TY - JOUR
T1 - Age-dependent evolution of the yeast protein interaction network suggests a limited role of gene duplication and divergence
AU - Wan, Kyu Kim
AU - Marcotte, Edward M.
PY - 2008/11
Y1 - 2008/11
N2 - Proteins interact in complex protein-protein interaction (PPI) networks whose topological properties -such as scale-free topology, hierarchical modularity, and dissortativity - have suggested models of network evolution. Currently preferred models invoke preferential attachment or gene duplication and divergence to produce networks whose topology matches that observed for real PPIs, thus supporting these as likely models for network evolution. Here, we show that the interaction density and homodimeric frequency are highly protein age-dependent in real PPI networks in a manner which does not agree with these canonical models. In light of these results, we propose an alternative stochastic model, which adds each protein sequentially to a growing network in a manner analogous to protein crystal growth (CG) in solution. The key ideas are (1) interaction probability increases with availability of unoccupied interaction surface, thus following an antipreferential attachment rule, (2) as a network grows, highly connected sub-networks emerge into protein modules or complexes, and (3) once a new protein is committed to a module, further connections tend to be localized within that module. The CG model produces PPI networks consistent in both topology and age distributions with real PPI networks and is well supported by the spatial arrangement of protein complexes of known 3-D structure, suggesting a plausible physical mechanism for network evolution.
AB - Proteins interact in complex protein-protein interaction (PPI) networks whose topological properties -such as scale-free topology, hierarchical modularity, and dissortativity - have suggested models of network evolution. Currently preferred models invoke preferential attachment or gene duplication and divergence to produce networks whose topology matches that observed for real PPIs, thus supporting these as likely models for network evolution. Here, we show that the interaction density and homodimeric frequency are highly protein age-dependent in real PPI networks in a manner which does not agree with these canonical models. In light of these results, we propose an alternative stochastic model, which adds each protein sequentially to a growing network in a manner analogous to protein crystal growth (CG) in solution. The key ideas are (1) interaction probability increases with availability of unoccupied interaction surface, thus following an antipreferential attachment rule, (2) as a network grows, highly connected sub-networks emerge into protein modules or complexes, and (3) once a new protein is committed to a module, further connections tend to be localized within that module. The CG model produces PPI networks consistent in both topology and age distributions with real PPI networks and is well supported by the spatial arrangement of protein complexes of known 3-D structure, suggesting a plausible physical mechanism for network evolution.
UR - http://www.scopus.com/inward/record.url?scp=57149118625&partnerID=8YFLogxK
U2 - 10.1371/journal.pcbi.1000232
DO - 10.1371/journal.pcbi.1000232
M3 - Article
C2 - 19043579
AN - SCOPUS:57149118625
SN - 1553-734X
VL - 4
JO - PLoS Computational Biology
JF - PLoS Computational Biology
IS - 11
M1 - e1000232
ER -