Trypsin: Difference between revisions

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== Ligand Binding and Catalysis ==

The structure of this particular bovine trypsin was determined in complex with <scene name='Sandbox_45/Btligand/1'>UB-THR 10</scene>, formula '''C'''20'''H'''29'''N'''5'''O'''2, along with two <scene name='Sandbox_45/Btsulfates/1'>sulfate ions</scene> (highlighted) and a ~~Calcium~~ ion (green). <scene name='10/100160/Cv/1'>Four key amino acids interact with ~~Calcium~~ at a subsite loop</scene>. The binding of ligand UB-THR 10 involves <scene name='10/100160/Cv/3'>water bridges</scene>, direct <scene name='10/100160/Cv/4'>hydrogen bonding, and a host of hydrophobic interactions</scene>. The figure below shows this binding in two dimensions.

The structure of this particular bovine trypsin was determined in complex with <scene name='Sandbox_45/Btligand/1'>UB-THR 10</scene>, formula '''C'''20'''H'''29'''N'''5'''O'''2, along with two <scene name='Sandbox_45/Btsulfates/1'>sulfate ions</scene> (highlighted) and a calcium ion (green). <scene name='10/100160/Calcium_site/1'>Four key amino acids interact with calcium at a subsite loop</scene>. The binding of ligand UB-THR 10 involves <scene name='10/100160/Ub-thr_10/1'>water bridges</scene>, direct <scene name='10/100160/Ub-thr_10/2'>hydrogen bonding, and a host of hydrophobic interactions</scene>. The figure below shows this binding in two dimensions.

The binding of trypsin to UB-THR 10 somewhat emulates the binding to its specific peptide substrates. The preference for lysine or arginine in trypsin catalysis is due to the composition of the trypsin <scene name='10/100160/Cv/5'>specificity pocket</scene>. Here (green), Asp 189 and one of two significant glycine backbones, Gly 216, interact with the ligand as they would with Arg or Lys.

The binding of trypsin to UB-THR 10 somewhat emulates the binding to its specific peptide substrates. The preference for lysine or arginine in trypsin catalysis is due to the composition of the trypsin <scene name='10/100160/Cv/8'>specificity pocket</scene>. Here (green), Asp 189 and one of two significant glycine backbones, Gly 216, interact with the ligand as they would with Arg or Lys.

[[Image:Ligand 3ljj ProteinPlus.png|thumb|left|upright=2.5|A two-dimensional representation of trypsin binding Ligand UB-THR 10]]

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@@ Line 19: / Line 19: @@
 == Ligand Binding and Catalysis ==
-The structure of this particular bovine trypsin was determined in complex with <scene name='Sandbox_45/Btligand/1'>UB-THR 10</scene>, formula '''C'''20'''H'''29'''N'''5'''O'''2, along with two <scene name='Sandbox_45/Btsulfates/1'>sulfate ions</scene> (highlighted) and a Calcium ion (green).  <scene name='10/100160/Cv/1'>Four key amino acids interact with Calcium at a subsite loop</scene>.  The binding of ligand UB-THR 10 involves <scene name='10/100160/Cv/3'>water bridges</scene>, direct <scene name='10/100160/Cv/4'>hydrogen bonding, and a host of hydrophobic interactions</scene>.  The figure below shows this binding in two dimensions.
+The structure of this particular bovine trypsin was determined in complex with <scene name='Sandbox_45/Btligand/1'>UB-THR 10</scene>, formula '''C'''20'''H'''29'''N'''5'''O'''2, along with two <scene name='Sandbox_45/Btsulfates/1'>sulfate ions</scene> (highlighted) and a calcium ion (green).  <scene name='10/100160/Calcium_site/1'>Four key amino acids interact with calcium at a subsite loop</scene>.  The binding of ligand UB-THR 10 involves <scene name='10/100160/Ub-thr_10/1'>water bridges</scene>, direct <scene name='10/100160/Ub-thr_10/2'>hydrogen bonding, and a host of hydrophobic interactions</scene>.  The figure below shows this binding in two dimensions.
-The binding of trypsin to UB-THR 10 somewhat emulates the binding to its specific peptide substrates.  The preference for lysine or arginine in trypsin catalysis is due to the composition of the trypsin <scene name='10/100160/Cv/5'>specificity pocket</scene>.  Here (green), Asp 189 and one of two significant glycine backbones, Gly 216, interact with the ligand as they would with Arg or Lys.
+The binding of trypsin to UB-THR 10 somewhat emulates the binding to its specific peptide substrates.  The preference for lysine or arginine in trypsin catalysis is due to the composition of the trypsin <scene name='10/100160/Cv/8'>specificity pocket</scene>.  Here (green), Asp 189 and one of two significant glycine backbones, Gly 216, interact with the ligand as they would with Arg or Lys.
 [[Image:Ligand 3ljj ProteinPlus.png|thumb|left|upright=2.5|A two-dimensional representation of trypsin binding Ligand UB-THR 10]]
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