Biology Reference
In-Depth Information
transport/sorting proteins and their cargo. Such transient interactions
are often mediated by much smaller interaction interfaces, or even just by
short peptide segments, and they probably do evolve
de novo
more easily
than stable interactions.
3. Networks That Include Indirect Associations
Simple protein-protein interaction networks, while very useful, represent
only one type of network out of several types currently in use in biology.
Other classes of networks include those that describe genetic interactions
between the various loci of an organism, or networks that describe the
relations between small organic metabolites and the enzymes that inter-
convert them (metabolic networks). Yet other networks describe the con-
nections between genes and the transcription factors that control them
(transcriptional regulation networks), or they describe specific types of
protein-protein interactions such as the interaction between protein
kinases and the substrates they phosphorylate. All of these networks are
being assembled for much the same reasons as for the protein-protein
interaction networks: visualization of complex relationships, data inte-
gration, simple browsing, or global evolutionary analysis.
Many of these networks are special instances of a more general type
of network: the protein-protein
association
network. In contrast to inter-
action networks, protein-protein association networks make no assertion
as to how exactly two proteins interact — in fact, they may not have to
interact at all, in a physical sense. Proteins can show a specific and pro-
ductive functional interaction without touching each other, for example,
by performing subsequent metabolic reactions in the same metabolic
pathway, or by regulating each other's abundance through transcription.
Even interactions that are thought to be direct physical interactions can
in fact be indirect associations, for example, in the case of two proteins
that have been isolated together from a protein complex but are in real-
ity located at opposite ends of the complex and may have no specific
interaction interface with each other.
In many ways, association networks are a more “natural” way of
describing proteins and their mutual interactions. First, many experimen-
tal techniques may not reveal whether an interaction is direct or indirect,
