|Reactions and kinetic parameters for the gene expression model|
|3||ka=150 for n>10, ka=30 for n≤10|
|15||ktrA=35, ktrB=8, ktrC=4.5|
|21||ktt is sequence dependent|
Chemical reactions, rate constants (in s−1), and delays (in s) used to model transcription and translation. Pro – promoter, Rp – RNA polymerase, Rib – ribosome, [RibR – number of translating ribosomes on RNA strand, P – complete protein, U – unoccupied nucleotide and O – nucleotide occupied by Rp, A – activated nucleotide; UR,OR,AR – corresponding ribonucleotides. n denotes the number of the nucleotide in the sequence. ΔP – range of nucleotides that Rp occupies, ΔP=25. ΔR – range of ribonucleotides that ribosome occupies, ΔR=31. Notation X∼N(μσ2) denotes that the values of X are drawn from normal distribution with a mean of μand variance of σ2. Parameter values are from measurements in E. coli, mainly for LacZ [3,20,24-34,53]. The duration of protein folding after translation is completed (τfold) is set according to measurements of a commonly used GFP mutant .
Emmert-Streib et al.
Emmert-Streib et al. BMC Bioinformatics 2012 13:152 doi:10.1186/1471-2105-13-152