039430
constant: false
boundary condition: false
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039529
constant: true
boundary condition: true
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 039309
type: Species

092649
stoichiometry: 1.0
species: 039429
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092547
local parameters: 092573
local parameters: 092560
notes: kf*LacZ_slash_elRIB-kb*LacZ_slash_Ribosome*LacZ_slash_Protein
type: KineticLaw

092757
stoichiometry: 1.0
species: 039430
type: SpeciesReference

092424
exponent: 1.0
scale: -6
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kind: MOLE
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units: 092315
value: 9.99893337111067E-14
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039349
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 039309
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092461
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species: 039369
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units: 092277
value: 0.0
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039369
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 039309
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092903
stoichiometry: 1.0
species: 039349
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092289
exponent: 1.0
scale: 0
multipler: 1.0
kind: LITRE
type: SBMLUnit

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

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

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species: 039469
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092302
exponent: -1.0
scale: 0
multipler: 1.0
kind: SECOND
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039309
constant: true
size: 9.9997E-16
spatial dimensions: 3.0
type: Compartment

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species: 039509
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exponent: -1.0
scale: 0
multipler: 1.0
kind: SECOND
type: SBMLUnit

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value: 6.419786E-20
type: LocalParameter

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

039549
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
type: Reaction

092509
stoichiometry: 1.0
species: 039389
type: SpeciesReference

MODEL4821294342
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
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reaction: 039709
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type: SBMLModel
substance units: 092412
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species: 039329
species: 039449
is described by: http://identifiers.org/pubmed/11062240
units def: 092412
species: 039509
species: 039429
species: 039349
reaction: 039669
length unit: length
reaction: 039649
species: 039529
compartment: 039298
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units def: 092363
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units def: 092277
reaction: 039549
area units: area
reaction: 039569
reaction: 039589
curated: false
compartment: 039309
volume units: metaid_0000217

093013
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species: 039430
type: SpeciesReference

092339
exponent: -1.0
scale: -6
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kind: MOLE
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species: 039329
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units: 092277
value: 4.99983333333333E-16
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039409
constant: false
boundary condition: false
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units: 092277
value: 9.99966666666667E-16
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093049
units: 092277
value: 2.9999E-16
type: LocalParameter

039509
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
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092842
local parameters: 092866
local parameters: 092854
notes: kf*LacZ_slash_RBS-kb*LacZ_slash_nucleotides
type: KineticLaw

092601
stoichiometry: 1.0
species: 039489
type: SpeciesReference

039329
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 039309
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092587
stoichiometry: 1.0
species: 039329
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092733
stoichiometry: 1.0
species: 039429
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093025
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species: 039529
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species: 039409
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039709
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
type: Reaction

092866
units: 092277
value: 0.0
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092818
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species: 039349
type: SpeciesReference

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

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

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

039609
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
type: Reaction

039589
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
type: Reaction

039649
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
type: Reaction

092878
stoichiometry: 1.0
species: 039369
type: SpeciesReference

092497
units: 092277
value: 2.249925E-15
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092709
units: 092277
value: 9.99966666666667E-15
type: LocalParameter

039629
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
type: Reaction
product: 092745
reactant: 092721
fast: false
product: 092769

092637
units: 092277
value: 0.0
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092745
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species: 039349
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039489
constant: true
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has only substance units: false
initial concentration: 0.0
initial amount: NaN
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092521
stoichiometry: 1.0
species: 039469
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039689
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
type: Reaction

092437
stoichiometry: 1.0
species: 039349
type: SpeciesReference

092769
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species: 039509
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092613
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notes: kf*LacZ_slash_Protein-kb*LacZ_slash_AAs
type: KineticLaw

039569
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
type: Reaction

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

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

039298
constant: true
size: 1.0E-18
spatial dimensions: 3.0
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species: 039529
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092806
units: 092363
value: 0.0
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092573
units: 092315
value: 0.0
type: LocalParameter

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

093001
units: 092277
value: 0.0
type: LocalParameter

039469
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
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092327
exponent: 2.0
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multipler: 1.0
kind: LITRE
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value: 0.0
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039449
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initial amount: NaN
in compartment: 039309
type: Species

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

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

092890
stoichiometry: 1.0
species: 039389
type: SpeciesReference

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

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

092952
stoichiometry: 1.0
species: 039409
type: SpeciesReference

039669
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
type: Reaction

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

092721
stoichiometry: 1.0
species: 039449
type: SpeciesReference