Daniel Eddelman Sandbox 1: Difference between revisions

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 ==The Mechanism of Trypsin==
+     Trypsin is a serine protease used in the human digestive system.  It is secreted by the pancrease into the duodenum (upper region of the small intestine).  It cleaves on the C-terminal side of Arg or Lys residues. Trypsin is comprised of just one polypeptide chain containing about 14 beta sheets and 2 alpha helices. , folded sort of into two domains.  Unlike chymotrypsin, which acts on large hydrophobic residues like Phe and Trp, trypsin acts on cationic residues like Lys and Arg.  As in the other serine proteases, trypsin relies on the catalytic triad of Ser-195, His-57, and Asp 102 in its active site.  This catalytic triad is essential to the protein’s ability to hydrolyze peptide bonds.  The mechanism of trypsin follows the general serine protease mechanism, and is comprised of 5 steps: 1) nucleophilic attack by active site Ser on carbonyl carbon of scissile peptide bond to form a tetrahedral intermediate; 2) decomposition of the tetrahedral intermediate to the acyl-enzyme intermediate through general acid catalysis by the active site Asp-polarized His; 3) loss of the amine product and its replacement by water; 4) the reversal of step 2 to form a second tetrahedral intermediate; 5) reversal of step 1 to yield the carboxyl product and the active enzyme.  Trypsin, like other serine proteases, preferentially binds the transition state leading to the tetrahedral intermediate.
 {{STRUCTURE_2agi |  PDB=2agi |  SCENE=  }}
-     Trypsin is a serine protease used in the human digestive system.  It is secreted by the pancrease into the duodenum (upper region of the small intestine).  It cleaves on the C-terminal side of Arg or Lys residues. Trypsin is comprised of just one polypeptide chain containing about 14 beta sheets and 2 alpha helices. , folded sort of into two domains.  Unlike chymotrypsin, which acts on large hydrophobic residues like Phe and Trp, trypsin acts on cationic residues like Lys and Arg.  As in the other serine proteases, trypsin relies on the catalytic triad of Ser-195, His-57, and Asp 102 in its active site.  This catalytic triad is essential to the protein’s ability to hydrolyze peptide bonds.  The mechanism of trypsin follows the general serine protease mechanism, and is comprised of 5 steps: 1) nucleophilic attack by active site Ser on carbonyl carbon of scissile peptide bond to form a tetrahedral intermediate; 2) decomposition of the tetrahedral intermediate to the acyl-enzyme intermediate through general acid catalysis by the active site Asp-polarized His; 3) loss of the amine product and its replacement by water; 4) the reversal of step 2 to form a second tetrahedral intermediate; 5) reversal of step 1 to yield the carboxyl product and the active enzyme.  Trypsin, like other serine proteases, preferentially binds the transition state leading to the tetrahedral intermediate.