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8.5.4 Protein–protein interactions

Given the complex network of pathways that exist in the cell (signalling pathways,

biosynthetic pathways, etc.), it is clear that all proteins must interact with other

molecules to fulfil their role. Indeed, it is now apparent that proteins do not exist in

isolation in the cell; proteins involved in a common pathway appear to exist in a loose

interaction, sometimes referred to as a biomodule. Therefore, if one can identify an

interaction between our unknown protein and a well-characterised protein, it can be

inferred that the former has a function somehow related to the latter. For example,

if the unknown protein is shown to interact with one or more proteins involved in

the biosynthetic pathways for arginine, then this strongly suggests that the

unknown protein is also involved in this pathway. Using this approach networks of

AB C D E

P1 111 0 0

P2 001 1 1

P3 101 1 0

P4 011 0 1

P5 110 0 1

P6 011 0 1

P7 100 1 0

P8 101 1 0

Fig. 8.8Phylogenic profile method. Five genomes, A–E, are shown (e.g.E. coli,S. cerevisiae, etc.). The presence (1)

or absence (0) of eight proteins (P1–P8) in each of these genomes is shown. It can be seen that proteins P3 and

P8 have the same phylogenic profile and therefore may have a functional linkage. P4 and P6 are similarly linked.

347 8.5 Proteomics and protein function