Table 2

Molecular amounts of initial species in the PRR model
Protein Total amount Reference Nuclear amount
Rad5 1520 [50] 1520
Rad6 2770 [50] 194
Rad18 206 [50] 206
Ubc13* 8970 [50] 628
Mms2* 2760 [50] 193
PCNA 22440 (7480 trimers) [52] 7480 trimers
Ubiquitin 124260 [50,52] 8698

The molecular amounts of the proteins initially occurring in the PRR model are here expressed as number of molecules per cell. Data in the second column were collected from log phase growing yeast cells, retrieved from the reference database reported in the third column. The amount of ubiquitin is calculated as the sum of molecular amounts deriving from the four genes coding for ubiquitin in yeast cells (namely, UBI1, UBI2, UBI3, UBI4). The fourth column reports the derived nuclear amounts of the proteins that are localized both in the nucleus and in the cytoplasm, scaled according to the 7% fraction of nuclear volume with respect to the total yeast cell volume [53]. This column specifies, in particular, the molecular amounts of proteins occurring in the initial state of the system. The proteins marked with the asterisk (Ubc13, Mms2) occur in the model as complex (Ubc13 : Mms2), whose initial amount is fixed at the minimum value between the amounts of the two proteins (namely, 193 molecules/cell).

Amara et al.

Amara et al. BMC Systems Biology 2013 7:24   doi:10.1186/1752-0509-7-24

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