Sandbox 50: Difference between revisions

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[[Image:Serine_protease_mechanism_by_snellios.png |thumb]]

===Active Site===

Trypsin's active site is composed of its catalytic triad, three amino acid residues that are crucial to the enzymes proteolytic function. The catalytic triad consists of Asp 102, His 57, and Ser 195. Serine is the major player in the cleaveage of the peptide bond, thus the name serine protease. His 57 aids in the cleavage of the peptide bond through hydrogen bonds, and Asp 102 aids in the cleavage by electrostatically stabalizing the positively charged form of His 57 in the transition state. Ser 195 performs a nucleophilic attack on the substrate's peptide carbonyl. This causes the oxyanion hole to form. The nucleophilic attack by the oxygen of Ser 195 also forms a tetrahedral intermediate. By reconstruction of the carbonyl double bound, the amino portion of the peptide leaves as a product, and an acyl-enzyme intermediate is left in the active site. Now the active site needs to be regenerated. To do this a water molecule nucleophillically attacks the carbonyl carbon, forming another tetrahedral intermediate and reforming the oxyanion hole. The nitrogen of the His 57 ring makes the oxygen of the water more nucleophilic by hydrogen bonding to one of water's hydrogens. By reforming the double bond of the carbonyl carbon, the carboxy end of the original substrate's peptide bond is released, and the active site has been regenerated. The picture in the thumbnail to the left shows the entire catalytic mechanism for a serine protease~~. A figure of the oxyanion hole can be seen in greater detail in the thumbnail on the left~~.

Trypsin's active site is composed of its catalytic triad, three amino acid residues that are crucial to the enzymes proteolytic function. The catalytic triad consists of Asp 102, His 57, and Ser 195. Serine is the major player in the cleaveage of the peptide bond, thus the name serine protease. His 57 aids in the cleavage of the peptide bond through hydrogen bonds, and Asp 102 aids in the cleavage by electrostatically stabalizing the positively charged form of His 57 in the transition state. Ser 195 performs a nucleophilic attack on the substrate's peptide carbonyl. This causes the oxyanion hole to form. The formation of the oxyanion hole is stabalizing because the carbonyl oxygen that has accepted electrons during the nucleophilic attack fits nicely into this hole, and is stabalized by hydrogen bonds to the backbone NH groups of Gly 193 and Ser 195. A figure of the oxyanion hole can be seen in greater detail in the thumbnail on the left.

The nucleophilic attack by the oxygen of Ser 195 also forms a tetrahedral intermediate. By reconstruction of the carbonyl double bound, the amino portion of the peptide leaves as a product, and an acyl-enzyme intermediate is left in the active site. Now the active site needs to be regenerated. To do this a water molecule nucleophillically attacks the carbonyl carbon, forming another tetrahedral intermediate and reforming the oxyanion hole. The nitrogen of the His 57 ring makes the oxygen of the water more nucleophilic by hydrogen bonding to one of water's hydrogens. By reforming the double bond of the carbonyl carbon, the carboxy end of the original substrate's peptide bond is released, and the active site has been regenerated. The picture in the thumbnail to the left shows the entire catalytic mechanism for a serine protease.

[[Image:Triad 1.jpg |thumb]]

==Zymogen: Trypsin Precursor==

Sandbox 50: Difference between revisions

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 [[Image:Serine_protease_mechanism_by_snellios.png |thumb]]
 ===Active Site===
-Trypsin's active site is composed of its catalytic triad, three amino acid residues that are crucial to the enzymes proteolytic function. The catalytic triad consists of Asp 102, His 57, and Ser 195. Serine is the major player in the cleaveage of the peptide bond, thus the name serine protease. His 57 aids in the cleavage of the peptide bond through hydrogen bonds, and Asp 102 aids in the cleavage by electrostatically stabalizing the positively charged form of His 57 in the transition state. Ser 195 performs a nucleophilic attack on the substrate's peptide carbonyl. This causes the oxyanion hole to form. The nucleophilic attack by the oxygen of Ser 195 also forms a tetrahedral intermediate. By reconstruction of the carbonyl double bound, the amino portion of the peptide leaves as a product, and an acyl-enzyme intermediate is left in the active site. Now the active site needs to be regenerated. To do this a water molecule nucleophillically attacks the carbonyl carbon, forming another tetrahedral intermediate and reforming the oxyanion hole. The nitrogen of the His 57 ring makes the oxygen of the water more nucleophilic by hydrogen bonding to one of water's hydrogens. By reforming the double bond of the carbonyl carbon, the carboxy end of the original substrate's peptide bond is released, and the active site has been regenerated. The picture in the thumbnail to the left shows the entire catalytic mechanism for a serine protease. A figure of the oxyanion hole can be seen in greater detail in the thumbnail on the left.
+Trypsin's active site is composed of its catalytic triad, three amino acid residues that are crucial to the enzymes proteolytic function. The catalytic triad consists of Asp 102, His 57, and Ser 195. Serine is the major player in the cleaveage of the peptide bond, thus the name serine protease. His 57 aids in the cleavage of the peptide bond through hydrogen bonds, and Asp 102 aids in the cleavage by electrostatically stabalizing the positively charged form of His 57 in the transition state. Ser 195 performs a nucleophilic attack on the substrate's peptide carbonyl. This causes the oxyanion hole to form. The formation of the oxyanion hole is stabalizing because the carbonyl oxygen that has accepted electrons during the nucleophilic attack fits nicely into this hole, and is stabalized by hydrogen bonds to the backbone NH groups of Gly 193 and Ser 195. A figure of the oxyanion hole can be seen in greater detail in the thumbnail on the left.
+The nucleophilic attack by the oxygen of Ser 195 also forms a tetrahedral intermediate. By reconstruction of the carbonyl double bound, the amino portion of the peptide leaves as a product, and an acyl-enzyme intermediate is left in the active site. Now the active site needs to be regenerated. To do this a water molecule nucleophillically attacks the carbonyl carbon, forming another tetrahedral intermediate and reforming the oxyanion hole. The nitrogen of the His 57 ring makes the oxygen of the water more nucleophilic by hydrogen bonding to one of water's hydrogens. By reforming the double bond of the carbonyl carbon, the carboxy end of the original substrate's peptide bond is released, and the active site has been regenerated. The picture in the thumbnail to the left shows the entire catalytic mechanism for a serine protease.
 [[Image:Triad 1.jpg |thumb]]
 ==Zymogen: Trypsin Precursor==