Fig. 4

Dynamic model for TOR signaling in budding yeast. a Molecular interactions represented in the core model (solid lines) and in hypothetical extensions (dashed lines), adapted from [33]. Nodes represent proteins or protein complexes (boxes; phosphorylation indicated by ’P’) as well as small molecules (ellipses). Arrows indicate reversible complex formation, while filled (open)circles adjacent to transition reactions denote protein phosphorylation (dephosphorylation). b, c Experimental data (symbols; mean and s.d.) and sample model trajectories (lines) for stimulation of TOR signaling with 500 nM (b) and 109 nM (c) rapamycin at t = 20 min. In (b), the abundance of phosphorylated Tap42 protein (red) was measured; in (c), complex formations of Tip41 with Tap42 (blue) and of Tap42 with Sit4 (green) were determined. All data are relative to steady-state concentrations prior to rapamycin addition; for details on model structure and experimental data, see [33]. Simulations in (b) and (c) represent viable parameter samples for a default negative log-likelihood scoring function with a 0.95 quantile as a threshold