The quaternary structure is that level of form in which units of tertiary structure aggregate to form homo- or hetero- multimers. This is found to be remarkably common, especially in the case of enzymes. The prokaryotic biosynthesis of tryptophan provides interesting examples which fall into each of the categories below. (See Branden & Tooze, 1991)
In this class of protein, domains are usually formed as modules covalently "strung together" on a single polypeptide chain. The individual chains of antibodies are like this, strings of immuno-globulin domains. However, light and heavy chains then combine to produce hetero-multimers, which may even associate into higher complexes, as with IgM.
In the case of the single polypeptide chain of pyruvate kinase there are four domains; the central TIM-barrel is the catalytic domain, whereas the other three play no direct role in enzymatic activity. However, the small N-terminal domain of 42 residues is involved in inter-subunit contacts when four copies associate to form a homo-tetramer.
E.coli produces a bifunctional enzyme which performs both the isomerisation of phospho-ribosyl anthranylate AND the synthesis of indole-glyceryl phosphate, two steps in tryptophan biosynthesis. It comprises two very similar eight-stranded a/b barrels, each barrel acting as a separate enzyme.
In this case we see different tertiary domains aggregating together to form a unit. The photoreaction centre is a good example.
Sometimes, we find that several domains are found in a single enzyme complex, either in a single polypeptide chain, or as an association of separate chains.
Often the domains have related functions, for instance, where one domain will be responsible for binding, another for regulation, and a third for enzymatic activity. Cellobiohydrolase provides anexample of such a protein. It is not uncommon to find more than once the same chain in a protein complex. A good example is the F-1 ATPase.
Two (further) steps in the biosynthetic pathway of tryptophan (in S.typhimirium) are catalysed by tryptophan synthase which consists of two separate chains, designated a and b, each of which is effectively a distinct enzyme.
The biologically active unit is a hetero-tetramer comprised of 2 a and 2 b units.
We sometimes find slightly different versions of the same protein associating. Thus, haemoglobin has both an A-chain and a B-chain, which come together to form a hetero-dimer. Two copies of this then associate to form the normal haemoglobin tetramer. Which is equivalent to an A-dimer associating with a B-dimer.
Also, it can happen that two different chains associate to form a bigger secondary structure. It is the case of the pea lectin, where a very large b-sheet is nade out of strands coming from different protein chains:
It is far more common to find copies of the same tertiary domain associating non-covalently. Such complexes are usually, though not always symmetrical. Because proteins are inherently asymmetrical objects, the multimers almost always exhibit rotational symmetry about one or more axes. The majority of the enzymes of the metabolic pathways seem to aggregate in this way, forming dimers, trimers, tetramers, pentamers, hexamers, octamers, decamers, dodecamers, (or even tetradecamers in the case of the chaperonin GroEL).
The reason for this is now thought to be the allosteric cooperativity that results in increased catalytic efficiency, effectively a "sharing" of the small conformational changes that accompany substrate binding and catalytic activity. A good well-studied example is the "breathing motion" observed in the haemoglobin tetramer.
Another interesting case study is found with the growth factors where we see dimers formed in 3 different ways, corresponding to two-fold axes in different directions.
There are other examples where dimerisation is necessary to actually create the active site of the enzyme in question. For instances the HIV protease, the viral (aspartic) protease responsible for excising the separate proteins from the single polyprotein that the virus produces once inside the cell.
In some instances, such as cytokines, homo-trimerisation leads to the formation of a functional ligand, which will pull together three single-chain receptors. Upon binding these receptors will trigger intra-cellular signals.
Examples of symmetrical enzyme multimers in the form usually found in cells have been especially prepared and archived at Brookhaven in a directory dedicated to these biological units. It may be accessed by anonymous ftp to ftp.pdb.bnl.gov and going to directory /user_group/biological_units/. The contents and associated README are worth a look.
The molecular machinery of the cell and indeed of assemblies of cells, rely on components made from multimeric assemblies of proteins, nucleic acids, and sugars. A few examples include :-
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