Evolution of the protein interaction network of budding yeast: Role of the protein family compatibility constraint

Understanding of how protein interaction networks (PIN) of living organisms have evolved or are organized can be the first stepping stone in unveiling how life works on a fundamental basis. Here, we introduce a new in-silico evolution model of the PIN of budding yeast, Saccharomyces cerevisiae; the model is composed of the PIN and the protein family network. The basic ingredient of the model includes family compatibility which constrains the potential binding ability of a protein, as well as the previously proposed gene duplication, divergence, and mutation. We investigate various structural properties of our model network with parameter values relevant to budding yeast and find that the model successfully reproduces the empirical data.