Protein function Chapter 5

Chapter 5: Function of Globular Proteins

• Importance of ligands and their reversible binding to proteins.

  • Specificity of ligands and binding sites.

  • Binding often leads to conformational changes (Induced Fit).

  • In multisubunit proteins, one subunit's conformational change can trigger effects in others (Cooperativity).

  • Detail of interactions can be regulated.

• Examples: Hemoglobin, antibodies, muscle contraction.

Functions of Globular Proteins

• Storage of Ions and Molecules

  • Example: Myoglobin, ferritin.

• Transport of Ions and Molecules

  • Example: Hemoglobin, serotonin transporter.

• Defense Against Pathogens

  • Example: Antibodies, cytokines.

• Muscle Contraction

  • Example: Actin, myosin.

• Biological Catalysis (Enzymes)

  • Example: Chymotrypsin, lysozyme.

Interaction with Other Molecules

• Reversible, transient process of chemical equilibrium: A + B → AB.

• Ligands: Molecules that bind to proteins, usually small.

  • Binding Site: Specific region within the protein where ligands attach.

• Binding is through noncovalent forces (similar to protein structure).

Binding: Quantitative Description

• Association and Dissociation Rates:

  • Association Rate Constant (ka): Rate at which ligand and protein form a complex.

    • Equation: Rate of association = ka [P][L].

  • Dissociation Rate Constant (kd): Rate at which the protein-ligand complex dissociates.

    • Equation: Rate of dissociation = kd [PL].

• Equilibrium:

  • At equilibrium, association and dissociation rates are equal.

  • Characterized by: Equilibrium Association Constant (Ka) and Equilibrium Dissociation Constant (Kd).

Binding: Analysis in Terms of the Bound Fraction

• Fraction of Occupied Binding Sites (θ): Proportion of total binding sites occupied by ligand.

• Equation for θ: [PL] / ([P] + [PL]).

Binding: Graphical Analysis

• Binding curve plotted against ligand concentration and θ.

• Shape: Rectangular hyperbola.

  • Key feature: θ = 0.5 at [L] = Kd.

Example: Oxygen Binding to Myoglobin

• Binding expressed in partial pressures: [L] / (Kd + pO2).

• Myoglobin's binding curve is hyperbolic; 50% saturation at P50 = 0.26 kPa.

• Under normal oxygen levels, myoglobin is highly saturated (94%).

Binding Strength: Protein Dissociation Constants

• Example Table: Protein vs. Ligand affinities.

• Notable examples include: Avidin-Biotin (1 x 10^-15 M) and Insulin Receptor-Insulin (1 x 10^-10 M).

• Interactions vary greatly based on conditions (pH, salt concentration).

Specificity: Lock-and-Key vs. Induced Fit Models

• Lock-and-Key Model: Assumes complementary surfaces are preformed.

• Induced Fit Model: Conformational changes occur upon binding, allowing tighter binding and higher affinity.

Globins: Oxygen-Binding Proteins and Heme Role

• Myoglobin: Main oxygen storage protein.

• Hemoglobin: Circulating oxygen-binding protein.

• Heme's iron can bind oxygen; however, free iron can generate free radicals.

Structures of Myoglobin

• Compact globular structure with a sequence of 153 amino acids.

• Composed mostly of α-helix structures, with significant hydrophobic and hydrophilic regions.

Binding of Carbon Monoxide

• CO binds to heme better than O2, causing toxicity.

• Binding mechanics adjusted when heme is protein-bound versus free.

Hemoglobin Characteristics

• Oligomeric protein in red blood cells (RBCs) designed for oxygen transport.

• Structure formed by two α and two β chains.

R and T States of Hemoglobin

• T State: Tense, low-affinity for oxygen.

• R State: Relaxed, high-affinity for oxygen.

• Oxygen binding triggers T → R conformational change.

Regulation of Muscle Contraction

• Myosin-binding sites on actin regulated by troponin and tropomyosin.

• Ca2+ release from nerve impulses exposes binding sites.

Chapter 5: Summary

• Covered: Ligand binding effects on proteins, quantitative binding analysis, oxygen storage by myoglobin, oxygen transport by hemoglobin, antibody foreign structure recognition, and muscle contraction mechanisms.