Sandbox 45
From Proteopedia
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= Structure of Trypsin = | = Structure of Trypsin = | ||
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| + | The various interactive tendencies and chemical characteristics of amino acids in this serine protease contribute to the protein's structure and catalytic function. The spacial arrangement of Trypsin's 223 residues in relation to themselves and their aqueous environment is displayed below. | ||
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| + | == Secondary Structure == | ||
| + | Bovine Trypsin contains 3? <scene name='Sandbox_45/Bt-helix/1'>alpha helices</scene> of lengths XYandZ. The two <scene name='Sandbox_45/Bt-sheet1/1'>beta sheets</scene>, A and B, are comprised of 7 and 6 strands. Although both appear as such, only B is technically a beta barrel. In the native conformation, these regular secondary structures interact with themselves and one another at a number of locations by numerous forces of attraction. A closer look at helix X,terminal, shows <scene name='Sandbox_45/Helixhold_vanderwaals/1'>van der Waals forces</scene>, <scene name='Sandbox_45/Helixhold_hbond/1'>hydrogen bonding and water bridges</scene> between it and local residues of the remaining peptide as significant to this portion of the 3D structure of the protein. | ||
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| + | Hydrophobic/hydrophilic residue composition The protein as a whole achieves its native conformation primarily by the hydrophobic collapse of supersecondary structure; hydrophobic side chains are internalized while water molecules interact with the water-soluble side chains pushed to the exterior. The red-colored water's <scene name='Sandbox_45/Bt-phillic_waters/2'>interaction</scene> with the surface of the protein shows this, as a <scene name='Sandbox_45/Bt-phillic_waters/3'>transparent</scene> view shows an absence of water within the hydrophobic core. | ||
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| + | <scene name='Sandbox_45/Disulfide_bonds/1'>Disulfide bonds</scene> also contribute to the stability of the protein. Typically, proteins in an extra-cellular, oxidizing environment contain disulfide bonds that hold the structure together through variable temperature and pH. It follows that trypsin, a digestive protease found in the digestive tract, would require this added stability. | ||
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| + | <applet load='3LJJ' size='300' frame='true' align='right' caption='Bovine Trypsin' /> | ||
| - | == Primary == | ||
| - | Bovine trypsin contains 223 amino acid residues of varied interactive tendencies and chemical characteristics, each of which contribute to the protein's structure and catalytic function. | ||
| - | == Secondary == | ||
| - | The spacial arrangement of hydrophobic and hydrophilic residues | ||
| - | <scene name='Sandbox_45/Bt-helix/1'>alpha helices</scene> | ||
| - | <scene name='Sandbox_45/Bt-sheet1/1'>beta sheets</scene> | ||
[[Image:Topographytrypsin.gif|thumb|center|upright=2.0]] | [[Image:Topographytrypsin.gif|thumb|center|upright=2.0]] | ||
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sig of disulfides in overall structure, helix to beta sheet, | sig of disulfides in overall structure, helix to beta sheet, | ||
| - | <scene name='Sandbox_45/Helixhold_hbond/1'>hydrogen bonding and water bridges</scene> | ||
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<scene name='Sandbox_45/Bt-phillic/1'>hydrophilic residues</scene> | <scene name='Sandbox_45/Bt-phillic/1'>hydrophilic residues</scene> | ||
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<scene name='Sandbox_45/Bt-phillic/3'>hydrophobic residues</scene> | <scene name='Sandbox_45/Bt-phillic/3'>hydrophobic residues</scene> | ||
| - | <scene name='Sandbox_45/Bt-phillic_waters/2'>water interaction</scene> | ||
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== Ligand Binding and Catalysis == | == Ligand Binding and Catalysis == | ||
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| + | <applet load='3LJJ' size='300' frame='true' align='right' caption='Bovine Trypsin' /> | ||
<scene name='Sandbox_45/Btligand/1'>ligands</scene> | <scene name='Sandbox_45/Btligand/1'>ligands</scene> | ||
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<scene name='Sandbox_45/Lig-metal/1'>metal</scene> | <scene name='Sandbox_45/Lig-metal/1'>metal</scene> | ||
| + | [http://http://www.ncbi.nlm.nih.gov/pubmed/19388054 calcium in regulation] | ||
<scene name='Sandbox_45/Lig-waterbridge/1'>water bridges</scene> | <scene name='Sandbox_45/Lig-waterbridge/1'>water bridges</scene> | ||
Revision as of 03:20, 29 October 2010
Structure of Trypsin
The various interactive tendencies and chemical characteristics of amino acids in this serine protease contribute to the protein's structure and catalytic function. The spacial arrangement of Trypsin's 223 residues in relation to themselves and their aqueous environment is displayed below.
Secondary Structure
Bovine Trypsin contains 3? of lengths XYandZ. The two , A and B, are comprised of 7 and 6 strands. Although both appear as such, only B is technically a beta barrel. In the native conformation, these regular secondary structures interact with themselves and one another at a number of locations by numerous forces of attraction. A closer look at helix X,terminal, shows , between it and local residues of the remaining peptide as significant to this portion of the 3D structure of the protein.
Hydrophobic/hydrophilic residue composition The protein as a whole achieves its native conformation primarily by the hydrophobic collapse of supersecondary structure; hydrophobic side chains are internalized while water molecules interact with the water-soluble side chains pushed to the exterior. The red-colored water's with the surface of the protein shows this, as a view shows an absence of water within the hydrophobic core.
also contribute to the stability of the protein. Typically, proteins in an extra-cellular, oxidizing environment contain disulfide bonds that hold the structure together through variable temperature and pH. It follows that trypsin, a digestive protease found in the digestive tract, would require this added stability.
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sig of disulfides in overall structure, helix to beta sheet,
Ligand Binding and Catalysis
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key amino acids
