MODEL4821294342
type: SBMLModel
notes: An approximation to the Kierzek AM. et al. J Biol Chem. (2001) 276(11):8165-72 model of LacZ gene expression in E. coli. They use stochastic simulation and model cell growth. Despite these discrepancies, the continuous fixed size model is within a factor of 3 of their results. Parameter values identical. This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2011 The BioModels.net Team. To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information. In summary, you are entitled to use this encoded model in absolutely any manner you deem suitable, verbatim, or with modification, alone or embedded it in a larger context, redistribute it, commercially or not, in a restricted way or not.. To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.
time units: 013121
reaction: 039689
species: 039369
species: 039489
units def: 092315
name: Kierzek2001_LacZ
species: 039409
reaction: 039709
species: 039389
substance units: 092412
species: 039430
reaction: 039629
species: 039329
species: 039449
is described by: http://identifiers.org/pubmed/11062240
units def: 092412
species: 039509
species: 039429
length unit: length
species: 039349
reaction: 039669
reaction: 039649
species: 039529
compartment: 039298
species: 039469
units def: 092363
reaction: 039609
units def: 092277
reaction: 039549
reaction: 039569
reaction: 039589
compartment: 039309
curated: false
area units: area
volume units: metaid_0000217

039689
type: Reaction
kinetic law: 092976
product: 092964
reactant: 092952
notes: Equation 3 from Kierzek et al. Isomerization of closed binary complex to open complex.
fast: false
reversible: true

092976
type: KineticLaw
local parameters: 093001
local parameters: 092989
notes: kf*LacZ_slash_P_RNAP-kb*LacZ_slash_TrRNAP

093001
type: LocalParameter
units: 092277
value: 0.0

092302
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 1.0
kind: SECOND

092289
type: SBMLUnit
exponent: 1.0
scale: 0
multipler: 1.0
kind: LITRE

092989
type: LocalParameter
units: 092277
value: 9.99966666666667E-16

092964
type: SpeciesReference
stoichiometry: 1.0
species: 039449

039449
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 039309

039309
type: Compartment
constant: true
size: 9.9997E-16
spatial dimensions: 3.0

092952
type: SpeciesReference
stoichiometry: 1.0
species: 039409

039409
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 039309

039369
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 039309

039489
type: Species
constant: true
boundary condition: true
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 039309

092351
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 1.0
kind: SECOND

092339
type: SBMLUnit
exponent: -1.0
scale: -6
multipler: 1.0
kind: MOLE

092327
type: SBMLUnit
exponent: 2.0
scale: 0
multipler: 1.0
kind: LITRE

039709
type: Reaction
kinetic law: 093037
product: 093025
reactant: 093013
notes: Also equation 8 from Kierzek et al. Since RBS is assumed to be the rate-limiting part of the protein synthesis, we don\'t really need to worry about the fate of the ElRNAP. For balance we degrade it at the same rate as the RBS.
fast: false
reversible: true

093037
type: KineticLaw
local parameters: 093061
local parameters: 093049
notes: kf*LacZ_slash_ElRNAP-kb*LacZ_slash_nucleotides

093061
type: LocalParameter
units: 092277
value: 0.0

093049
type: LocalParameter
units: 092277
value: 2.9999E-16

093025
type: SpeciesReference
stoichiometry: 1.0
species: 039529

039529
type: Species
constant: true
boundary condition: true
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 039309

093013
type: SpeciesReference
stoichiometry: 1.0
species: 039430

039430
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 039309

039389
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 039309

092424
type: SBMLUnit
exponent: 1.0
scale: -6
multipler: 1.0
kind: MOLE

039629
type: Reaction
product: 092757
product: 092733
notes: Equation 4 from Kierzek et al. They say: To clear the promoter region, active RNA polymerase must move 30 to 60 nucleotides (ref Record et al 1996 E coli and Salmonella 2nd ed pp 792-821 ASM Press, Washington DC) Since rate of polymerase movement is about 40 nucleotides/sec, this step takes about 1 sec. The length of the mRNA chain that is synthesized during this time corresponds roughly to the length of the leader region containing the ribosome binding site (RBS). Therefore the synthesis of the RBS and promotor clearance occur at approximately the same rate of 1 per sec. .... Therefore we modeled these two processes by the single first order reaction with a rate constant of 1 sec.
reversible: true
kinetic law: 092782
product: 092745
reactant: 092721
fast: false
product: 092769

092757
type: SpeciesReference
stoichiometry: 1.0
species: 039430

092733
type: SpeciesReference
stoichiometry: 1.0
species: 039429

039429
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.00166672222407414
initial amount: NaN
in compartment: 039309

092782
type: KineticLaw
local parameters: 092806
local parameters: 092794
notes: kf*LacZ_slash_TrRNAP-kb*LacZ_slash_P*LacZ_slash_RBS*LacZ_slash_ElRNAP*LacZ_slash_RNAP

092806
type: LocalParameter
units: 092363
value: 0.0

092400
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 1.0
kind: SECOND

092388
type: SBMLUnit
exponent: -3.0
scale: -6
multipler: 1.0
kind: MOLE

092376
type: SBMLUnit
exponent: 4.0
scale: 0
multipler: 1.0
kind: LITRE

092794
type: LocalParameter
units: 092277
value: 9.99966666666667E-16

092745
type: SpeciesReference
stoichiometry: 1.0
species: 039349

039349
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 039309

092721
type: SpeciesReference
stoichiometry: 1.0
species: 039449

092769
type: SpeciesReference
stoichiometry: 1.0
species: 039509

039509
type: Species
notes: RNA Polymerase. Kierzek et al assume mean 35 and delta = 3.5 molecules. Turns out they assume that this buffered.
constant: true
boundary condition: true
has only substance units: false
initial concentration: 0.0583352778425947
initial amount: NaN
in compartment: 039309

039329
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 039309

039669
type: Reaction
kinetic law: 092915
product: 092903
product: 092890
reactant: 092878
notes: Equation 7 from Kierzek et al. Based on Draper , DE 1996 E coli and Salmonella 2nd Ed pp 902-908 ASM Press, Washington DC. This is the rate at which the RBS cleared.
fast: false
reversible: true

092915
type: KineticLaw
local parameters: 092939
local parameters: 092927
notes: kf*LacZ_slash_RibRBS-kb*LacZ_slash_elRIB*LacZ_slash_RBS

092939
type: LocalParameter
units: 092315
value: 0.0

092927
type: LocalParameter
units: 092277
value: 4.99983333333333E-16

092903
type: SpeciesReference
stoichiometry: 1.0
species: 039349

092890
type: SpeciesReference
stoichiometry: 1.0
species: 039389

092878
type: SpeciesReference
stoichiometry: 1.0
species: 039369

039649
type: Reaction
kinetic law: 092842
product: 092830
reactant: 092818
notes: Equation 8 from Kierzek et al, set equal to transcription initiaton frequency. This is the decay rate of RBS.
fast: false
reversible: true

092842
type: KineticLaw
local parameters: 092866
local parameters: 092854
notes: kf*LacZ_slash_RBS-kb*LacZ_slash_nucleotides

092866
type: LocalParameter
units: 092277
value: 0.0

092854
type: LocalParameter
units: 092277
value: 2.9999E-16

092830
type: SpeciesReference
stoichiometry: 1.0
species: 039529

092818
type: SpeciesReference
stoichiometry: 1.0
species: 039349

039298
type: Compartment
constant: true
size: 1.0E-18
spatial dimensions: 3.0

039469
type: Species
notes: Ribosome pool The language in the paper is a little ambiguous, but from simulation it turns out that they assume that the number of free ribosomes is held fixed at 350. In other buffered.
constant: true
boundary condition: true
has only substance units: false
initial concentration: 0.583352778425947
initial amount: NaN
in compartment: 039309

039609
type: Reaction
kinetic law: 092685
product: 092673
reactant: 092661
reactant: 092649
notes: Equations 1 and 2 from Kierzek et al. Reversible RNA binding.
fast: false
reversible: true

092685
type: KineticLaw
local parameters: 092709
local parameters: 092697
notes: kf*LacZ_slash_P*LacZ_slash_RNAP-kb*LacZ_slash_P_RNAP

092709
type: LocalParameter
units: 092277
value: 9.99966666666667E-15

092697
type: LocalParameter
units: 092315
value: 9.99893337111067E-14

092673
type: SpeciesReference
stoichiometry: 1.0
species: 039409

092661
type: SpeciesReference
stoichiometry: 1.0
species: 039509

092649
type: SpeciesReference
stoichiometry: 1.0
species: 039429

039549
type: Reaction
kinetic law: 092473
product: 092461
reactant: 092449
reactant: 092437
notes: Equations 5 and 6 from Kierzek et al. Association rate set to order of magnitude of diffusion-limited aggregation. Dissociation rate set to reproduce translation frequency.
fast: false
reversible: true

092473
type: KineticLaw
local parameters: 092497
local parameters: 092485
notes: kf*LacZ_slash_RBS*LacZ_slash_Ribosome-kb*LacZ_slash_RibRBS

092497
type: LocalParameter
units: 092277
value: 2.249925E-15

092485
type: LocalParameter
units: 092315
value: 9.99893337111067E-14

092461
type: SpeciesReference
stoichiometry: 1.0
species: 039369

092449
type: SpeciesReference
stoichiometry: 1.0
species: 039469

092437
type: SpeciesReference
stoichiometry: 1.0
species: 039349

039569
type: Reaction
kinetic law: 092547
product: 092534
product: 092521
reactant: 092509
notes: Equation 9 from Kierzek et al. They say that this step should be RibRBS-> Protein, but based on text and the logic of the synthesis, it should really be ElRIB, the Ribosome elongating protein chain, that should give rise to the protein. The calculation is: ribosome moves at 15 AAs /sec. The protein is 1024 AAs long. So protein is formed 0.015/sec.
fast: false
reversible: true

092547
type: KineticLaw
local parameters: 092573
local parameters: 092560
notes: kf*LacZ_slash_elRIB-kb*LacZ_slash_Ribosome*LacZ_slash_Protein

092573
type: LocalParameter
units: 092315
value: 0.0

092560
type: LocalParameter
units: 092277
value: 1.49995E-17

092534
type: SpeciesReference
stoichiometry: 1.0
species: 039329

092521
type: SpeciesReference
stoichiometry: 1.0
species: 039469

092509
type: SpeciesReference
stoichiometry: 1.0
species: 039389

039589
type: Reaction
kinetic law: 092613
product: 092601
reactant: 092587
notes: Equation 10 from Kierzek et al. Assume a half-life of 3 hours for beta-galactosidase in E coli, from Berquist and Truman 1978 Mol. Cell. Genet. 164, 105-108.
fast: false
reversible: true

092613
type: KineticLaw
local parameters: 092637
local parameters: 092625
notes: kf*LacZ_slash_Protein-kb*LacZ_slash_AAs

092637
type: LocalParameter
units: 092277
value: 0.0

092625
type: LocalParameter
units: 092277
value: 6.419786E-20

092601
type: SpeciesReference
stoichiometry: 1.0
species: 039489

092587
type: SpeciesReference
stoichiometry: 1.0
species: 039329