  We study how the dynamic equilibrium of the reversible protein-protein
binding network in yeast Saccharomyces cerevisiae responds to large changes in
abundances of individual proteins. The magnitude of shifts between free and
bound concentrations of their immediate and more distant neighbors in the
network is influenced by such factors as the network topology, the distribution
of protein concentrations among its nodes, and the average binding strength.
Our primary conclusion is that, on average, the effects of a perturbation are
strongly localized and exponentially decay with the network distance away from
the perturbed node, which explains why, despite globally connected topology,
individual functional modules in such networks are able to operate fairly
independently. We also found that under specific favorable conditions, realized
in a significant number of paths in the yeast network, concentration
perturbations can selectively propagate over considerable network distances (up
to four steps). Such "action-at-a-distance" requires high concentrations of
heterodimers along the path as well as low free (unbound) concentration of
intermediate proteins.
