Protein Structure Class: 3. Tertiary
tertiary structure of proteins
- Interactions between amino acid residue side chains form the 3D structure of proteins.
- The tertiary structure is where the protein begins to take on its final three-dimensional shape via polypeptide side chain interactions, as opposed to primary and secondary structure wherein the amino and carboxy groups create the bonds.
- Tertiary structure interactions are not limited to localized regions of the polypeptide chain: amino acids on opposite ends of the chain may interact – unlike in primary and secondary structure, where residues in close proximity interact.
- Tertiary structure comprises four types of covalent and non-covalent interactions:
- Tertiary structures are sensitive to environmental changes (called denaturing agents) such as: temperature, pH, and strong oxidizing/reducing agents. These denaturing agents are so-named because they cause the protein's structure to fall apart.
- Many of these changes are reversible because primary structure is sufficient to dictate tertiary structure, meaning: once the denaturing agent is removed, the protein will reassemble itself into its tertiary structure.
Tertiary Structure
- Tertiary structure interactions involve parts of the protein that are not always close together in the polypeptide sequence, so here we draw our entire polypeptide chain and then add the representative tertiary structure bonds.
- Here, we draw a tertiary protein sequence as follows: a beta strand, a short alpha helix, two anti-parallel beta strands, another alpha helix, another beta sheet, two alpha helices separated by a turn and a third alpha helix separated by a loop.
- Tertiary molecular interactions occur between non-adjacent secondary elements.
- The side chains of the amino acid residues are the only participants in our molecular interactions.
Hydrogen bond
- Serine residue on beta strand 3 forms a hydrogen bond to a glutamate residue on beta strand 4. The hydrogen from serine is "donated" to the carbonyl oxygen on glutamate.
Ionic bond
Ionic bonds form between oppositely charged side chains of amino acid residues.*
- We show this between alpha helix 5 and beta strand 6.
- We draw an aspartic acid residue on alpha helix 5, which forms an ionic bond with a lysine residue on beta strand 6. The negatively charged carbonyl oxygen of aspartate binds to the positively charged epsilon amino of lysine.
Hydrophobic interaction
- We draw a leucine residue on beta strand 4 and show that it forms a hydrophobic interaction with a valine residue on alpha helix 7. Interactions between these hydrophobic residues excludes water: they are not truly bonds in the sense that they do not occur from attraction of the amino acid side chains to one another.
Disulfide bond
- The disulfide bond between two cysteine residues on beta strand 1 and alpha helix 8 helps "lock" the protein into its shape.
- Disulfide bonds are covalent bonds between two cysteine residues that are difficult to break. Because these bonds are so secure, they are believed to be the last bonds formed in tertiary structure and help set the final shape of the protein.
Bonds: Review
- Hydrogen: two polar residues (or polar + water).
- Ionic: negatively and positively charged side chains.
- Hydrophobic: hydrophobic residues.
- Disulfide: cysteine residues.