Mechanisms of Catalysis

Mechanisms of Catalysis

• Enzymes speed up reactions by increasing the rate of collisions between substrates within the active site.
• Enzyme active sites are pre-organized to form near-attack complexes (NACs) where reacting atoms are in Van der Waals contact at an angle resembling the bond to be formed in the transition state.
• The presence of an enzyme increases the substrate collision rate from 0.0001% to 1-70%.
• NACs are characterized by reacting atoms within 3.2 Å and an approach angle of ±15° of the bonding angle in the transition state.
• Protein Motions Are Essential to Enzyme Catalysis
  • Proteins are constantly moving: bonds vibrate, side chains bend and rotate, backbone loops wiggle and sway, and whole domains move as a unit.
  • Active site conformation changes:
    • assist substrate binding
    • bring catalytic groups into position
    • induce formation of NACs
    • assist in bond making and bond breaking
    • facilitate conversion of substrate to product

Covalent Catalysis

• Active site residues form a temporary covalent bond with the substrate.
• At the end of the reaction, the covalent bond is broken to regenerate the enzyme.
• Often occurs due to nucleophilic attack by amino acid side chains on electrophilic groups on substrates.
• Can also involve prosthetic groups.
• Facilitates electron transfer.
• Double Displacement
  • Two substrates bind and react separately in a ping pong manner.
  • The product of the enzyme's reaction with the first substrate is released prior to the reaction with the second substrate, e.g., Enzyme-substrate Intermediates.

General Acid-Base Catalysis

• Proton transfer in the transition state.
• Transferring an H+ can:
  • Activate nucleophiles
  • Stabilize charged groups
  • Improve electrostatic interactions that stabilize the transition state
• Facilitates proton transfer
• Specific Acid-Base Catalysis
  • H+ or OH- that has diffused into the active site.
• Candidate amino acids are Glu, Asp, or His.
  • Histidine can be deprotonated by another group and then act as a base accepting a proton from the substrate.
• Water often plays a role as an acid or base at the active site through proton transfer with an assisting active-site residue.

Metal Ion Catalysis

• Common metal ions involved in catalysis include zinc, magnesium, and iron.
• Metal atoms lose electrons easily and exist as cations.
• Positive charge allows them to:
  • Stabilize transient and intermediate structures.
  • Assist in forming strong nucleophilic species.
  • Hold the substrate inside the active site.
  • Stabilize charge.

Low-Barrier Hydrogen Bonds (LBHBs)

• Typical H-bond strength is 10-30 kJ/mol, and the O-O separation is typically 0.28 nm.
• As the distance between heteroatoms becomes smaller, the H-bond becomes stronger, and the barrier to proton transfer decreases.
  • The lower the barrier, the stronger the bond.

Secondary Roles of Amino Acids

• About half of the amino acids engage directly in catalytic effects in enzyme active sites.
• Other residues may function in secondary roles in the active site:
  • Raising or lowering catalytic residue pKa values.
  • Orientation of catalytic residues.
  • Charge stabilization.
  • Proton transfers via hydrogen tunneling.