1. Serine Proteases Components of the enzymatic pocket:
Oxyanion hole
Components of the enzymatic pocket:
1. Catalytic triad
(asp-his-ser)
2. Oxyanion hole
3. Specificity pocket
Specificity pocket
Catalytic triad

2. Basic mechanism

3. Aspartyl Proteases Components of the enzymatic pocket:
1. Two aspartate residues
2. Enzyme bound water
3. Specificity for hydrophobic amino acids
Charge repulsion of the two aspartate residues decreases side chain acidity

4. Basic mechanism
-There is no enzyme-substrate intermediate!

5. Be able to compare the mechanisms of the two protease types:
Catalytic residues
Catalytic triad (asp-his-ser)
Dual aspartate residues
Intermediate
Enyzme-bound
Tetrahedral, geminal diol
Specificity
Basic amino acids (arginine, lysine
Nonpolar amino acids (e.g. valine, leucine)

6. Be able to use the mechanisms of these two proteases to develop inhibitors
Serine proteases: make use of the enzyme bound intermediate to covalently trap the enzyme
-identify inhibitors by basic amino acids and good leaving groups/electrophilic sites
Aspartyl proteases: no enzyme bound intermediate
-mimic the tetrahedral nature of the bound intermediate (transition state analog)

7. N-terminal hydrolases
Examples include the proteasome, penicillin acylase, glutamine PPP amidohydrolase
Catalytic domain consists of a bound water molecule and an N-terminal serine, threonine, or cysteine

8. Autoproteolysis Similar mechanism to N-terminal hydrolases
Initial attack of amide by adjacent threonine is slow, rate limiting step