Model output under normal conditions. (a) Stochastic variation. Simulations were repeated 100 times and the mean for two of the species plotted. The black lines show the mean values, the green and red lines show the upper and lower 95% confidence interval respectively. (i) Native protein (NatP). (ii) Misfolded protein (MisP). (b) Results are shown for a typical simulation, for a 10 hour period. (i) Level of native protein (NatP), misfolded protein (MisP), and misfolded protein bound to E3 (E3_MisP). (ii) Ubiquitin pools. (iii) Ubiquitin bound to E1 and E2 (E1_Ub and E2_Ub respectively). (iv) Cumulative number of degradation reactions for different length of ubiquitin chains bound to substrate. (v) Accumulation of aggregated protein (AggP), sequestered aggregated protein (SeqAggP) and aggregated protein bound to proteasomes (AggP_Proteasome). (vi) Available pool of proteasomes, number of proteasomes bound by substrates and number of proteasomes bound by aggregated proteins.