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Sandbox 30
From Proteopedia
(Difference between revisions)
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= Trypsin = | = Trypsin = | ||
| - | (Specifically 1QLQ) | + | (Specifically PDB: 1QLQ) |
<applet load='1QLQ' size='450' frame='true' align='right' caption='Click on the links to the left to view different structural aspects. Ligand shown: SO4' /> | <applet load='1QLQ' size='450' frame='true' align='right' caption='Click on the links to the left to view different structural aspects. Ligand shown: SO4' /> | ||
| - | == | + | ==Structure Quick Links== |
An easy way to distinguish between main structural components of the protein is to view it using <scene name='Sandbox_30/Trypsin_cartoon_rainbow/2'>rainbow coloration.</scene> To see various other specific structures of Trypsin, click on their links. | An easy way to distinguish between main structural components of the protein is to view it using <scene name='Sandbox_30/Trypsin_cartoon_rainbow/2'>rainbow coloration.</scene> To see various other specific structures of Trypsin, click on their links. | ||
* <scene name='Sandbox_30/Trypsin_cartoon_rainbow/2'>Rainbow Coloration</scene> | * <scene name='Sandbox_30/Trypsin_cartoon_rainbow/2'>Rainbow Coloration</scene> | ||
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==Structure== | ==Structure== | ||
| - | Trypsin's primary amino acid sequence forms two <scene name='Sandbox_30/Helixs_maroon/3'>α helices</scene> and two <scene name='Sandbox_30/Sheets_green/4'>β sheets</scene>. Both of the α helices are right handed and the β sheets are anti-parallel. The order of the secondary structures is easily visible when using the <scene name='Sandbox_30/Trypsin_cartoon_rainbow/2'>rainbow coloration</scene> scheme to identify secondary structures. The N-terminus (blue) is the beginning of trypsin and the C-terminus (agua-green) is the end. | + | Trypsin's primary amino acid sequence (RPDFCLEPPYAGACRARIIRYFYNAKAGLCQTFVYGGCRAKRNNFKSAEDCLRTCGGA) <ref> 1qlq [http://bip.weizmann.ac.il/oca-bin/send-seq?1qlq_A]</ref> forms the <scene name='Sandbox_30/Backbone/1'>backbone</scene> of the protein, which then folds into secondary structures, consisting of two <scene name='Sandbox_30/Helixs_maroon/3'>α helices</scene> and two <scene name='Sandbox_30/Sheets_green/4'>β sheets</scene>. Both of the α helices are right handed and the β sheets are anti-parallel. The order of the secondary structures is easily visible when using the <scene name='Sandbox_30/Trypsin_cartoon_rainbow/2'>rainbow coloration</scene> scheme to identify secondary structures. The N-terminus (blue) is the beginning of trypsin and the C-terminus (agua-green) is the end. |
| - | + | ==Polar and Nonpolar Residues== | |
| - | Polar residues are typically hydrophobic, and seek to be sheltered from the aqueous environments that proteins typically inhibit. The polarity of an amino acid is determined by its <scene name='Sandbox_30/Side_chains/1'>side | + | Polar residues are typically hydrophobic, and seek to be sheltered from the aqueous environments that proteins typically inhibit. The polarity of an amino acid is determined by its <scene name='Sandbox_30/Side_chains/1'>side chain</scene> (orange). When considering the <scene name='Sandbox_30/Polar_and_nonpolar/1'>ball and stick model</scene> it may look like the polar (blue) and nonpolar (crimson) residues are not organized in a specific manner, but when you consider the <scene name='Sandbox_30/Polar_and_nonpolar/2'>space filling model,</scene> it is evident that the majority of the polar residues are shielded by they nonpolar residues. |
Another way to show this principle is by looking at the location of the <scene name='Sandbox_30/Hydrophobic_red/1'>hydrophobic sections</scene> of Trypsin (red). The hydrophobic portions desire to be shielded from the water in the smallest area possible in order to minimize its interaction with water, thereby maximizing the entropy of the water. It is evident that basically all water molecules are kept outside the protein when viewing a <scene name='Sandbox_30/Ball_and_stick_with_water/1'>rendering with water</scene> (water-blue, trypsin-orange). This form of trypsin (PDB 1QLQ), has been modified to help enable its crystalization, and thus has four water molecules inside of it instead of the normal three which is present in the wild-type trpsin<ref> Czapinska, Honorata et al. "High-resolution structure of bovine pancreatic trypsin inhibitor with altered binding loop sequence." ''Journal of Molecular Biology.'' Volume 295, Issue 5, 4 February 2000, Pages 1237-1249 [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WK7-45F4TXM-2W&_user=4187488&_coverDate=02/04/2000&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000062504&_version=1&_urlVersion=0&_userid=4187488&md5=221a9d3b8b66f6f908a8d93c6b10f18f&searchtype=a#secx12 doi:10.1006/jmbi.1999.3445] </ref>. | Another way to show this principle is by looking at the location of the <scene name='Sandbox_30/Hydrophobic_red/1'>hydrophobic sections</scene> of Trypsin (red). The hydrophobic portions desire to be shielded from the water in the smallest area possible in order to minimize its interaction with water, thereby maximizing the entropy of the water. It is evident that basically all water molecules are kept outside the protein when viewing a <scene name='Sandbox_30/Ball_and_stick_with_water/1'>rendering with water</scene> (water-blue, trypsin-orange). This form of trypsin (PDB 1QLQ), has been modified to help enable its crystalization, and thus has four water molecules inside of it instead of the normal three which is present in the wild-type trpsin<ref> Czapinska, Honorata et al. "High-resolution structure of bovine pancreatic trypsin inhibitor with altered binding loop sequence." ''Journal of Molecular Biology.'' Volume 295, Issue 5, 4 February 2000, Pages 1237-1249 [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WK7-45F4TXM-2W&_user=4187488&_coverDate=02/04/2000&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000062504&_version=1&_urlVersion=0&_userid=4187488&md5=221a9d3b8b66f6f908a8d93c6b10f18f&searchtype=a#secx12 doi:10.1006/jmbi.1999.3445] </ref>. | ||
| - | + | ||
| + | ==Intramolecular and Intermolecular Forces== | ||
The structure of trypsin is stabilized by a variety of intramolecular and intermolecular forces. For example, the first α-helix in trypsin's structure is stabilized by several other <scene name='Sandbox_30/1_a_helix_hydrophobic_interact/1'>hydrophobic residues</scene> in the molecule itself. | The structure of trypsin is stabilized by a variety of intramolecular and intermolecular forces. For example, the first α-helix in trypsin's structure is stabilized by several other <scene name='Sandbox_30/1_a_helix_hydrophobic_interact/1'>hydrophobic residues</scene> in the molecule itself. | ||
Revision as of 22:16, 29 October 2010
| Please do NOT make changes to this Sandbox. Sandboxes 30-60 are reserved for use by Biochemistry 410 & 412 at Messiah College taught by Dr. Hannah Tims during Fall 2012 and Spring 2013. |
Contents |
Trypsin
(Specifically PDB: 1QLQ)
|
Structure Quick Links
An easy way to distinguish between main structural components of the protein is to view it using To see various other specific structures of Trypsin, click on their links.
- - Ball and stick
- - Space filling model
Structure
Trypsin's primary amino acid sequence (RPDFCLEPPYAGACRARIIRYFYNAKAGLCQTFVYGGCRAKRNNFKSAEDCLRTCGGA) [1] forms the of the protein, which then folds into secondary structures, consisting of two and two . Both of the α helices are right handed and the β sheets are anti-parallel. The order of the secondary structures is easily visible when using the scheme to identify secondary structures. The N-terminus (blue) is the beginning of trypsin and the C-terminus (agua-green) is the end.
Polar and Nonpolar Residues
Polar residues are typically hydrophobic, and seek to be sheltered from the aqueous environments that proteins typically inhibit. The polarity of an amino acid is determined by its (orange). When considering the it may look like the polar (blue) and nonpolar (crimson) residues are not organized in a specific manner, but when you consider the it is evident that the majority of the polar residues are shielded by they nonpolar residues. Another way to show this principle is by looking at the location of the of Trypsin (red). The hydrophobic portions desire to be shielded from the water in the smallest area possible in order to minimize its interaction with water, thereby maximizing the entropy of the water. It is evident that basically all water molecules are kept outside the protein when viewing a (water-blue, trypsin-orange). This form of trypsin (PDB 1QLQ), has been modified to help enable its crystalization, and thus has four water molecules inside of it instead of the normal three which is present in the wild-type trpsin[2].
Intramolecular and Intermolecular Forces
The structure of trypsin is stabilized by a variety of intramolecular and intermolecular forces. For example, the first α-helix in trypsin's structure is stabilized by several other in the molecule itself.
|
References
- ↑ 1qlq [1]
- ↑ Czapinska, Honorata et al. "High-resolution structure of bovine pancreatic trypsin inhibitor with altered binding loop sequence." Journal of Molecular Biology. Volume 295, Issue 5, 4 February 2000, Pages 1237-1249 doi:10.1006/jmbi.1999.3445
