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

Chapter 6: The Three-Dimensional Structure of Proteins

Four Levels of Protein Structure

Proteins exhibit a hierarchical organization, with four distinct levels of structure that determine their shape and function. Each level contributes to the overall architecture and biological activity of the protein.

• Primary Structure: The linear sequence of amino acids in a polypeptide chain, linked by peptide bonds. This sequence is genetically determined and dictates all higher levels of structure.

• Secondary Structure: Local regions of regular, repeating structure stabilized by hydrogen bonds between backbone atoms. The most common elements are the α-helix and β-sheet.

• Tertiary Structure: The overall three-dimensional arrangement of all atoms in a single polypeptide chain, including interactions between secondary structure elements.

• Quaternary Structure: The spatial arrangement of multiple polypeptide chains (subunits) in a multisubunit protein complex.

Example: Hemoglobin exhibits all four levels: its primary sequence, α-helices and β-sheets, the folding of these elements, and the assembly of four subunits.

Common Secondary Structure Elements

Secondary structure refers to regular, repeating patterns within the polypeptide backbone, stabilized by hydrogen bonding.

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

• β-Sheet: Composed of β-strands aligned side-by-side, stabilized by interchain hydrogen bonds. Side chains alternate above and below the plane of the sheet. Sheets can be parallel (strands run in the same direction) or antiparallel (strands run in opposite directions).

Example: Silk fibroin is rich in β-sheets, while keratin contains α-helices.

Side Chain Positions in Secondary Structures

• In an α-helix, side chains radiate away from the helical axis, and the center consists of closely packed backbone atoms. 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

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. It forms a coiled-coil structure, with large hydrophobic residues repeating every four positions, creating a hydrophobic interface between helices.

• Fibroin: The main protein in silk cocoons, composed of extensive close-packed β-sheets interrupted by compact folded regions, providing elasticity.

• Collagen: The most abundant connective tissue protein, forming a triple helix structure. It serves as matrix material in bone, where mineral components precipitate.

Globular Proteins: Tertiary Structure and Functional Diversity

Globular proteins are compact, generally soluble proteins with diverse tertiary structures and functions.

• They contain varying amounts of α-helix, β-sheet, and loop regions.

• Larger proteins often consist of two or more distinct domains, each a compact folded region with a specific function (e.g., DNA recognition, oligomerization, cofactor binding).

• A typical domain is about 200 amino acids and can fold independently.

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

Factors Determining Secondary and Tertiary Structure

The folding and stability of proteins are governed by thermodynamic principles and various molecular 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 proteins have high entropy due to many possible conformations.

  • Folding restricts conformational freedom, resulting in lower entropy.

• Favorable Gain of Solvent Entropy (Hydrophobic Effect):

  • Burying hydrophobic side chains in the protein interior releases ordered water molecules, increasing overall entropy.

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

• Binding of Ions or Prosthetic Groups: Association with metal ions or non-protein groups (e.g., heme) can stabilize protein structure.

Equation:

Protein folding is driven by the change in Gibbs free energy:

$riangle G = riangle H - T riangle S$

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

Quaternary structure describes the arrangement and symmetry of multiple polypeptide chains in a protein complex.

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

• Point-Group Symmetry:

  • $C_2$: One axis of symmetry (2-fold)

  • $C_3$: One 3-fold axis

  • $D_2$: Three 2-fold axes

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

• Examples:

  • Transthyretin dimer exhibits $C_2$ symmetry (β-sandwich structure).

  • Phosphofructokinase tetramer displays $D_2$ symmetry (three 2-fold axes).

Table: Common Symmetries in 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 tetramer

Additional info: Symmetry in quaternary structure is important for protein function, assembly, and regulation.