Sandbox Wabash14
From Proteopedia
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==The Mechanism of Trypsin by Austin Dukes, Isaac Empson, Michael Miller== | ==The Mechanism of Trypsin by Austin Dukes, Isaac Empson, Michael Miller== | ||
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''> | <StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''> | ||
| - | Trypsin is a serine protease that hydrolyzes proteins in two sequential steps. The first acylation occurs when the nucleophilic serine attacks the substrate at the scissle bond (bond later to be broken). The tetrahedral intermediate is formed. Next, the C-terminal fragment is released, leaving only a covalently bound acyl-enzyme. A second deacylation reaction occurs after a water molecule attacks the acyl-enzyme. This series of events leads to the formation of a second terminal intermediate. Then, the N-terminal fragment is released. The histidine residue acts as a base in the first step by accepting a proton to activate serine as a nucleophile. The histidine later acts as an acid by donating the proton to the nitrogen of the peptide leaving group. <ref>PMID:16636277</ref> | + | Trypsin is a serine protease that hydrolyzes proteins in two sequential steps. The first acylation occurs when the nucleophilic serine 195 attacks the substrate at the scissle bond (bond later to be broken). The tetrahedral intermediate is formed by the His 57 forming a hydrogen bond with the substrate polypeptide. His 57 itself is stabilized by a hydrogen bond from Asp 103 (along with Ser 195 forming the catalytic triad). The various conformation changes often leaves His 57 represented as two ring complexes. This representation is due to its nearly equally abundant conformations it is found in. Next, the C-terminal fragment is released, leaving only a covalently bound acyl-enzyme. A second deacylation reaction occurs after a water molecule attacks the acyl-enzyme. This series of events leads to the formation of a second terminal intermediate. Then, the N-terminal fragment, which is often stabilized by the oxyanion hole, is released. The histidine residue acts as a base in the first step by accepting a proton to activate serine as a nucleophile. The histidine later acts as an acid by donating the proton to the nitrogen of the peptide leaving group. <ref>PMID:16636277</ref> |
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue. | You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue. | ||
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<scene name='72/725337/His_57/1'>His 57</scene> | <scene name='72/725337/His_57/1'>His 57</scene> | ||
<scene name='72/725337/Catalytic_triad/1'>Catalytic Triad</scene> | <scene name='72/725337/Catalytic_triad/1'>Catalytic Triad</scene> | ||
| + | <scene name='72/725337/Oxyanion_hole/1'>Oxyanion Hole</scene> | ||
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes. | This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes. | ||
Current revision
The Mechanism of Trypsin by Austin Dukes, Isaac Empson, Michael Miller
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References
- ↑ Radisky ES, Lee JM, Lu CJ, Koshland DE Jr. Insights into the serine protease mechanism from atomic resolution structures of trypsin reaction intermediates. Proc Natl Acad Sci U S A. 2006 May 2;103(18):6835-40. Epub 2006 Apr 24. PMID:16636277
- ↑ Hanson, R. M., Prilusky, J., Renjian, Z., Nakane, T. and Sussman, J. L. (2013), JSmol and the Next-Generation Web-Based Representation of 3D Molecular Structure as Applied to Proteopedia. Isr. J. Chem., 53:207-216. doi:http://dx.doi.org/10.1002/ijch.201300024
- ↑ Herraez A. Biomolecules in the computer: Jmol to the rescue. Biochem Mol Biol Educ. 2006 Jul;34(4):255-61. doi: 10.1002/bmb.2006.494034042644. PMID:21638687 doi:10.1002/bmb.2006.494034042644
