Quaternary Structure
Whereas all proteins have primary, secondary and tertiary strucuture, not all proteins possess quaternary structure. Quaternary structure occurs when proteins are made of two or more polypeptides (called subunits or chains).
When a protein consists of two subunits, and both subunits are identical, it is called a homodimer (homo=same; di=two). If it consists of two subunits which are different, it is called a heterodimer (hetero=other). Some proteins, such as RNA polymerase, are quite large, containing many different subunits. These are called multimeric proteins.
Insulin is a heterodimer, containing, an A chain and a B chain.
A chain of insulin The A chain of insulin is shown in medium spring green (2HIU.pdb) I am not sure Oppenheimer would approve of this color.
B chain of insulin The B chain of insulin is shown in hot pink. (2HIU.pdb) This is Barbie's favorite accessory.
The subunits in proteins with quaternary structure are held together by the same types of interactions as in the tertiary structure, except the interactions occur between chains, instead of within a single chain. Explore these interactions in the proteins below.
Hydrophobic Interactions Hemoglobin carries oxygen in the blood. You explored the beta subunit (beta globin) earlier in this tutorial (1A3N.pdb). It consists of two alpha subunits and two beta subunits. Only one of each of the two different subunits is displayed here. Two pairs of interactions are shown here; sidechains are in cpk, and the backbone atoms of interaction sidechains are colored green or blue.
Salt Bridges Triose phosphate isomerase (TPI) is an enzyme in the glycolytic pathway. (2YPI.pdb) TPI is a homodimer. Three salt bridges between the subunits are shown here; the backbone of each pair of interacting subunits is colored differently.
Hydrogen Bonds TPI (2YPI.pdb). Although two hydrophobic sidechains are shown here, hydrogen bonds form between the polar backbone atoms of these residues. Note that two hydrogen bonds form between each pair. Remember that hydrogen atoms are not displayed, but are present between the N and O atoms shown here.
Sulfur-Sulfur Bonds Insulin is a peptide hormone involved in regulating blood glucose levels. (2HIU.pdb) Insulin is a heterodimer; two interchain disulfide bonds (inter=between, as in interstate highway) join the A and B chains; a third intrachain disulfide bond (intra=within) stabilizes the A chain.
Thusfar you have reviewed the four levels of protein structure and have become familar with visualizing proteins using computer models. Now you will look at specific interactions between two proteins and a protein and DNA. These are the same types of interactions that occur between enzymes and substrates.
Remember that enzymes are proteins in which the amino acid sidechains serve as the binding site by holding the substrate in the correct orientation, and also serve as the catalytic group that changes the substrate to the product.