When hundreds or thousands of proteins are displayed on the same map, the network diagram becomes bewilderingly complicated, serving to illustrate the enormous challenges that face scientists attempting to understand the cell (Figure 3–80). Much more useful are small subsections of these maps, centered on a few proteins of interest.
We have previously described the structure and mode of action of the SCF ubiquitin ligase, using it to illustrate how protein complexes are constructed from interchangeable parts (see Figure 3–71). Figure 3–81 shows a network of protein– protein interactions for the five proteins that form this protein complex in a yeast cell. Four of the subunits of this ligase are located at the bottom right of this figure. The remaining subunit, the F-box protein that serves as its substrate-binding arm, appears as a set of 15 different gene products that bind to adaptor protein 2 (the Skp1 protein). Along the top and left of the figure are sets of additional protein interactions marked with yellow and green shading: as indicated, these protein sets function at the origin of DNA replication, in cell cycle regulation, in methionine synthesis, in the kinetochore, and in vacuolar H+-ATPase assembly. We shall use this figure to explain how such protein interaction maps are used, and what they do and do not mean.
1.
Protein interaction maps are useful for identifying the likely function of previously uncharacterized proteins. Examples are the products of the genes that have thus far only been inferred to exist from the yeast genome sequence, which are the three proteins in the figure that lack a simple three-letter abbreviation (white letters beginning with Y). The three in this diagram are F-box proteins that bind to Skp1; these are therefore likely to function as part of the ubiquitin ligase, serving as substrate-binding arms that recognize different target proteins. However, as we discuss next, neither assignment can be considered certain without additional data.
2.
Protein interaction networks need to be interpreted with caution because, as a result of evolution making efficient use of each organism’s genetic information, the same protein can be used as part of different protein complexes that have different types of functions. Thus, although protein A binds to protein B and protein B binds to protein C, proteins A and C need not function in the same process. For example, we know from detailed biochemical studies that the functions of Skp1 in the kinetochore and in
Figure 3–80 a network of protein-binding interactions in a yeast cell.
Each line connecting a pair of dots (proteins) indicates a protein–protein interaction. (From A. Guimerá and
M. Sales–Pardo, Mol. Syst. Biol. 2:42, 2006. With permission from Macmillan Publishers Ltd.)
Figure 3–81 a map of some protein–protein interactions of the SCF ubiquitin ligase and other proteins in the yeast
S. cerevisiae. The symbols and/or colors used for the five proteins of the ligase are those in Figure 3–71. Note that 15 different F-box proteins are shown (purple); those with white lettering (beginning with Y) are known from the genome sequence as open reading frames. For additional details, see text. (Courtesy of Peter Bowers and David Eisenberg, UCLA-DOE Institute for Genomics and Proteomics, UCLA.) vacuolar H+-ATPase assembly (yellow shading) are separate from its function in the SCF ubiquitin ligase. In fact, only the remaining three functions of Skp1 illustrated in the diagram—methionine synthesis, cell cycle regulation, and origin of replication (green shading)—involve ubiquitylation.
3. In cross-species comparisons, those proteins displaying similar patterns of interactions in the two protein interaction maps are likely to have the same function in the cell. Thus, as scientists generate more and more highly detailed maps for multiple organisms, the results will become increasingly useful for inferring protein function. These map comparisons will be a particularly powerful tool for deciphering the functions of human proteins, because a vast amount of direct information about protein function can be obtained from genetic engineering, mutational, and genetic analyses in experimental organisms—such as yeast, worms, and flies—that are not feasible in humans.