Protein Structure: From Amino Acids to Quaternary Levels

Primary Structure

Primary Structure: Amino acid sequence, description of all main covalent disulfide bonds and peptide bonds.

• Superfamily: Homology 30%.
• Families: Greater than 50% homology and usually the same function.

Enzymes that break peptide bonds:

• Trypsin
• Chymotrypsin
• Pepsin
• Papain

Predictions from primary structure:

• Homology
• Hydrophobicity
• Secondary structure
• HPLC chromatographic retention
• Accessible and hidden residues
• Mutability

Secondary Structure

Secondary Structure: Folding of the polypeptide chain that occurs due to the formation of hydrogen bonds between the atoms forming the peptide bond.

Structures formed:

• Alpha-helix
• Beta-sheet
• Beta-turn

Examples:

• Alpha-helix: Myoglobin (globular protein), Fibrinogen (fibrous protein)
• Beta-sheet: Fibroin (fibrous protein)

Supersecondary Structures

• Helix-turn-helix
• Seven transmembrane helices and amphipathic helix
• Leucine zipper
• Beta-alpha-beta unit
• Beta-meander
• Zn Finger
• EF Hand

Determination of Secondary Structure

Physical methods:

• X-ray Crystallography
• Nuclear Magnetic Resonance (NMR)

Other techniques: Circular dichroism

Tertiary Structure

Tertiary Structure: Three-dimensional structure of the protein.

Forces Maintaining Tertiary Structure

Noncovalent:

• Hydrophobic effect: Nonpolar amino acids are placed in the interior of the protein and polar amino acids are placed outward.
• Hydrogen bonds:
  • Acceptor: Histidine, Cysteine, Methionine, Glutamic Acid, Glycine, Asparagine
  • Donor: Tyrosine, Serine, Threonine, Lysine, Arginine, Glutamine
• Ionic interactions or salt bridges: Lysine, Arginine, Histidine, Glutamic Acid

Covalent:

• Disulfide bond
• Amide bond

Protein Classes

• Class 1: Alpha, non-bundled, small-peptide
• Class 2: Beta. Examples: Barrel porin, propeller hemopexin, solenoid pectate lyase
• Class 3: Alpha-beta. Examples: Barrel triosephosphate isomerase, horseshoe-ribonuclease inhibitor
• Class 4: Irregular. Example: Pisum sativum lectin

Quaternary Structure

Quaternary Structure: The spatial arrangement of different polypeptide chains of a multimeric protein.

Forces Maintaining Quaternary Structure

The same forces that maintain tertiary structure.

Proteins with Quaternary Structure

• Hemoglobin
• Concanavalin
• Aspartate transcarbamylase
• Glycogen phosphorylase