Chapter 9: Catalytic Strategies of Enzymes

Catalytic Strategies of Enzymes establishes fundamental principles such as the use of binding energy to stabilize transition states and promote induced fit, alongside chemical strategies including covalent catalysis, general acid-base catalysis, catalysis by approximation, and metal ion catalysis. The text details the mechanism of serine proteases like chymotrypsin, which facilitates the hydrolysis of kinetically stable peptide bonds using a catalytic triad of serine, histidine, and aspartate. This triad activates serine into a potent alkoxide nucleophile, leading to a covalent acyl-enzyme intermediate stabilized by the oxyanion hole. Substrate specificity is shown to depend on the S1 binding pocket, distinguishing chymotrypsin from homologs like trypsin and elastase, while convergent evolution is illustrated by subtilisin. The discussion extends to cysteine, aspartyl, and metalloproteases, highlighting the clinical importance of protease inhibitors like Indinavir for HIV treatment. The chapter then explores carbonic anhydrases, which accelerate carbon dioxide hydration to near-diffusion-limited rates by using a zinc ion to lower the pKa of a bound water molecule, generating a reactive hydroxide nucleophile. To bypass proton diffusion limits, these enzymes employ a histidine proton shuttle to transfer protons to the buffer. Specificity mechanisms are further examined through restriction endonucleases like EcoRV, which cleave specific DNA sequences to protect host bacteria from viral infection. EcoRV demonstrates that specificity can arise from catalytic activation rather than binding affinity; only cognate DNA is distorted (kinked) to position a magnesium ion for direct hydrolysis, a mechanism confirmed by the inversion of stereochemistry at the phosphorus atom. Host DNA protection is achieved through methylation, which prevents this critical distortion. Finally, the chapter investigates myosins, which harness the free energy of ATP hydrolysis to drive mechanical motion. Using transition-state analogs like vanadate, structural studies reveal that ATP hydrolysis is reversible within the active site and that the release of the phosphate product is the rate-limiting step. Myosins are identified as members of the P-loop NTPase family, utilizing conformational changes to perform work.