User:Ann Taylor/Sandbox Trypsin: Difference between revisions

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==The Mechanism of Trypsin==

One of the ways we know about the mechanism of enzymes is through the use of xray crystallography structures of trapped intermediates or inhibitors bound to enzymes. In a paper by Radisky and Koshland<ref>PMID: 16636277</ref>, an acyl intermediate of trypsin (PDB code [[2AGG]] was characterized.

Serine proteases use a covalent mechanism to catalyze the hydrolysis of a peptide bond. A covalent bond is formed between <scene name='72/725330/Ser195/1'>Ser195</scene> and a substrate <scene name='72/725330/Substrate_and_ser/1'>peptide</scene>.

Serine proteases use a covalent mechanism to catalyze the hydrolysis of a peptide bond. A covalent bond is formed between <scene name='72/725330/Ser195/1'>Ser195</scene> and a substrate <scene name='72/725330/Substrate_and_ser/1'>peptide</scene>. The <scene name='72/725330/Ser_o_lys_bond_length/1'>distance</scene> between one of the Ser O configurations and the alpha carbon of the substrate lysine is the distance of a C-O bond, indicating that the covalent intermediate is indeed formed. There is a <scene name='72/725330/Water/2'>water</scene> situated in the active site, primed to cleave the acyl intermediate by the same <scene name='72/725330/Water_his_57/1'>histidine</scene> that participates in the catalytic triad.

~~Specificity~~ of the ~~proteases~~ is ~~determined~~ by ~~a binding pocket~~.

Specificity of the proteases is determined by a binding pocket. Trypsin is specific for large, basic amino acids; its binding pocket contains an <scene name='72/725330/Binding_pocket/1'>aspartic acid</scene> residue at the base of the pocket.

@@ Line 1: / Line 1: @@
 ==The Mechanism of Trypsin==
-<StructureSection load='1agg' size='340' side='right' caption='Acyl intermediate of trypsin catalyzed hydrolysis' scene=''>
+<StructureSection load='2agg' size='340' side='right' caption='Acyl intermediate of trypsin catalyzed hydrolysis' scene=''>
 One of the ways we know about the mechanism of enzymes is through the use of xray crystallography structures of trapped intermediates or inhibitors bound to enzymes. In a paper by Radisky and Koshland<ref>PMID: 16636277</ref>, an acyl intermediate of trypsin (PDB code [[2AGG]] was characterized.
-Serine proteases use a covalent mechanism to catalyze the hydrolysis of a peptide bond.  A covalent bond is formed between <scene name='72/725330/Ser195/1'>Ser195</scene> and a substrate <scene name='72/725330/Substrate_and_ser/1'>peptide</scene>.
+Serine proteases use a covalent mechanism to catalyze the hydrolysis of a peptide bond.  A covalent bond is formed between <scene name='72/725330/Ser195/1'>Ser195</scene> and a substrate <scene name='72/725330/Substrate_and_ser/1'>peptide</scene>.  The <scene name='72/725330/Ser_o_lys_bond_length/1'>distance</scene> between one of the Ser O configurations and the alpha carbon of the substrate lysine is the distance of a C-O bond, indicating that the covalent intermediate is indeed formed.  There is a <scene name='72/725330/Water/2'>water</scene> situated in the active site, primed to cleave the acyl intermediate by the same <scene name='72/725330/Water_his_57/1'>histidine</scene> that participates in the catalytic triad.
-Specificity of the proteases is determined by a binding pocket.
+Specificity of the proteases is determined by a binding pocket.  Trypsin is specific for large, basic amino acids; its binding pocket contains an <scene name='72/725330/Binding_pocket/1'>aspartic acid</scene> residue at the base of the pocket.