Protein Folding

Protein Denaturation

Denaturation: Disrupting the native conformation of a protein.
Examples:
- Cooking eggs (heat denaturation): Egg whites turn from clear to white.
- Common denaturing agents: Urea, Potassium cyanate, Detergents (e.g., SDS), Acid (e.g., lemon juice, vinegar in cheese making).
Melting Temperature (TM):
- Temperature at which there is 50% folded and 50% unfolded protein.
- Most proteins in biological systems have a TM between 40-60°C.
- Thermophiles (heat-loving organisms): TM can be >100°C.

Example: Ribonuclease A
- Denatured with Urea; takes about 1 minute to refold to native structure.
Folding is not by random sampling of all conformations but driven by specific factors.

Thermodynamics:
- ΔG = ΔH - TΔS
- ΔS (Entropy): Negative (decreasing entropy from random chain to folded protein).
- ΔH (Enthalpy): Negative (exothermic from intermolecular forces like hydrogen bonding, dipole-dipole interactions, Van der Waals interactions).
- Hydrophobic Effect: Water molecules excluded upon folding increase disorder (favorable ΔS).
- Overall: Protein folding is spontaneous (negative ΔG), but not instantaneous.

Proteins are not static; they are in motion in solution.
Folding towards the lowest energy conformation (energy funnel model).
- Intermediate lower energy forms can exist.
- Enzymes help escape false low-energy intermediates.
Energy Well Model:
- Rapid, reversible secondary structure formation (alpha helices and beta sheets) to final native structure.

Facilitate proper protein folding.
- Prevent misfolding or aggregation.
- Energetically required process (uses ATP).
- ATP → ADP leads to natively folded protein.

Some caused by simple mutations (e.g., incorrect polypeptide chain sequence).
Others due to protein misfolding independent of mutations.
- Often amyloid-related diseases (protein aggregation).
- Important for human health to prevent misfolding and aggregation.