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Table 1 Constants used in the Simple Gene Expression Model

From: TABASCO: A single molecule, base-pair resolved gene expression simulator

Constant Tabasco Species-Level
kon (M-1s-1). 4E7 4E7
koff (s-1). 4 4
kiniton (s-1). 1.2 1.2
% runoff 0 N/A
krecyc (s-1). 0 N/A
kelong (s-1) 0.23 0.23
kprot (s-1) 0.645 0.645
kribon (M-1s-1) 1.15E4 1.15E4
kclear (s-1). 0.14* 0.1308
rib elongation (s-1) 20 20
mRNA deg (s-1). 2.5E-3 2.5E-3
protein deg (s-1) 7E-4 7E-4
  1. We compared two models of expression of a single-gene varying only if mRNA and protein elongation reactions are treated as series of individual steps or a single lumped reaction (Figure 3; Figure 6). The kclear rates do not exactly match because of small differences in the model structures (see text). The Tabasco constant for kclear was adjusted to ensure the steady-state levels of mRNA and protein were equivalent in both simulations.