Chapter 6: The Three-Dimensional Structure of Proteins – Study Notes

Four Levels of Protein Structure

Overview of Protein Structural Organization

Proteins exhibit a hierarchical organization, classified into four distinct structural levels. Each level contributes to the overall shape and function of the protein molecule.

• Primary Structure: The linear sequence of amino acids in a polypeptide chain, determined by genetic information. This sequence dictates all higher levels of structure.

• Secondary Structure: Localized regions of repeating main chain structure, stabilized by hydrogen bonds. Common elements include α-helix and β-sheet.

• Tertiary Structure: The overall three-dimensional arrangement of secondary structural elements within a single polypeptide chain.

• Quaternary Structure: The spatial arrangement of multiple polypeptide chains (subunits) to form multisubunit complexes.

Example: Hemoglobin is a classic example of a protein with quaternary structure, consisting of four polypeptide subunits.

Common Secondary Structure Elements

α-Helix and β-Sheet

Secondary structures are stabilized by hydrogen bonding patterns and are fundamental to protein folding.

• α-Helix: A right-handed coil where side chains radiate outward from the helix axis. Hydrogen bonds are nearly parallel to the helix axis, often resulting in distinct hydrophilic and hydrophobic faces.

• β-Sheet: Composed of β-strands stabilized by interchain hydrogen bonds. Side chains alternate above and below the plane of the sheet. Strands can be parallel (same N→C direction) or antiparallel (opposite N→C directions).

Example: Silk fibroin is rich in β-sheet structure, contributing to its strength and flexibility.

Side Chain Positions in Secondary Structures

• In an α-helix, side chains radiate away from the helical axis, with backbone atoms closely packed in the center. Hydrogen bonds stabilize the helix.

• In a β-sheet, neighboring side chains are located on opposite faces of the sheet, stabilized by hydrogen bonds between adjacent β-strands.

Fibrous Proteins: Structural Materials of Cells and Tissues

Characteristics and Examples

Fibrous proteins are elongated molecules with well-defined secondary structures, serving as structural materials in cells and tissues.

• Keratin: Found in hair, fingernails, feathers, scales, and intermediate filaments. Features a coiled-coil structure with hydrophobic residues repeating every four positions.

• Fibroin: The main protein in silk cocoons, characterized by extensive close-packed β-sheets interrupted by folded regions for elasticity.

• Collagen: The most abundant connective tissue protein, forming a triple helix and serving as matrix material in bone.

Globular Proteins: Tertiary Structure and Functional Diversity

Three-Dimensional Structure and Domains

Globular proteins fold into compact, diverse three-dimensional structures, often containing multiple domains with specific functions.

• Domains are independently folding units, typically ~200 amino acids in length.

• Domains may be responsible for DNA recognition, oligomerization, or cofactor binding.

Example: Human ubiquitin is a small globular protein with a well-defined tertiary structure.

Factors Determining Secondary and Tertiary Structure

Thermodynamics, Folding, and Stability

Protein folding is governed by a balance of enthalpic and entropic factors, as well as specific stabilizing interactions.

• Favorable intramolecular enthalpic interactions:

  • Charge-charge interactions (ionic bonds)

  • Intramolecular hydrogen bonds

  • Van der Waals interactions (dense packing of atoms)

• Unfavorable loss of conformational entropy:

  • Unfolded state has high entropy (many conformations)

  • Folded state has low entropy (few conformations)

• Favorable gain of solvent entropy:

  • Burying hydrophobic groups releases ordered water molecules (hydrophobic effect)

• Disulfide bonds: Covalent bonds between cysteine residues greatly increase protein stability.

• Binding of ions or prosthetic groups: These interactions further stabilize protein structure.

Key Equations

• Gibbs Free Energy of Folding: $riangle G = riangle H - T riangle S$ where $riangle G$ is the change in free energy, $riangle H$ is the change in enthalpy, $T$ is temperature, and $riangle S$ is the change in entropy.

Quaternary Structures—Symmetries

Types of Symmetry in Multisubunit Proteins

Quaternary structure often involves symmetrical arrangements of subunits, classified by point-group symmetry.

• Helical symmetry: Structures such as actin and tobacco mosaic virus can grow indefinitely in length.

• Point-group symmetries:

  • $C_2$: one 2-fold axis

  • $C_3$: one 3-fold axis

  • $D_2$: three 2-fold axes

  • $D_4$: one 4-fold axis and two 2-fold axes

Example: The tetrameric enzyme phosphofructokinase displays $D_2$ symmetry.

Table: Common Symmetries in Protein Quaternary Structure

Symmetry Type	Description	Example
Helical	Indefinite growth in length	Actin, Tobacco mosaic virus
$C_2$	One 2-fold axis	Transthyretin dimer
$D_2$	Three 2-fold axes	Phosphofructokinase

Additional info: Symmetry in quaternary structure is crucial for the assembly and function of many protein complexes, including enzymes and structural proteins.