Sandbox 39: Difference between revisions

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== Composition of Papain ==

Proteins only consist of certain elements: carbon, hydrogen, nitrogen, oxygen, and sulfur. Enzymes' primary structures allow them to fold optimally and interact with their substrates maximally in order to efficiently catalyze biological reactions. The <scene name='Sandbox_39/Elemental/2'>elemental composition</scene> of papain shows carbon atoms outlined in grey, oxygen atoms in red, nitrogen atoms in blue, and sulfur atoms in yellow.

Proteins only consist of certain elements: carbon, hydrogen, nitrogen, oxygen, and sulfur. Enzymes' primary structures allow them to fold optimally and interact with their substrates maximally in order to efficiently catalyze biological reactions. The <scene name='Sandbox_39/Elemental/2'>elemental composition</scene> of papain, seen to the right as a space-fill model, shows carbon atoms outlined in grey, oxygen atoms in red, nitrogen atoms in blue, and sulfur atoms in yellow.

In addition, the entirety of the secondary structure of papain can be traced from the <scene name='Sandbox_39/Elemental/3'>N- to C-terminus.</scene> As shown to the left, the red end begins the protein at the

N-terminus, and can be traced through the colors of the rainbow to the ~~purple~~ end at the C-terminus.

N-terminus, and can be traced through the colors of the rainbow to the blue end at the C-terminus.

== Active Site ==

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== Papain Inhibition ==

Substances that inhibit enzymes have sequences that resemble the normal substrate of that enzyme. Some substances that act to inhibit the enzymatic activity of papain are able to do so because of their structural and chemical similarity to polypeptides normally degraded by papain. One example of a papain inhibitor is cystatin. According to this model, the N terminal of the cystatin interacts with the active site and the S1-S3 sites of papain. At the same time, two hairpin loops bind to the S1’-S2’ sites. The interaction between systatin and papain can be seen below. The inactivation of the cysteine proteases, including papain, occurs by competitive, noncovalent, reversible inhibition.

Substances that inhibit enzymes have sequences that resemble the normal substrate of that enzyme. Some substances that act to inhibit the enzymatic activity of papain are able to do so because of their structural and chemical similarity to polypeptides normally degraded by papain.

[[Image:Inhibitor.jpg|~~center~~]]

One example of a papain inhibitor is cystatin. According to this model, the N terminal of the cystatin interacts with the active site and the S1-S3 sites of papain. At the same time, two hairpin loops bind to the S1’-S2’ sites. The interaction between systatin and papain can be seen below. The inactivation of the cysteine proteases, including papain, occurs by competitive, noncovalent, reversible inhibition.

[[Image:Inhibitor.jpg|left]]

<ref>Image from:

Hans-Hartwig Otto, and Tanja Schirmeister (1997) Cysteine Proteases and Their Inhibitors. Chemical Reviews. No. 97, 133-171.</ref>]]

Another example of a papain inhibitor is <scene name='Sandbox_39/Inhibitor/1'>ZLFG-DAM</scene>, a diazomethylketone inhibitor. As shown in the Jmol to the right, the methylene carbon atom of the inhibitor (shown as a grey sphere, is covalently bound to the Cys-25 of papain. The hydrophobic S2 pocket is occupied by the inhibitor's P2 side chain, shown as a pink chain. Extensive hydrogen bonding and hydrophobic interactions are responsible for the interaction of the inhibitor with the enzyme.

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@@ Line 32: / Line 32: @@
 == Composition of Papain ==
-Proteins only consist of certain elements: carbon, hydrogen, nitrogen, oxygen, and sulfur. Enzymes' primary structures allow them to fold optimally and interact with their substrates maximally in order to efficiently catalyze biological reactions.  The <scene name='Sandbox_39/Elemental/2'>elemental composition</scene> of papain shows carbon atoms outlined in grey, oxygen atoms in red, nitrogen atoms in blue, and sulfur atoms in yellow.
+Proteins only consist of certain elements: carbon, hydrogen, nitrogen, oxygen, and sulfur. Enzymes' primary structures allow them to fold optimally and interact with their substrates maximally in order to efficiently catalyze biological reactions.  The <scene name='Sandbox_39/Elemental/2'>elemental composition</scene> of papain, seen to the right as a space-fill model, shows carbon atoms outlined in grey, oxygen atoms in red, nitrogen atoms in blue, and sulfur atoms in yellow.
 In addition, the entirety of the secondary structure of papain can be traced from the <scene name='Sandbox_39/Elemental/3'>N- to C-terminus.</scene> As shown to the left, the red end begins the protein at the
-N-terminus, and can be traced through the colors of the rainbow to the purple end at the C-terminus.
+N-terminus, and can be traced through the colors of the rainbow to the blue end at the C-terminus.
 ==  Active Site ==
@@ Line 51: / Line 51: @@
 == Papain Inhibition ==
-Substances that inhibit enzymes have sequences that resemble the normal substrate of that enzyme. Some substances that act to inhibit the enzymatic activity of papain are able to do so because of their structural and chemical similarity to polypeptides normally degraded by papain. One example of a papain inhibitor is cystatin. According to this model, the N terminal of the cystatin interacts with the active site and the S1-S3 sites of papain. At the same time, two hairpin loops bind to the S1’-S2’ sites. The interaction between systatin and papain can be seen below. The inactivation of the cysteine proteases, including papain, occurs by competitive, noncovalent, reversible inhibition.
+Substances that inhibit enzymes have sequences that resemble the normal substrate of that enzyme. Some substances that act to inhibit the enzymatic activity of papain are able to do so because of their structural and chemical similarity to polypeptides normally degraded by papain.
-[[Image:Inhibitor.jpg|center]]
+One example of a papain inhibitor is cystatin. According to this model, the N terminal of the cystatin interacts with the active site and the S1-S3 sites of papain. At the same time, two hairpin loops bind to the S1’-S2’ sites. The interaction between systatin and papain can be seen below. The inactivation of the cysteine proteases, including papain, occurs by competitive, noncovalent, reversible inhibition.
+[[Image:Inhibitor.jpg|left]]
 <ref>Image from:
 Hans-Hartwig Otto, and Tanja Schirmeister (1997) Cysteine Proteases and Their Inhibitors. Chemical Reviews. No. 97, 133-171.</ref>]]
+Another example of a papain inhibitor is <scene name='Sandbox_39/Inhibitor/1'>ZLFG-DAM</scene>, a diazomethylketone inhibitor. As shown in the Jmol to the right, the methylene carbon atom of the inhibitor (shown as a grey sphere, is covalently bound to the Cys-25 of papain. The hydrophobic S2 pocket is occupied by the inhibitor's P2 side chain, shown as a pink chain. Extensive hydrogen bonding and hydrophobic interactions are responsible for the interaction of the inhibitor with the enzyme.