Biochem- Lec Protein & Folding 5

Protein Structures and Folding

Part A: Globular Protein Structures

• Green Fluorescent Protein (GFP)

  • Structure: β-barrel with 11 antiparallel strands and an α-helix at the center.

  • Contains fluorescent group made from three protein side-chains: Ser-Tyr-Gly.

  • The protein modifies itself to create the chromophore located in the middle of the central helix.

  • Origin: Derived from the jellyfish, Aequorea victoria.

  • Key feature: Self-contained, single protein which can have its gene cloned into other organisms.

• Heme-Containing Proteins

  • Porphyrin: Large, rigid hydrophobic ring that binds a metal ion (e.g., Fe2+, Mg2+, or Zn2+).

  • Commonly found in:

    • Myoglobin

    • Hemoglobin

    • Cytochromes

    • Catalase

  • Brightly colored due to the presence of metal ions and conjugated aromatic ring electrons.

• Myoglobin

  • Length: 153 amino acids.

  • Function: Stores oxygen in muscle tissues.

  • Structure: Monomeric with 8 α-helices; heme binds in a hydrophobic pocket within the protein.

Part B: Fibrous Protein Structures

• Fibrous Proteins

  • Characterized by long, regular secondary structure arrays and repeating sequences.

  • In contrast to globular proteins, which have complex primary sequences and shorter stretches of secondary structure.

• α-Keratin

  • Structure: Forms a coiled-coil structure with two wrapped α-helices.

  • Composition: 3.6 residues per turn; 7 residue pseudorepeat.

  • Features: Nonpolar residues pack together between helices, resulting in a non-polar core for folding, leading to long and stiff fibers.

Part C: Higher-Order Structures

• Keratin

  • Coiled-coils are bundled and stabilize through disulfide linkages.

  • Perming involves chemical treatment to break and reshape these linkages.

• Collagen

  • Structure: Triple helix formed by three repeated amino acids (Gly-Pro-xxx).

  • Modifications: Pro residues are often converted to hydroxyproline (Hyp).

  • Features: Non-alpha helix structure provides stiffness and strength, making it ideal for bones and tendons.

Collagen Diseases

• Scurvy: Vitamin C deficiency affecting collagen formation, leading to fragile blood vessels and bleeding.

• Ehler’s-Danlos Syndrome: Genetic replacement of Gly with Ser in the collagen Col1A gene results in loose joints and skin.

• Osteogenesis Imperfecta: Gly replaced by Ser/Cys in collagen gene Col5A leads to brittle bones.

Part D: Protein Folding

• Proteins begin in an unfolded state post-ribosome synthesis.

• Secondary structure formation aids in collapsing proteins into their stable, folded forms.

• The native folded structure is the thermodynamically most stable state, though protein folding pathways often have intermediate steps.

• Weak non-covalent attractions, such as the hydrophobic effect and van der Waals forces, maintain tertiary structure.

• Higher entropy in unfolded proteins opposes the folding process.

Part E: Unfolding and Chaperonins

• Unfolding Agents: Ethanol, heat, and detergents can lead to protein unfolding.

• Chaperonins: Assist folding by recognizing and repairing misfolded proteins.

  • Example: GroEL/GroES complex helps proteins refold through a barrel-like structure that protects misfolded proteins and requires ATP hydrolysis for release.

Key Terms

• Tertiary Structure: Three-dimensional structure formed by folding of the protein.

• Globular Proteins: Proteins with compact, spherical shapes.

• Fibrous Proteins: Proteins with elongated structures and less folding complexity.

• Heme: The iron-containing component of hemoglobin and myoglobin.

• Protein Folding: Process of achieving a stable three-dimensional structure involving interactions between non-polar side chains, hydrogen bonds, and entropy dynamics.