Sandbox 32: Difference between revisions

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=='''Catalytic Mechanism'''==

As a sulfhydryl protease, ~~Papain~~ has a catalytic site with three important residues --Cysteine-25, Histidine-159,and Asparganine176 (4). The catalytic site is located in the <scene name='Sandbox_32/Binding_cleft/2'>binding cleft</scene> between the L and R domains of the protein The <scene name='Sandbox_32/Catalytic_site/1'>catalytic site</scene> centers around Cysteine-25 as it is a sulfhydryl protease. Sulfur on the cysteine will nucelophilically attack its substrate. Histidine acts to deprotonate sulfur (Cys-25), allowing it to be negatively charged. Once sulfur attacks the peptide,the tetrahedral intermediate is stabilized by a proposed oxyanion hole, specifically by asparganine (Asn-176) (1). The charged imidazolium ion of papain will in turn protanate the nitrogen in the peptide bond, releasing the C-terminal part of the peptide (5). Water enters the active site and ultimately regenerates the enzyme and allowing for the release of the N-terminal portion of the cleaved peptide.

As a sulfhydryl protease, papain has a catalytic site with three important residues --Cysteine-25, Histidine-159,and Asparganine176 (4). The catalytic site is located in the <scene name='Sandbox_32/Binding_cleft/2'>binding cleft</scene> between the L and R domains of the protein The <scene name='Sandbox_32/Catalytic_site/1'>catalytic site</scene> centers around Cysteine-25 as it is a sulfhydryl protease. Sulfur on the cysteine will nucelophilically attack its substrate. Histidine acts to deprotonate sulfur (Cys-25), allowing it to be negatively charged. Once sulfur attacks the peptide,the tetrahedral intermediate is stabilized by a proposed oxyanion hole, specifically by asparganine (Asn-176) (1). The charged imidazolium ion of papain will in turn protanate the nitrogen in the peptide bond, releasing the C-terminal part of the peptide (5). Water enters the active site and ultimately regenerates the enzyme and allowing for the release of the N-terminal portion of the cleaved peptide.

Papain is very non-specific in the type of peptide bonds that it cleaves. It will cleave bonds of most basic amino acids. It will also cleave after leucine or glycine residues and will hydrolyze esters and amides (3).

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=='''Inhibition'''==

Papain is inactivated by oxygen iodine, hydrogen peroxide, and EDTA (4). Also, it is is irreversibly inhibited by N-ethylmaleimide and iodoacetate. Other inhibitors of ~~Papain~~ are <scene name='Sandbox_32/Inhibition/1'>ICP</scene> (inhibitor of cysteine protease) and <scene name='Sandbox_32/Khq/1'>ZLFG-DAM </scene> (1). With ZLFG-DAM(diazomethylketone), the methylene carbon will covalently bind to the cysteine-25 carbon and the hydrophobic pocket near the active site will also be inhibited (1).

Papain is inactivated by oxygen iodine, hydrogen peroxide, and EDTA (4). Also, it is is irreversibly inhibited by N-ethylmaleimide and iodoacetate. Other inhibitors of papain are <scene name='Sandbox_32/Inhibition/1'>ICP</scene> (inhibitor of cysteine protease) and <scene name='Sandbox_32/Khq/1'>ZLFG-DAM </scene> (1). With ZLFG-DAM(diazomethylketone), the methylene carbon will covalently bind to the cysteine-25 carbon and the hydrophobic pocket near the active site will also be inhibited (1).

This scene should show the contacts between papain and its inhibitor <scene name='Sandbox_32/Inhibitor/1'>ZLFG-DAM</scene>

Water and methanol can be considered other ligands to ~~Papain~~. When obtaining the crystal structure of the enzyme, the solvent becomes part of the stabilized structure. Another ligand that can be considered for ~~Papain~~ is water. Water molecules play an important role in maintaining structural stability. There are 21 water molecules that are located in contact areas between adjacent papain molecule (2).

Water and methanol can be considered other ligands to papain. When obtaining the crystal structure of the enzyme, the solvent becomes part of the stabilized structure. Another ligand that can be considered for papain is water. Water molecules play an important role in maintaining structural stability. There are 21 water molecules that are located in contact areas between adjacent papain molecule (2).

=='''References'''==

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@@ Line 13: / Line 13: @@
 =='''Catalytic Mechanism'''==
-As a sulfhydryl protease, Papain has a catalytic site with three important residues --Cysteine-25, Histidine-159,and Asparganine176 (4). The catalytic site is located in the <scene name='Sandbox_32/Binding_cleft/2'>binding cleft</scene> between the L and R domains of the protein  The <scene name='Sandbox_32/Catalytic_site/1'>catalytic site</scene> centers around Cysteine-25 as it is a sulfhydryl protease. Sulfur on the cysteine will nucelophilically attack its substrate. Histidine acts to deprotonate sulfur (Cys-25), allowing it to be negatively charged. Once sulfur attacks the peptide,the tetrahedral intermediate is stabilized by a proposed oxyanion hole, specifically by asparganine (Asn-176) (1). The charged imidazolium ion of papain will in turn protanate  the nitrogen in the peptide bond, releasing the C-terminal part of the peptide (5). Water enters the active site and ultimately regenerates the enzyme and allowing for the release of the N-terminal portion of the cleaved peptide.
+As a sulfhydryl protease, papain has a catalytic site with three important residues --Cysteine-25, Histidine-159,and Asparganine176 (4). The catalytic site is located in the <scene name='Sandbox_32/Binding_cleft/2'>binding cleft</scene> between the L and R domains of the protein  The <scene name='Sandbox_32/Catalytic_site/1'>catalytic site</scene> centers around Cysteine-25 as it is a sulfhydryl protease. Sulfur on the cysteine will nucelophilically attack its substrate. Histidine acts to deprotonate sulfur (Cys-25), allowing it to be negatively charged. Once sulfur attacks the peptide,the tetrahedral intermediate is stabilized by a proposed oxyanion hole, specifically by asparganine (Asn-176) (1). The charged imidazolium ion of papain will in turn protanate  the nitrogen in the peptide bond, releasing the C-terminal part of the peptide (5). Water enters the active site and ultimately regenerates the enzyme and allowing for the release of the N-terminal portion of the cleaved peptide.
 Papain is very non-specific in the type of  peptide bonds that it cleaves. It will cleave bonds of most basic amino acids. It will also cleave after leucine or glycine residues and will hydrolyze esters and amides (3).
@@ Line 19: / Line 19: @@
 =='''Inhibition'''==
-Papain is inactivated by oxygen iodine, hydrogen peroxide, and EDTA (4).  Also, it is is irreversibly inhibited by N-ethylmaleimide and iodoacetate. Other inhibitors of Papain are <scene name='Sandbox_32/Inhibition/1'>ICP</scene> (inhibitor of cysteine protease) and <scene name='Sandbox_32/Khq/1'>ZLFG-DAM </scene> (1). With ZLFG-DAM(diazomethylketone), the methylene carbon will covalently bind to the cysteine-25 carbon and the hydrophobic pocket near the active site will also be inhibited (1).
+Papain is inactivated by oxygen iodine, hydrogen peroxide, and EDTA (4).  Also, it is is irreversibly inhibited by N-ethylmaleimide and iodoacetate. Other inhibitors of papain are <scene name='Sandbox_32/Inhibition/1'>ICP</scene> (inhibitor of cysteine protease) and <scene name='Sandbox_32/Khq/1'>ZLFG-DAM </scene> (1). With ZLFG-DAM(diazomethylketone), the methylene carbon will covalently bind to the cysteine-25 carbon and the hydrophobic pocket near the active site will also be inhibited (1).
 This scene should show the contacts between papain and its inhibitor <scene name='Sandbox_32/Inhibitor/1'>ZLFG-DAM</scene>
-Water and methanol can be considered other ligands to Papain. When obtaining the crystal structure of the enzyme, the solvent becomes part of the stabilized structure. Another ligand that can be considered for Papain is water. Water molecules play an important role in maintaining structural stability. There are 21 water molecules that are located in contact areas between adjacent papain molecule (2).
+Water and methanol can be considered other ligands to papain. When obtaining the crystal structure of the enzyme, the solvent becomes part of the stabilized structure. Another ligand that can be considered for papain is water. Water molecules play an important role in maintaining structural stability. There are 21 water molecules that are located in contact areas between adjacent papain molecule (2).
 =='''References'''==