  The relationship between the regulatory design and the functionality of
molecular networks is a key issue in biology. Modules and motifs have been
associated to various cellular processes, thereby providing anecdotal evidence
for performance based localization on molecular networks. To quantify
structure-function relationship we investigate similarities of proteins which
are close in the regulatory network of the yeast Saccharomyces Cerevisiae. We
find that the topology of the regulatory network show weak remnants of its
history of network reorganizations, but strong features of co-regulated
proteins associated to similar tasks. This suggests that local topological
features of regulatory networks, including broad degree distributions, emerge
as an implicit result of matching a number of needed processes to a finite
toolbox of proteins.
