  Proteins in organisms, rather than act alone, usually form protein complexes
to perform cellular functions. We analyze the topological network structure of
protein complexes and their component proteins in the budding yeast in terms of
the bipartite network and its projections, where the complexes and proteins are
its two distinct components. Compared to conventional protein-protein
interaction networks, the networks from the protein complexes show more
homogeneous structures than those of the binary protein interactions, implying
the formation of complexes that cause a relatively more uniform number of
interaction partners. In addition, we suggest a new optimization method to
determine the abundance and function of protein complexes, based on the
information of their global organization. Estimating abundance and biological
functions is of great importance for many researches, by providing a
quantitative description of cell behaviors, instead of just a "catalogues" of
the lists of protein interactions. With our new optimization method, we present
genome-wide assignments of abundance and biological functions for complexes, as
well as previously unknown abundance and functions of proteins, which can
provide significant information for further investigations in proteomics. It is
strongly supported by a number of biologically relevant examples, such as the
relationship between the cytoskeleton proteins and signal transduction and the
metabolic enzyme Eno2's involvement in the cell division process. We believe
that our methods and findings are applicable not only to the specific area of
proteomics, but also to much broader areas of systems biology with the concept
of optimization principle.
