Subunits & Quaternary Structure

Proteins containing more than one polypeptide chain exhibit an additional level of structural organisation.

In this case, each polypeptide chain is a "subunit". Quaternary (4^o) structure describes the way the subunits are arranged together and the nature of their contacts.

Subunits associate by non-covalent interactions similar to those involved in tertiary structure:

Hydrophobic Interactions Hydrogen bonds Salt Bridges / Ion Pairs

Haemoglobin consists of 2a subunits (each 141 amino acids) - the green and the dark blue chains. There are also 2b subunits (each 146 amino acids) - the orange and light blue chains. Together these make a tetramer described as: "a₂b₂".

Note also that each subunit of haemoglobin has a haem group associated with it. (Grey and red molecule in each subunit.) Remember also that each subunit of haemoglobin is quite similar in structure to the single chain of myoglobin. However myoglobin does not associate to form a tetramer. This property of haemoglobin gives it some important characteristics in the way in which it binds oxygen. These will be looked at later in the tutorial

Proteins with subunits are called oligomeric proteins. Because haemoglobin has subunits of two types, a and b, it is called a "hetero-oligomer". Oligomeric proteins with identical subunits are called "homo-oligomers".

There are also proteins with a great many subunits (not just 4 as for haemoglobin).

Choleratoxin consists of 6 subunits, described AB₅. There is a ring of 5 B subunits which form a "base" (Red, gold, yellow, green and cyan.) upon which the A subunit (light and dark blue) sits.

The B subunits attach to the host cell membrane (usually an intestinal cell as cholera is a pathogen of the digestive tract) and form a pore through which the A subunit passes to enter the host cell cytosol. When the A subunit enters the cell it catalyses a reaction which inactivates one of the proteins of the cell membrane. This causes a massive loss of Na⁺ and water from the cell into the gut and causes the symptoms of cholera.

Rhinovirus (causes a cold) and Poliovirus (causes Polio) have a genome which is encapsulated in a protein coat of 180 subunits. There are 60 VP1 , 60 VP2 and 60 VP3 subunits in the coat. On the inside, are 60 VP4 subunits which house the RNA genome, unitl it is release inside the infected cell to cause the cell to more viral particles. Because it is such a huge protein complex, there have been no crystals made of it yet. For a good representation, see Stryer (4th Ed), Figure 2-47, p36.

Domains

Sometimes a single polypeptide may fold into two or more compact regions called domains. These can be from 100 to 300 residues in size.

A good example of proteins with well-defined domain structure are the immunoglobulins, the antibody proteins which circulate in the blood and combine with and neutralise foreign antigens. You looked at immunoglobulins in the first part of the tutorial but here is the structure again:

The domain structure of the heavy and light chains of the molecule should be obvious, especially if you turn on rotation. The light chains are blue and yellow and the heavy chains are red and cyan.

Some proteins can have quite complex folding and domain patterns. The structure of lactoferrin, an iron binding protein from milk, was determined here at Massey by Professor Ted Baker and his group.

Lactoferrin is an iron-binding protein from milk. The structure shown is that of the protein from human milk. The single polypeptide chain (691 residues) folds into two lobes domains (of approximately 345 residues each) (green and red) joined by a short linking helix (yellow). Each lobe has a binding site for a single iron (Fe³⁺) atom (magenta). The sequence of each lobe is quite similar, suggesting that the ancestral protein may have been half the size and had a single lobe and iron binding site.

Each lobe of lactoferrin has two domains and the iron binding site is located in a cleft between them. However in lactoferrin each domain is not a single linear length of the peptide sequence as the domains in immunoglobulins are. In the N-terminal lobe of lactoferrin the sequence starts in one domain, moves into the second domain and then back into the first domain before running through a short connecting helix to the C-lobe where the folding pattern is repeated. This is shown in the next image.

The two domains of the N-lobe of lactoferrin are shown in blue and yellow with the Fe³⁺ in magenta. If the rotation function is turned on you will be able to see the cleft that the iron sits in and also the way the peptide chain runs from one domain (the green one) into the second (red) and then back to the first (green again).

The two domains of the N-lobe of lactoferrin can move independently of each other and release the iron atom.



Often proteins fold into domains and each domain is associated with a particular function of the protein.

The steroid hormone receptors are located in the cytosol of cells which are targets of the particular hormone. The steroid hormone is released into the blood from the tissue where it is made and is carried round the body in the blood. The steroid homones can anter all cells, but in their specific target cells there is a protein receptor to which the hormone binds. The receptor plus hormone is transported into the nucleus and binds DNA at specific target sequences and brings about changes to the expression of aghacent genes..

Steroid receptors can all these tasks even though they are only a single polypeptide. (p)The first 100 or so residues form an activation domain, the next 60 residues or so comprise the DNA binding domain, and the last 250 or so residues make a hormone binding domain. The entire protein has not been able to form crystals, and so a picture is not available. However individual domains of the steroid receptor have been crystallise and the structures determined.

By now you should have a good idea how a protein folds and the various shapes that they can assume.

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