Catalytic Strategies

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Catalytic Strategies

• Covalent catalysis
• Form covalent intermediates
• Acid-base catalysis
• Use of molecule other than water as a proton
  donor or acceptor
• Metal ion catalysis
• At least one-third of enzymes contain metals
• Catalysis by approximation
• Bring two substrates together.

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Examples

• Proteases
• Carbonic Anhydrases
• Restriction enzymes

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Proteases

• Ingest system
• Blood coagulation
• Programmed cell death apoptosis

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Proteases
Peptide bonds are very stable. Proteases cleave
the bonds in milliseconds
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Chymotrypsin is a good example
Phe, Trp, Tyr, Met
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Chymotrypsin
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Kinetics of Chymotrypsin
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Irreversible Inhibitor of Chymotrypsin
diisopropylphosphofluoridate
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Chain A green Chain B orange Chain C blue
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Catalytic Triad in Chymotrypsin
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Binding state
Resting state
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Nucleophilic attack
donating both bonding electrons to electrophile.
Tetrahedral state
Binding state
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Tetrahedral state
Acyl-E state
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Acyl-E state
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Tetrahedral state
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Recovery
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Variations of Oxyanion Hole
Subtilisin (from Bacillus amyloliquefaciens)
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Other Serine Proteases
Trypsin, blue Chymotrypsin, red
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Specificity of Chymotrypsin
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Specificity of Other Serine Proteases
(V8 protease)
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Specificity of Serine Proteases may be Defined by
Multiple Binding Pockets
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Cysteine Proteases

• Cysteine, instead of serine, is activated by
  histidine, and plays the role of the nucleophile.

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Papain is isolated from papaya
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Caspases are Cysteine Proteases
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Aspartyl Proteases
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Aspartyl Proteases
pKa 1.2
pKa 3.9
Important in regulating blood pressure
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Aspartyl Proteases
HIV protease
The enzyme is essential for activation of viral
proteins.
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Specificity of HIV Protease and Inhibitors

• Hydrophobic residue-Proline-hydrophobic residues
• Inhibitors must be specific to HIV protease

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HIV Protease-Inhibitor Complex
Cocktail drug
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Metalloproteases
Carboxypeptidase A Matrix proteases
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Summary of Proteases

• Serine or Threonine protease
• Chymotrypsin, trypsin, elastase, subtilisin.
• Cysteine protease
• Papain, caspases
• Aspartic protease
• Renin, HIV proteases
• Zn protease
• Carboxypeptidase, matrix proteases