Mechanisms of Catalysis

Study Notes

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

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.

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.

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.

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.

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.