Sandbox 30: Difference between revisions

Line 3:

= '''Papain''' =

Note: For some reason, using the "hydrogen bonds" link in the structure section breaks the jmol display and results in scenes after that point having random disulfide bonds and solvent molecules floating in mid-air. I've tried to fix it but to no avail, so if this happens just refresh the page and everything should work again.

Note: For some reason, using the "hydrogen bonds" link in the structure section breaks the jmol display and results in scenes after that point having random disulfide bonds and solvent molecules floating in mid-air. I've tried to fix it but to no avail, so if this happens just refresh the page and everything should work again. Oh look, now the new h-bond link in the substrate binding section does the same thing. If you see disembodied floating solvent molecules after clicking it, just refresh the page.

==Overview==

Line 34:

===Substrate Binding===

In order to investigate binding of protein substrates to papain, the enzyme was crystallized with the broad-spectrum competitive protease inhibitor leupeptin, shown in blue in the ribbon diagram. It has the structure Ac-Leu-Leu-Arginal, where Ac is an acetyl group attached to the nitrogen of the first leucine. The inhibitor functions by binding to the enzyme's active site, where the catalytic nucleophile (cysteine in papain) attacks the arginal aldehyde. This forms a tight-binding transition state from which the normal catalytic mechanism cannot proceed, due to this carbonyl having no potential leaving groups bonded to it. Analysis of the resulting structure revealed that the

<scene name='Sandbox_30/Papain_inhibitor_activesite/3'>substrate binding pocket</scene> of papain consists primarily of a variety of <scene name='Sandbox_30/Papain_inhibitor_hydrophobics/1'>hydrophobic residues</scene>, including tyrosine, tryptophan, and valine, which coordinate the bound leuptin. Some of the enzyme's residues also make <scene name='Sandbox_30/Papain_inhibitor_h-bonds/2'>hydrogen bonds</scene> with some of the leupeptin atoms. These hydrogen bonds, shown in yellow, include interactions between both hydrogens on both Gln19 and the amide nitrogen of the catalytic Cys25 with the arginal carbanion, forming the catalytically important oxyanion hole. In addition, Gly66 interacts with the second leucine in leupeptin while Asp158 interacts with a hydrogen on the arginal. These interaction further stabilize and orient the substrate in the binding pocket. ~~Finally,~~

<scene name='Sandbox_30/Papain_inhibitor_activesite/3'>substrate binding pocket</scene> of papain consists primarily of a variety of <scene name='Sandbox_30/Papain_inhibitor_hydrophobics/1'>hydrophobic residues</scene>, including tyrosine, tryptophan, and valine, which coordinate the bound leuptin. Some of the enzyme's residues also make <scene name='Sandbox_30/Papain_inhibitor_h-bonds/2'>hydrogen bonds</scene> with some of the leupeptin atoms. These hydrogen bonds, shown in yellow, include interactions between both hydrogens on both Gln19 and the amide nitrogen of the catalytic Cys25 with the arginal carbanion, forming the catalytically important oxyanion hole. In addition, Gly66 interacts with the second leucine in leupeptin while Asp158 interacts with a hydrogen on the arginal. These interaction further stabilize and orient the substrate in the binding pocket.

Sandbox 30: Difference between revisions

Navigation menu

Page actions

Page actions

Personal tools

Navigation

Search

Tools

@@ Line 3: / Line 3: @@
 <!-- PLEASE ADD YOUR CONTENT BELOW HERE -->
 = '''Papain''' =
-Note: For some reason, using the "hydrogen bonds" link in the structure section breaks the jmol display and results in scenes after that point having random disulfide bonds and solvent molecules floating in mid-air.  I've tried to fix it but to no avail, so if this happens just refresh the page and everything should work again.
+Note: For some reason, using the "hydrogen bonds" link in the structure section breaks the jmol display and results in scenes after that point having random disulfide bonds and solvent molecules floating in mid-air.  I've tried to fix it but to no avail, so if this happens just refresh the page and everything should work again.  Oh look, now the new h-bond link in the substrate binding section does the same thing.  If you see disembodied floating solvent molecules after clicking it, just refresh the page.
 ==Overview==
@@ Line 34: / Line 34: @@
 ===Substrate Binding===
 In order to investigate binding of protein substrates to papain, the enzyme was crystallized with the broad-spectrum competitive protease inhibitor leupeptin, shown in blue in the ribbon diagram.  It has the structure Ac-Leu-Leu-Arginal, where Ac is an acetyl group attached to the nitrogen of the first leucine.  The inhibitor functions by binding to the enzyme's active site, where the catalytic nucleophile (cysteine in papain) attacks the arginal aldehyde.  This forms a tight-binding transition state from which the normal catalytic mechanism cannot proceed, due to this carbonyl having no potential leaving groups bonded to it.  Analysis of the resulting structure revealed that the
-<scene name='Sandbox_30/Papain_inhibitor_activesite/3'>substrate binding pocket</scene> of papain consists primarily of a variety of <scene name='Sandbox_30/Papain_inhibitor_hydrophobics/1'>hydrophobic residues</scene>, including tyrosine, tryptophan, and valine, which coordinate the bound leuptin.  Some of the enzyme's residues also make <scene name='Sandbox_30/Papain_inhibitor_h-bonds/2'>hydrogen bonds</scene> with some of the leupeptin atoms.  These hydrogen bonds, shown in yellow, include interactions between both hydrogens on both Gln19 and the amide nitrogen of the catalytic Cys25 with the arginal carbanion, forming the catalytically important oxyanion hole.  In addition, Gly66 interacts with the second leucine in leupeptin while Asp158 interacts with a hydrogen on the arginal.  These interaction further stabilize and orient the substrate in the binding pocket.  Finally,
+<scene name='Sandbox_30/Papain_inhibitor_activesite/3'>substrate binding pocket</scene> of papain consists primarily of a variety of <scene name='Sandbox_30/Papain_inhibitor_hydrophobics/1'>hydrophobic residues</scene>, including tyrosine, tryptophan, and valine, which coordinate the bound leuptin.  Some of the enzyme's residues also make <scene name='Sandbox_30/Papain_inhibitor_h-bonds/2'>hydrogen bonds</scene> with some of the leupeptin atoms.  These hydrogen bonds, shown in yellow, include interactions between both hydrogens on both Gln19 and the amide nitrogen of the catalytic Cys25 with the arginal carbanion, forming the catalytically important oxyanion hole.  In addition, Gly66 interacts with the second leucine in leupeptin while Asp158 interacts with a hydrogen on the arginal.  These interaction further stabilize and orient the substrate in the binding pocket.