Sandbox 30: Difference between revisions
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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>. | 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>. | ||
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> | 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> | ||
==Structure== | ==Structure== | ||
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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). | 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). | ||
[[Image:SO4_Ligand.JPG|right|180px]] | |||
===Ligands=== | ===Ligands=== | ||
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. | |||
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 | |||
==Cleavage Mechanism== | ==Cleavage Mechanism== | ||
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>. You are able to view the <scene name='Sandbox_30/Active_site/1'>actual binding site</scene> | 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/2'>substrate in the binding site</scene>. | ||
[[Image:Serine_cleavage.jpg|left|150px]] | |||
==Trypsinogen== | ==Trypsinogen== | ||
