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| - | = '''Trypsin''' = | + | ==Your Heading Here (maybe something like 'Structure')==<StructureSection load='9pap' size='500' side='right' caption='Structure of Papain (PDB entry [[9pap]])' scene=''>Anything in this section will appear adjacent to the 3D structure and will be scrollable.</StructureSection> |
| - | [[Image:1qlq.jpg|left|200px]] | + | |
| - | (Specifically PDB: 1QLQ)
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| - | ==Overview==
| + | <scene name='Sandbox_30/Hydrophobic_highlights/1'>Green text</scene> |
| - | Trypsin was first isolated by Wilhelm Kühne in 1867<ref>[https://www.doria.fi/bitstream/handle/10024/2142/trypsinr.pdf?sequence=1 ISBN 952-10-1863-1]</ref>. Trypsin is a serine protease synthesized in the pancreas but is not activated until the zymogen form of trypsin is activated. This prevents trypsin from digesting actual body tissue<ref> [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TGT-49S6WV8-1&_user=4187488&_coverDate=12/31/2003&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000062504&_version=1&_urlVersion=0&_userid=4187488&md5=a7d7e1b154a43b709d5228c4852e5d10&searchtype=a doi:10.1016/j.theochem.2003.08.072]</ref>. Serine proteases were instrumental in the discovery and subsequent study of enzymes due to there high stability and large quantities in digestive juices. One of the first proteins to be studied via X-ray crystallography was Chymotrypsin. Trypsin cleaves on the C-terminus side of lysine and arginine<ref>[http://www.pdb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb46_1.html Protein Data Bank]</ref>.
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| - | 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>
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| - | ==Structure==
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| - | <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' />
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| - | Trypsin's primary amino acid sequence (RPDFCLEPPYAGACRARIIRYFYNAKAGLCQTFVYGGCRAKRNNFKSAEDCLRTCGGA) <ref>[http://bip.weizmann.ac.il/oca-bin/send-seq?1qlq_A 1qlq]</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.
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| - | ==Polar and Nonpolar Residues==
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| - | 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 nonpolar residues are shielded by the polar residues.
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| - | 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). Alternatively, for a more in depth analysis of trypsin, you can view
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| - | <scene name='Sandbox_30/Space_fill_charge_and_polar/1'>charged (Blue +)(Red -), uncharged polar (purple), and hydrophobic (gray) space filling rendering</scene> which can be even more informing. 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>.
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| - | ==Intramolecular and Intermolecular Forces==
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| - | The structure of trypsin is stabilized by a variety of intramolecular and intermolecular forces. Trypsin has three <scene name='Sandbox_30/Disulfied_bonds/2'>disulfide bonds,</scene> which form between the cysteine amino acids. The cysteine amino acids are shown as pink, and you can see how they are placed in the proper 3-dimensional space to bond with each other. The bond they form is represented by the yellow bar in between them, as each of their sulfurs bind to one another. Disulfide bonds are especially important for structural stability in extracellular environments, where conditions are more prone to fluctuation. Secondary structures are stabilized via interactions that compliment their specific side chains. For example, the first α helix in trypsin's structure is stabilized by several other
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| - | <scene name='Sandbox_30/A_helix_hydrophobic/1'>hydrophobic residues</scene> in the molecule itself. The ball and stick amino acids marked with an * are part of α helix while the space filling molecules stabilize the α helix. the The α helix is also stabilized by <scene name='Sandbox_30/A_helix_hydrogen_bonds/1'>intramolecular hydrogen bonding,</scene> as well as
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| - | <scene name='Sandbox_30/A_helix_hydrogen_bonds/2'>the addition of hydrogen bonding to water molecules</scene> (water is dark blue).
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| - | The <scene name='Sandbox_30/Beta_sheet_interactions/1'>β sheets</scene> (β sheets are ball and stick) have a more bilaterally divided type of bonding. One side of the β sheets are exposed to water (pink), and are stabilized by hydrogen bonding. Additionally, there are many hydrophobic interactions (gray) on the internal side of the β sheets. There are some intramolecular hydrogen bonding which is shown as light blue(oxygen) and blue(nitrogen).
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| - | [[Image:SO4_Ligand.JPG|right|180px]]
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| - | ===Ligands===
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| - | There are four <scene name='Sandbox_30/So4_ligands/1'>ligands</scene> present in 1QLQ, which are stabilized mostly by hydrogen bonding. For example, <scene name='Sandbox_30/So4_ligand_62_a/1'>SO4 62 A</scene> is stabilized by hydrogen bonds using the oxygens on SO4. There is a image to the right showing the bonding interaction.
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| - | ==Cleavage Mechanism==
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| - | Serine proteases cleave using what is commonly called a catalytic triad. This catalytic triad consists of Asp 102, His 57, and Ser 195<ref>Polgár L. "The catalytic triad of serine peptidases". Cell. Mol. Life Sci. October 2005. 62 (19-20): 2161–72. [http://www.springerlink.com/content/l3t068x156682u55/ doi:10.1007/s00018-005-5160-x]</ref>. The cleavage mechanism is shown to the left. First, the substrate binds to trypsin, and then the side chain oxygen of Ser 195 nucleophilicly attacks, with assist from His 57. Next, the peptide bond is cleaved, with His 57 assisting again with stabilization. After cleavage, the first product is released. Next there is a nucleophilic attack of H20 on the acyl-enzye intermediate (assistance of His 57). This is followed by the decomposition of the acyl intermediate and release of the second product<ref>Polgár L. "The catalytic triad of serine peptidases". Cell. Mol. Life Sci. October 2005. 62 (19-20): 2161–72. [http://www.springerlink.com/content/l3t068x156682u55/ doi:10.1007/s00018-005-5160-x]</ref>. <applet scene='Sandbox_30/Big_trypsin_rainbow/1' size='300' frame='true' align='right' caption='Bovine trypsin in complex with UB-THR 10' /> You are able to view the <scene name='Sandbox_30/Active_site/1'>actual binding site</scene>. Additionally, you may see the <scene name='Sandbox_30/Active_site/3'>substrate in the binding site</scene>.
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| - | [[Image:Serine_cleavage.jpg|left|150px]]
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| - | ==Trypsinogen==
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| - | Trypsin's zymogen form is called trypsinogen, and can actually activate itself. Zymogens require a biochemical change to activate. Only an activated form of trypsin can activate the trypsinogen, and this initial activation is carried out by enteropeptidase, which is a serine protease as well. Because activated forms of trypsin can activate others, trypsin is said to be autocatalytic<ref>Voet, Donald et al. Fundamentals of Biochemistry - Life at the Molecular Level. 3rd ed. John Wiley & Sons, Inc. 2008</ref>. In addition to activating itself, it can also activate [http://www.proteopedia.org/wiki/index.php/Chymotrypsin chymotrypsin] and [http://www.proteopedia.org/wiki/index.php/Elastase elastase].
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| - | ==References==
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| - | <references />
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