23.1 Interactomics

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regulation can be quantified by looking at the effects of controlled environmental

perturbations on gene expression, or the number of regulatory proteins needed to

achieve a desired outcome. The trade-offs between different types of regulatory

strategies can be quantified by looking at the efficiency of the network, defined as

how well the network is able to respond to environmental changes. This efficiency

can be determined by looking at how quickly the network is able to change its

response to external stimuli, and how reliably it is able to maintain its response over

time. Efficiency can also be measured by looking at the amount of energy (or other

resources, provided that they are accounted for consistently) needed to maintain the

network, and how well it is able to optimize its response to a given set of inputs.

23.1 Interactomics

In the examples of previous section—and in numerous others in which the com-

munication channels along which information flows are conducting wires carrying

electrons—the elements constituting the regulated system are physically connected

by levers, wires, or pipes. In the living cell, the equivalent signal (Chap. 22) is typi-

cally a transformed molecule, such as an activated enzyme (e.g., by phosphorylation),

that simply diffuses away from where it is generated. Rather like certain male fish

mating by merely dispersing their sperm in the water around them, to be picked up

by any females of that species that happen to be in the vicinity, the transformed,

information-bearing molecules will only catalyse the reaction for which they are

activated if they encounter their specific substrate, to which they must first bind. ⁵

Hence, physicochemical affinities (interactions) between molecules play an essen-

tial rôle in regulation. From the base-pairing of nucleic acids, to the formation of

the bilayer lipid membranes enclosing organelles and cells, through to the protein–

protein interactions building up supramolecular complexes serving structural ends,

or for carrying out reactions, the regulation of gene expression by transcription fac-

tors binding to promotors, the operation of the immune system—the list seems to

be almost endless—one observes the molecules of life linked together in a web of

interactions. The set of all these interactions (i.e., a list of all the molecules, asso-

ciated with all the other molecules with which some kind of specific association is

found) constitutes the interactome (the repertoire of interactions). ⁶ With advancing

understanding of the interactome, chemists are now looking to design and engi-

5 Eukaryotic cells in particular are in a great deal more structured than the simple picture sug-

gests: Filaments of various kinds (e.g., microtubules) appear to function inter alia as tracks along

which certain molecules are transported to specific destinations. However, even in this case, the

information-bearing (“signalling”) molecule has first to encounter, and bind to, the carrier molecule

that will convey it along the track.

6 McConkey (1982) has coined the term “quinary structure” (of proteins) for this web of interactions.