Sandbox 31: Difference between revisions

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Papain is formed from a peptide that is 212 amino acids in length.<ref>http://www.pdb.org/pdb/explore/explore.do?structureId=9PAP</ref> It consists of 25% <scene name='Sandbox_31/Alpha_helices/4'>Alpha helices</scene> and 21% <scene name='Sandbox_31/Beta_sheet/2'>Beta Sheet</scene>. The structure also consists of three <scene name='Sandbox_31/Disulfide/3'>Disulfide bonds</scene>(seen in yellow) between <scene name='Sandbox_31/Cys_with_labels/2'>Cysteine Residues</scene>. The disulfide bonds exist between Cys 63 and Cys 22, Cys 200 and Cys 153, and Cys 56 and Cys 95. Another important residue to the structure is Cysteine 25 which has a sulfhydryl group that plays a major role in the active site activity[[http://www.sigmaaldrich.com/life-science/metabolomics/enzyme-explorer/analytical-enzymes/papain.html]].

The <scene name='Sandbox_31/~~Hydrophobic_residues~~/2'>Hydrophobic Residues</scene> in papain are primarily located toward the inside of the enzyme or paired by hydrophobic interactions with other hydrophobic residues to exclude water. The <scene name='Sandbox_31/Polar_residues/1'>Polar Residues</scene> are located facing the exterior, in the active site, or paired with other charged residues(seen in orange). The polar residues seen in orange predominantly fill the space surrounding the exterior of the enzyme. This is because they are hydrophillic and interact with polar water molecules. The <scene name='Sandbox_31/Positive/1'>Negatively</scene> charged residues (shown in green) and the <scene name='Sandbox_31/Basic_positive/1'>Positively</scene> charged residues (shown in red) make up the polar residues. The charged and polar residues are hydrophilic therefore do not orient themselves to exclude water or solvent. The charged <scene name='Sandbox_31/Termini/4'>Termini</scene> face outward due to their hydrophilic nature.

The <scene name='Sandbox_31/Hydrophobic_residues2/1'>Hydrophobic Residues</scene>(seen in pink) in papain are primarily located toward the inside of the enzyme or paired by hydrophobic interactions with other hydrophobic residues to exclude water. The <scene name='Sandbox_31/Polar_residues/1'>Polar Residues</scene> are located facing the exterior, in the active site, or paired with other charged residues(seen in orange). The polar residues seen in orange predominantly fill the space surrounding the exterior of the enzyme. This is because they are hydrophillic and interact with polar water molecules. The <scene name='Sandbox_31/Positive/1'>Negatively</scene> charged residues (shown in green) and the <scene name='Sandbox_31/Basic_positive/1'>Positively</scene> charged residues (shown in red) make up the charged polar residues. The charged and polar residues are hydrophilic therefore do not orient themselves to exclude water or solvent. The charged <scene name='Sandbox_31/Termini/4'>Termini</scene> face outward due to their hydrophilic nature.

==Inhibitors==

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'''Leupeptin (PDB ID #: 1pop)'''

<scene name='Sandbox_31/Leupeptin/1'>Leupeptin</scene> is a commonly studied inhibitor of proteases (seen in the Jmol as ball and stick model). It inhibits by binding and interacting with the active site which allows it to block the enzyme's desired protein substrate. There are many <scene name='Sandbox_31/1popligand_contacts/1'>Residues</scene> that interact with Leupeptin in the active site. The predominant interaction is from hydrophobic interactions between Leupeptin and <scene name='Sandbox_31/1pophydrointeract/1'>active site residues</scene>. In addition to hydrophobic interactions, there are also some hydrogen bonding interactions to hold Leupeptin in the active site of papain. Leupeptin works well at blocking papain from its enzymatic duties. A recent study has shown that Leupeptin actually forms a covalent bond between its <scene name='Sandbox_31/Leupeptin_active/1'>Carbonyl Carbon</scene> and CYS 25. In addition, the residues Gln 19 and CYS 25 form <scene name='Sandbox_31/Leupeptin_active/2'>hydrogen bonds</scene>with the Leupeptin molecule

<scene name='Sandbox_31/Leupeptin/1'>Leupeptin</scene> is a commonly studied inhibitor of proteases (seen in the Jmol as ball and stick model). It inhibits by binding and interacting with the active site which allows it to block the enzyme's desired protein substrate. There are many <scene name='Sandbox_31/1popligand_contacts/1'>Residues</scene> that interact with Leupeptin in the active site. The predominant interaction is from hydrophobic interactions between Leupeptin and <scene name='Sandbox_31/1pophydrointeract/1'>active site residues</scene>. In addition to hydrophobic interactions, there are also some hydrogen bonding interactions to hold Leupeptin in the active site of papain. Leupeptin works well at blocking papain from its enzymatic duties. A recent study has shown that Leupeptin actually forms a covalent bond between its <scene name='Sandbox_31/Leupeptin_active/1'>Carbonyl Carbon</scene> and CYS 25. In addition, the residues Gln 19 and CYS 25 form <scene name='Sandbox_31/Leupeptin_active/2'>hydrogen bonds</scene> with the Leupeptin molecule

'''Cathepsin L (PDB ID #: 1CVZ)'''

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@@ Line 23: / Line 23: @@
 Papain is formed from a peptide that is 212 amino acids in length.<ref>http://www.pdb.org/pdb/explore/explore.do?structureId=9PAP</ref> It consists of 25% <scene name='Sandbox_31/Alpha_helices/4'>Alpha helices</scene> and 21% <scene name='Sandbox_31/Beta_sheet/2'>Beta Sheet</scene>. The structure also consists of three <scene name='Sandbox_31/Disulfide/3'>Disulfide bonds</scene>(seen in yellow) between <scene name='Sandbox_31/Cys_with_labels/2'>Cysteine Residues</scene>.  The disulfide bonds exist between Cys 63 and Cys 22, Cys 200 and Cys 153, and Cys 56 and Cys 95.  Another important residue to the structure is Cysteine 25 which has a sulfhydryl group that plays a major role in the active site activity[[http://www.sigmaaldrich.com/life-science/metabolomics/enzyme-explorer/analytical-enzymes/papain.html]].
-The <scene name='Sandbox_31/Hydrophobic_residues/2'>Hydrophobic Residues</scene> in papain are primarily located toward the inside of the enzyme or paired by hydrophobic interactions with other hydrophobic residues to exclude water.  The <scene name='Sandbox_31/Polar_residues/1'>Polar Residues</scene> are located facing the exterior, in the active site, or paired with other charged residues(seen in orange).  The polar residues seen in orange predominantly fill the space surrounding the exterior of the enzyme.  This is because they are hydrophillic and interact with polar water molecules.  The <scene name='Sandbox_31/Positive/1'>Negatively</scene> charged residues (shown in green) and the <scene name='Sandbox_31/Basic_positive/1'>Positively</scene> charged residues (shown in red) make up the polar residues. The charged and polar residues are hydrophilic therefore do not orient themselves to exclude water or solvent.  The charged <scene name='Sandbox_31/Termini/4'>Termini</scene> face outward due to their hydrophilic nature.
+The <scene name='Sandbox_31/Hydrophobic_residues2/1'>Hydrophobic Residues</scene>(seen in pink) in papain are primarily located toward the inside of the enzyme or paired by hydrophobic interactions with other hydrophobic residues to exclude water.  The <scene name='Sandbox_31/Polar_residues/1'>Polar Residues</scene> are located facing the exterior, in the active site, or paired with other charged residues(seen in orange).  The polar residues seen in orange predominantly fill the space surrounding the exterior of the enzyme.  This is because they are hydrophillic and interact with polar water molecules.  The <scene name='Sandbox_31/Positive/1'>Negatively</scene> charged residues (shown in green) and the <scene name='Sandbox_31/Basic_positive/1'>Positively</scene> charged residues (shown in red) make up the charged polar residues. The charged and polar residues are hydrophilic therefore do not orient themselves to exclude water or solvent.  The charged <scene name='Sandbox_31/Termini/4'>Termini</scene> face outward due to their hydrophilic nature.
 ==Inhibitors==
@@ Line 30: / Line 30: @@
 '''Leupeptin (PDB ID #: 1pop)'''
-<scene name='Sandbox_31/Leupeptin/1'>Leupeptin</scene> is a commonly studied inhibitor of proteases (seen in the Jmol as ball and stick model).  It inhibits by binding and interacting with the active site which allows it to block the enzyme's desired protein substrate.  There are many <scene name='Sandbox_31/1popligand_contacts/1'>Residues</scene> that interact with Leupeptin in the active site.  The predominant interaction is from hydrophobic interactions between Leupeptin and <scene name='Sandbox_31/1pophydrointeract/1'>active site residues</scene>.  In addition to hydrophobic interactions, there are also some hydrogen bonding interactions to hold Leupeptin in the active site of papain.  Leupeptin works well at blocking papain from its enzymatic duties.  A recent study has shown that Leupeptin actually forms a covalent bond between its <scene name='Sandbox_31/Leupeptin_active/1'>Carbonyl Carbon</scene> and CYS 25.  In addition, the residues Gln 19 and CYS 25 form <scene name='Sandbox_31/Leupeptin_active/2'>hydrogen bonds</scene>with the Leupeptin molecule
+<scene name='Sandbox_31/Leupeptin/1'>Leupeptin</scene> is a commonly studied inhibitor of proteases (seen in the Jmol as ball and stick model).  It inhibits by binding and interacting with the active site which allows it to block the enzyme's desired protein substrate.  There are many <scene name='Sandbox_31/1popligand_contacts/1'>Residues</scene> that interact with Leupeptin in the active site.  The predominant interaction is from hydrophobic interactions between Leupeptin and <scene name='Sandbox_31/1pophydrointeract/1'>active site residues</scene>.  In addition to hydrophobic interactions, there are also some hydrogen bonding interactions to hold Leupeptin in the active site of papain.  Leupeptin works well at blocking papain from its enzymatic duties.  A recent study has shown that Leupeptin actually forms a covalent bond between its <scene name='Sandbox_31/Leupeptin_active/1'>Carbonyl Carbon</scene> and CYS 25.  In addition, the residues Gln 19 and CYS 25 form <scene name='Sandbox_31/Leupeptin_active/2'>hydrogen bonds</scene> with the Leupeptin molecule
 '''Cathepsin L (PDB ID #: 1CVZ)'''