Sandbox 46: Difference between revisions

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=Trypsin=
=Trypsin=
Trypsin, a member of the serine protease family, is produced in the pancreas and found in the digestive tracks of vertebrates.  To avoid pancreatic self-degradation, trypsin is synthesized as trypsinogen, a zymogen.  Cleavage by enteropeptidase allows tryspin to enter its active form.  As a serine protease, trypsin contains a serine residue in its active site.  
Trypsin, a member of the serine protease family, is produced in the pancreas and found in the digestive tracks of vertebrates.  To avoid pancreatic self-degradation, trypsin is synthesized as trypsinogen, a zymogen.  Cleavage by enteropeptidase allows tryspin to enter its active form.  As a serine protease, trypsin contains a serine residue in its active site.<ref name="pmid7845208">{{"Trypsin." Wikipedia, the Free Encyclopedia. Web. 30 Oct. 2010. <http://en.wikipedia.org/wiki/Trypsin#Structure_and_function>.}}</ref>




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In addition to disulphide bonds, Hydrogen bonding plays a large role in stability.  As this <scene name='Sandbox_46/Hbonds_backbone/1'>model</scene> suggests, hydrogen bonds (orange) are most prominent in alpha helices and beta sheets of the backbone.  In alpha helices, hydrogen bonds form between an H-N and a C-O 4 residue away; complementing the specific turn length (3.6 residues).  Hydrogen bonds between the <scene name='Sandbox_46/H_bonds_r_groups/1'>sidechain residues</scene> (R groups) provide further stability for the trypsin moiety.   
In addition to disulphide bonds, Hydrogen bonding plays a large role in stability.  As this <scene name='Sandbox_46/Hbonds_backbone/1'>model</scene> suggests, hydrogen bonds (orange) are most prominent in alpha helices and beta sheets of the backbone.  In alpha helices, hydrogen bonds form between an H-N and a C-O 4 residue away; complementing the specific turn length (3.6 residues).  Hydrogen bonds between the <scene name='Sandbox_46/H_bonds_r_groups/1'>sidechain residues</scene> (R groups) provide further stability for the trypsin moiety.   


The yellow and red molecules represent <scene name='Sandbox_46/So4/1'>SO4 (2-) molecules</scene> which are not part of the traditional trypsin structure; they were added during crystallization to freeze Trypsin in a specific conformation.  Each SO4 molecule is bound to an active site (ball and stick display) in order to prevent interaction with another substrate.  Active site inhibition is a prominent method for studying enzymes.   
The yellow and red molecules represent <scene name='Sandbox_46/So4/1'>SO4 (2-) molecules</scene> which are not part of the traditional trypsin structure; they were added during crystallization to freeze Trypsin in a specific conformation.  Each SO4 molecule is bound to an active site (ball and stick display) in order to prevent interaction with another substrate. <ref>{{Czapinska, H., J. Otlewski, S. Krzywda, G. M. Sheldrick, and M. Jaskolski. "RCSB Protein Data Bank - Structure Summary for 1QLQ - BOVINE PANCREATIC TRYPSIN INHIBITOR (BPTI) MUTANT WITH ALTERED BINDING LOOP SEQUENCE." Http://www.rcsb.org/pdb/explore/explore.do?structureId=1QLQ. (1999) J.Mol.Biol. 295: 1237. Web. 30 Oct. 2010. <http://www.rcsb.org/pdb/explore.do?structureId=1qlq>.}}</ref> Active site inhibition is a prominent method for studying enzymes.   


==Function==
==Function==
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Enteropeptidase cleaves after Lysine if it is preceded by 4 Aspartic Acid residues and not followed by a Proline residue.  This particular cleavage converts trypsinogen (zymogen) into trypsin.   
Enteropeptidase cleaves after Lysine if it is preceded by 4 Aspartic Acid residues and not followed by a Proline residue.  This particular cleavage converts trypsinogen (zymogen) into trypsin.   
Once activated, trypsin catalyzes the hydrolysis of peptides into amino acids which the body can absorb during digestion.  Trypsin has an affinity for positively charged molecules; thus, it specifically cleaves on the carboxyl end (after) of Lysine and Arginine, unless Proline follows the residue.  Trypsin's active site normally contains a triad of residues: Histidine, Serine, and Apartic Acid.  The particular mutant form discussed here does not contain this particular active site, but rather 4 different active sites.  Click on any of the following links to view a specific active site: <scene name='Sandbox_46/Ac1/1'>Active Site 1</scene> (light blue); <scene name='Sandbox_46/Ac2/1'>Active Site 2</scene> (pink); <scene name='Sandbox_46/Ac3/1'>Active Site 3</scene>(yellow); <scene name='Sandbox_46/Ac4/1'>Active Site 4</scene> (dark blue).  This <scene name='Sandbox_46/Ac_all/1'>model</scene> compares the orientation of all four active sites.  Site 1 and 3 share a small portion (Arginine residue 42) which is shown in maroon.  Active site three most closely resembles the traditional composition of trypsin's active site.
Once activated, trypsin catalyzes the hydrolysis of peptides into amino acids which the body can absorb during digestion.  Trypsin has an affinity for positively charged molecules; thus, it specifically cleaves on the carboxyl end (after) of Lysine and Arginine, unless Proline follows the residue.  Trypsin's active site normally contains a triad of residues: Histidine, Serine, and Apartic Acid.  The particular mutant form discussed here does not contain this particular active site, but rather 4 different active sites.  Click on any of the following links to view a specific active site: <scene name='Sandbox_46/Ac1/1'>Active Site 1</scene> (light blue); <scene name='Sandbox_46/Ac2/1'>Active Site 2</scene> (pink); <scene name='Sandbox_46/Ac3/1'>Active Site 3</scene>(yellow); <scene name='Sandbox_46/Ac4/1'>Active Site 4</scene> (dark blue).  This <scene name='Sandbox_46/Ac_all/1'>model</scene> compares the orientation of all four active sites.  Site 1 and 3 share a small portion (Arginine residue 42) which is shown in maroon.  Active site three most closely resembles the traditional composition of trypsin's active site.
==References==
{{Reflist}}
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