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. 2013 Jul 8;8(7):e66446. doi: 10.1371/journal.pone.0066446

Table 1. Model parameters used in simulations.

Symbol value unit Comment
First-order rate constant for ADP-ribosylation k cat 0.0045 s−1 assumed1
Total EF2 in the system [EF2]t 0.6 µM/cell [36]
Total ribosomes engaging in mRNA translation [R]t 0.5 µM/cell [37] 2
EF1-initiated peptidyl insertion rate constant k 0,max 4 s−1 [38]
Association rate constant between E GTP and R k 1 96 µM−1 s−1 [8], [9] 3
Dissociation rate constant for Inline graphic Inline graphic 0.3 s−1 assumed
Translocation rate constant for Inline graphic k 2 35 s−1 [8], [9]
EF2•GDP release rate constant for Inline graphic k 3 5 s−1 [8], [9] 4
GTP exchange rate constant for E GDP k 4 12.8 µM s−1 [39]
EF2•GDP dissociation constant K d,GDP 0.5 µM [24]
EF2•GTP dissociation constant K d,GTP 2.68 µM [24]
Free GTP concentration [GTP] 400 µM [35]
Free GDP concentration [GDP] 40 µM assumed5
Polysomal density m 10 # ORF−1 assumed
Threshold for dead-end translocation block in f f c 0.09 [17]
Basal fraction of translocation-active ribosomes Inline graphic 0.29 modeled
Basal stalling coefficient Inline graphic 0.14 modeled

The rate constant Inline graphic is set equal to k 3 throughout the work, whereas Inline graphic, and Inline graphic may differ from their native counterparts.

1

Calculated from λ cat [T], using λ cat = 1.7×109 M−1 min−1 [34] and [T] = 0.16 nM (equivalent to 250 toxin molecules in the cytosol of a cell, with a cell cytosol volume equal to 2.6 pL [35].

2

Obtained by the ratio of [EF2]t : [R]t = 1.2∶ 1 [37] using the estimated [EF2]t.

3

Calculated as k 1 = k a k GTP/(k d+k GTP) = 150*250/(140+250) = 96 s−1.

4

Taken as the rate constant for relocking [8], [9].

5

Based on [GTP]:[GDP] = 10∶1 [32].