenderizer because of its ability to hydrolyze esters and amides.<ref>IUBMB Enzyme Nomenclature: www.chem.qmul.ac.uk/iubmb/enzyme/EC3/4/22/2.html</ref> Another common use is as a digestive aid. Papaya is commonly referenced as a preferred fruit for those suffering from gastroesophageal reflux disease due to its ability to help the the stomach with digestion of complex proteins.

=== History ===

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=== Ligands ===

Papain binds many <scene name='Sandbox_34/Entire_protein_with_ligands/2'>methanol molecules</scene> via hydrogen bonding.

Papain binds many <scene name='Sandbox_34/Entire_protein_with_ligands/2'>methanol molecules</scene> via hydrogen bonding. In addition to the methanol molecules, papain also has an interesting hydrogen bonding with water molecules. A refined crystal structure of papain, involving a restrained least-squares procedure at 1.65 A, with an estimated accuracy of 0.1 A, revealed that water forms something almost like a hydration shell around individual molecules of papain. The interaction of papain with these water molecules leads to less interaction between papain molecules, and contributes to the stability of the crystal structure of papain.<ref name="Structure" />

=== Specificity ===

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 === Introduction ===
 <Structure load='9pap' size='500' frame='true' align='right' caption='Papain' scene='Sandbox_34/Entire_protein_with_ligandscys/1' />
-'''Papain''' is a [[cysteine protease]], also known as '''papaya proteinase I''', from the peptidase C1 family with E.C. 3.4.22.2. It functions as a hydrolase, endopeptidase, and thiol protease.<ref name="UniProt">http://www.uniprot.org/uniprot/P00784</ref> Its optimal activity values for pH lie between 6.0 and 7.0, and 65 °C as its optimal temperature for activity. Its pI values are 8.75 and 9.55. Papain is best visualized at a wavelength of 278 nm. <ref>http://www.sigmaaldrich.com/life-science/metabolomics/enzyme-explorer/analytical-enzymes/papain.html</ref> Naturally found in the latex of the papaya fruit, one of the most common uses of papain is as a meat tenderizer because of its ability to hydrolyze esters and amides.<ref>IUBMB Enzyme Nomenclature: www.chem.qmul.ac.uk/iubmb/enzyme/EC3/4/22/2.html</ref> Another common use is as a digestive aid. Papaya is commonly referenced as a preferred fruit for those suffering from gastroesophageal reflux disease due to its ability to help the the stomach with digestion of complex proteins.
+'''Papain''' is a cysteine protease, also known as '''papaya proteinase I''', from the peptidase C1 family referenced as E.C. 3.4.22.2. It functions as a hydrolase, endopeptidase, and thiol protease.<ref name="UniProt">http://www.uniprot.org/uniprot/P00784</ref> Its optimal activity values for pH lie between 6.0 and 7.0, and 65 °C as its optimal temperature for activity. Its pI values are 8.75 and 9.55. Papain is best visualized at a wavelength of 278 nm. <ref>http://www.sigmaaldrich.com/life-science/metabolomics/enzyme-explorer/analytical-enzymes/papain.html</ref> Naturally found in the latex of the papaya fruit, one of the most common uses of papain is as a meat tenderizer because of its ability to hydrolyze esters and amides.<ref>IUBMB Enzyme Nomenclature: www.chem.qmul.ac.uk/iubmb/enzyme/EC3/4/22/2.html</ref> Another common use is as a digestive aid. Papaya is commonly referenced as a preferred fruit for those suffering from gastroesophageal reflux disease due to its ability to help the the stomach with digestion of complex proteins.
 === History ===
@@ Line 20: / Line 20: @@
 === Ligands ===
-Papain binds many <scene name='Sandbox_34/Entire_protein_with_ligands/2'>methanol molecules</scene> via hydrogen bonding.
+Papain binds many <scene name='Sandbox_34/Entire_protein_with_ligands/2'>methanol molecules</scene> via hydrogen bonding. In addition to the methanol molecules, papain also has an interesting hydrogen bonding with water molecules. A refined crystal structure of papain, involving a restrained least-squares procedure at 1.65 A, with an estimated accuracy of 0.1 A, revealed that water forms something almost like a hydration shell around individual molecules of papain. The interaction of papain with these water molecules leads to less interaction between papain molecules, and contributes to the stability of the crystal structure of papain.<ref name="Structure" />
 === Specificity ===