Lecture: Tertiary Structures of Proteins (Part 2)

Overview

• Discussion on the tertiary structures of proteins.
• Focus on interactions between the side groups of amino acids (distinct from secondary structure which involves peptide bonds).

Types of Interactions

Dipole-Dipole Interactions

• Occur between polar side chains of amino acids that are not sufficiently polar for hydrogen bonding.
• Example: Serine and Methionine.
  • Serine: CH2-OH
  • Methionine: CH2-CH2-S-CH3
• Interaction between positive ends (hydrogen of serine) and negative ends (sulfur of methionine).
• Generally weak but significant in large numbers.

Dispersion Forces (Hydrophobic Forces)

• Involve non-polar side groups (C-H based structures).
• Protein solubility depends on the solvent (polar or non-polar).
  • Non-polar solvent (e.g., lipids):
    • Non-polar side groups on the exterior of the protein.
    • Polar side groups on the interior.
  • Polar solvent (e.g., water):
    • Polar side groups on the exterior, interacting with water.
    • Non-polar side groups on the interior, avoiding water.
• Hydrophobic and hydrophilic nature helps maintain protein structure.

Ionic Interactions

• Certain amino acids can form ions through their side groups (functional groups like amine or carboxylic acid).
• Example: Aspartic Acid and Lysine.
  • Aspartic Acid: COO-
  • Lysine: NH3+
  • Form electrostatic attraction.
• Ionic interactions can also involve metal ions (e.g., iron in hemoglobin).
  • Can link different parts of the same protein or multiple proteins.
  • Example: Iron holding together four heme units in hemoglobin.

Key Points

• Tertiary structures are determined by the specific interactions between the side chains of amino acids.
• Different environments (solvent types) affect the protein folding and stability.
• Multiple types of interactions (dipole-dipole, hydrophobic, ionic) work together to establish the protein's three-dimensional structure.