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BIOMD0000000147 - ODea2007_IkappaB

 

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Reference Publication
Publication ID: 17486138
O'Dea EL, Barken D, Peralta RQ, Tran KT, Werner SL, Kearns JD, Levchenko A, Hoffmann A.
A homeostatic model of IkappaB metabolism to control constitutive NF-kappaB activity.
Mol. Syst. Biol. 2007; 3: 111
Signaling Systems Laboratory, Department of Chemistry and Biochemistry, UCSD, La Jolla, CA 92037, USA.  [more]
Model
Original Model: BIOMD0000000147.origin
Submitter: Molecular Systems Biology
Submission ID: MODEL2784772048
Submission Date: 06 Sep 2007 08:06:28 UTC
Last Modification Date: 26 May 2014 23:05:35 UTC
Creation Date: 04 Sep 2007 10:35:41 UTC
Encoders:  Harish Dharuri
   Hoffman Alexander
set #1
bqmodel:isDerivedFrom BioModels Database Hoffmann2002_WT_IkBNFkB_Signaling
BioModels Database Hoffmann2002_KnockOut_IkBNFkB_Signaling
set #2
bqbiol:hasTaxon Taxonomy Mus musculus
set #3
bqbiol:is Gene Ontology I-kappaB kinase/NF-kappaB signaling
bqbiol:isPartOf KEGG Pathway T cell receptor signaling pathway - Mus musculus (mouse)
Notes

O'Dea, E.L., Barken, D., Peralta, R.Q., Tran K.T., Werner, S.L., Kearns, J.D., Levchenko, A., Hoffmann, A. A homeostatic model of IkB metabolism to control constitutive activity. Molecular Systems Biology, 3:111, pp. 1-7. 2007

Questions concerning the paper should be addressed to the corresponding author. Alexander Hoffmann (ahoffmann@ucsd.edu)


The original model was written and simulated within MathWorks MatLab 2006a using the ode15s (stiff/NDF) solver. It is highly recommended that those wanting to model this system use the MatLab version which we will freely provide upon request. As always, simulation results vary according to the numerical solver used.

Translation to SBML Level 2.1 was performed via reconstruction of the model within MathWorks SimBiology Desktop (version 2.1) followed by an Export to SBML. Please address questions about this SBML model to Jeff Kearns (jkearns@ucsd.edu).

BioModels DB curation: The model reproduces the values of diffferent species depicted in Fig 3A and 3B (wt) of the paper corresponding to Model1.1. To depict the the total IkB alpha, beta epsilon species, three additional parameters and their corresponding assignment rules have been introduced in this model by the creator. Model succesfully tested on MathSBML.

This model originates from BioModels Database: A Database of Annotated Published Models. It is copyright (c) 2005-2010 The BioModels Team.
For more information see the terms of use.
To cite BioModels Database, please use Le Novère N., Bornstein B., Broicher A., Courtot M., Donizelli M., Dharuri H., Li L., Sauro H., Schilstra M., Shapiro B., Snoep J.L., Hucka M. (2006) BioModels Database: A Free, Centralized Database of Curated, Published, Quantitative Kinetic Models of Biochemical and Cellular Systems Nucleic Acids Res., 34: D689-D691.

Model
Publication ID: 17486138 Submission Date: 06 Sep 2007 08:06:28 UTC Last Modification Date: 26 May 2014 23:05:35 UTC Creation Date: 04 Sep 2007 10:35:41 UTC
Mathematical expressions
Reactions
txn_a mdeg_a tsl_a int_ai
int_an int_an_n int_2ani int_2ain
deg_a deg_a_n deg_an_n deg_an
deg_ai deg_ain loc_a loc_an
loc_bn loc_b deg_bin deg_bi
deg_bn deg_bn_n deg_b_n deg_b
int_2bin int_2bni int_bn_n int_bn
int_bi tsl_b mdeg_b txn_b
loc_n txn_e mdeg_e tsl_e
int_ei int_en int_en_n int_2eni
int_2ein deg_e deg_e_n deg_en_n
deg_en deg_ei deg_ein loc_e
loc_en IKK_deg itxn_a  
Rules
Assignment Rule (variable: Total_IkBalpha) Assignment Rule (variable: Total_IkBbeta) Assignment Rule (variable: Total_IkBeps)  
Physical entities
Compartments Species
cytoplasm IkBa IkBaIKK IkBaNFkB
IkBaIKKNFkB NFkB IKK
IkBbIKK IkBbIKKNFkB IkBbNFkB
IkBb IkBe IkBeNFkB
IkBeIKKNFkB IkBeIKK  
nucleus IkBat IkBan IkBaNFkBn
NFkBn IkBbNFkBn IkBbn
IkBbt IkBet IkBen
IkBeNFkBn    
Global parameters
Total_IkBalpha Total_IkBbeta Total_IkBeps  
Reactions (51)
 
 txn_a  → [IkBat];  
 
 mdeg_a [IkBat] → ;  
 
 tsl_a [IkBat] → [IkBat] + [IkBa];  
 
 int_ai [IkBa] + [IKK] ↔ [IkBaIKK];  
 
 int_an [IkBa] + [NFkB] ↔ [IkBaNFkB];  
 
 int_an_n [IkBan] + [NFkBn] ↔ [IkBaNFkBn];  
 
 int_2ani [IkBaNFkB] + [IKK] ↔ [IkBaIKKNFkB];  
 
 int_2ain [IkBaIKK] + [NFkB] ↔ [IkBaIKKNFkB];  
 
 deg_a [IkBa] → ;  
 
 deg_a_n [IkBan] → ;  
 
 deg_an_n [IkBaNFkBn] → [NFkBn];  
 
 deg_an [IkBaNFkB] → [NFkB];  
 
 deg_ai [IkBaIKK] → [IKK];  
 
 deg_ain [IkBaIKKNFkB] → [NFkB] + [IKK];  
 
 loc_a [IkBa] ↔ [IkBan];  
 
 loc_an [IkBaNFkBn] → [IkBaNFkB];  
 
 loc_bn [IkBbNFkBn] → [IkBbNFkB];  
 
 loc_b [IkBb] ↔ [IkBbn];  
 
 deg_bin [IkBbIKKNFkB] → [NFkB] + [IKK];  
 
 deg_bi [IkBbIKK] → [IKK];  
 
 deg_bn [IkBbNFkB] → [NFkB];  
 
 deg_bn_n [IkBbNFkBn] → [NFkBn];  
 
 deg_b_n [IkBbn] → ;  
 
 deg_b [IkBb] → ;  
 
 int_2bin [IkBbIKK] + [NFkB] ↔ [IkBbIKKNFkB];  
 
 int_2bni [IkBbNFkB] + [IKK] ↔ [IkBbIKKNFkB];  
 
 int_bn_n [IkBbn] + [NFkBn] ↔ [IkBbNFkBn];  
 
 int_bn [IkBb] + [NFkB] ↔ [IkBbNFkB];  
 
 int_bi [IkBb] + [IKK] ↔ [IkBbIKK];  
 
 tsl_b [IkBbt] → [IkBbt] + [IkBb];  
 
 mdeg_b [IkBbt] → ;  
 
 txn_b  → [IkBbt];  
 
 loc_n [NFkB] ↔ [NFkBn];  
 
 txn_e  → [IkBet];  
 
 mdeg_e [IkBet] → ;  
 
 tsl_e [IkBet] → [IkBet] + [IkBe];  
 
 int_ei [IkBe] + [IKK] ↔ [IkBeIKK];  
 
 int_en [IkBe] + [NFkB] ↔ [IkBeNFkB];  
 
 int_en_n [IkBen] + [NFkBn] ↔ [IkBeNFkBn];  
 
 int_2eni [IkBeNFkB] + [IKK] ↔ [IkBeIKKNFkB];  
 
 int_2ein [IkBeIKK] + [NFkB] ↔ [IkBeIKKNFkB];  
 
 deg_e [IkBe] → ;  
 
 deg_e_n [IkBen] → ;  
 
 deg_en_n [IkBeNFkBn] → [NFkBn];  
 
 deg_en [IkBeNFkB] → [NFkB];  
 
 deg_ei [IkBeIKK] → [IKK];  
 
 deg_ein [IkBeIKKNFkB] → [NFkB] + [IKK];  
 
 loc_e [IkBe] ↔ [IkBen];  
 
 loc_en [IkBeNFkBn] → [IkBeNFkB];  
 
 IKK_deg [IKK] → ;  
 
 itxn_a  → [IkBat];   {NFkBn}
 
Rules (3)
 
 Assignment Rule (name: Total_IkBalpha) Total_IkBalpha = IkBa_cytoplasm+IkBa_nucleus+IkBaIKK+IkBaIKKNFkB+IkBaNFkB_cytoplasm+IkBaNFkB_nucleus
 
 Assignment Rule (name: Total_IkBbeta) Total_IkBbeta = IkBb_cytoplasm+IkBb_nucleus+IkBbIKK+IkBbIKKNFkB+IkBbNFkB_cytoplasm+IkBbNFkB_nucleus
 
 Assignment Rule (name: Total_IkBeps) Total_IkBeps = IkBe_cytoplasm+IkBe_nucleus+IkBeIKK+IkBeIKKNFkB+IkBeNFkB_cytoplasm+IkBeNFkB_nucleus
 
 cytoplasm Spatial dimensions: 3.0  Compartment size: 1.0
 
 IkBa
Compartment: cytoplasm
Initial concentration: 0.0  (Units: substance)
 
 IkBaIKK
Compartment: cytoplasm
Initial concentration: 0.0  (Units: substance)
 
 IkBaNFkB
Compartment: cytoplasm
Initial concentration: 0.06  (Units: substance)
 
 IkBaIKKNFkB
Compartment: cytoplasm
Initial concentration: 0.0  (Units: substance)
 
 NFkB
Compartment: cytoplasm
Initial concentration: 0.0  (Units: substance)
 
 IKK
Compartment: cytoplasm
Initial concentration: 0.001  (Units: substance)
 
 IkBbIKK
Compartment: cytoplasm
Initial concentration: 0.0  (Units: substance)
 
 IkBbIKKNFkB
Compartment: cytoplasm
Initial concentration: 0.0  (Units: substance)
 
 IkBbNFkB
Compartment: cytoplasm
Initial concentration: 0.03  (Units: substance)
 
 IkBb
Compartment: cytoplasm
Initial concentration: 0.0  (Units: substance)
 
 IkBe
Compartment: cytoplasm
Initial concentration: 0.0  (Units: substance)
 
 IkBeNFkB
Compartment: cytoplasm
Initial concentration: 0.01  (Units: substance)
 
 IkBeIKKNFkB
Compartment: cytoplasm
Initial concentration: 0.0  (Units: substance)
 
 IkBeIKK
Compartment: cytoplasm
Initial concentration: 0.0  (Units: substance)
 
 nucleus Spatial dimensions: 3.0  Compartment size: 1.0
 
   IkBat
Compartment: nucleus
Initial concentration: 0.0  (Units: substance)
 
 IkBan
Compartment: nucleus
Initial concentration: 0.0  (Units: substance)
 
 IkBaNFkBn
Compartment: nucleus
Initial concentration: 0.0  (Units: substance)
 
 NFkBn
Compartment: nucleus
Initial concentration: 0.0  (Units: substance)
 
 IkBbNFkBn
Compartment: nucleus
Initial concentration: 0.0  (Units: substance)
 
 IkBbn
Compartment: nucleus
Initial concentration: 0.0  (Units: substance)
 
   IkBbt
Compartment: nucleus
Initial concentration: 0.0  (Units: substance)
 
   IkBet
Compartment: nucleus
Initial concentration: 0.0  (Units: substance)
 
 IkBen
Compartment: nucleus
Initial concentration: 0.0  (Units: substance)
 
 IkBeNFkBn
Compartment: nucleus
Initial concentration: 0.0  (Units: substance)
 
Global Parameters (3)
 
   Total_IkBalpha  
 
   Total_IkBbeta  
 
   Total_IkBeps  
 
txn_a (1)
 
   tr2a
Value: 1.848E-4   (Units: uM_per_min)
Constant
 
mdeg_a (1)
 
   tr3a
Value: 0.0168   (Units: per_min)
Constant
 
tsl_a (1)
 
   tr1a
Value: 0.2448   (Units: per_min)
Constant
 
int_ai (2)
 
   a1
Value: 1.35   (Units: per_uM_per_min)
Constant
 
   d1_1
Value: 0.075   (Units: per_min)
Constant
 
int_an (2)
 
   a4_1
Value: 30.0   (Units: per_uM_per_min)
Constant
 
   d4_1
Value: 6.0E-5   (Units: per_min)
Constant
 
int_an_n (2)
 
   a4_2
Value: 30.0   (Units: per_uM_per_min)
Constant
 
   d4_2
Value: 6.0E-5   (Units: per_min)
Constant
 
int_2ani (2)
 
   a7
Value: 11.1   (Units: per_uM_per_min)
Constant
 
   d1_2
Value: 0.075   (Units: per_min)
Constant
 
int_2ain (2)
 
   a4_3
Value: 30.0   (Units: per_uM_per_min)
Constant
 
   d4_3
Value: 6.0E-5   (Units: per_min)
Constant
 
deg_a (1)
 
   deg1_c
Value: 0.12   (Units: per_min)
Constant
 
deg_a_n (1)
 
   deg1_n
Value: 0.12   (Units: per_min)
Constant
 
deg_an_n (1)
 
   deg4_n
Value: 6.0E-5   (Units: per_min)
Constant
 
deg_an (1)
 
   deg4_c
Value: 6.0E-5   (Units: per_min)
Constant
 
deg_ai (1)
 
   r1
Value: 0.072   (Units: per_min)
Constant
 
deg_ain (1)
 
   r4
Value: 0.36   (Units: per_min)
Constant
 
loc_a (2)
 
   tp1a
Value: 0.018   (Units: per_min)
Constant
 
   tp2a
Value: 0.012   (Units: per_min)
Constant
 
loc_an (1)
 
   k2_a
Value: 0.828   (Units: per_min)
Constant
 
loc_bn (1)
 
   k2_b
Value: 0.414   (Units: per_min)
Constant
 
loc_b (2)
 
   tp1b
Value: 0.018   (Units: per_min)
Constant
 
   tp2b
Value: 0.012   (Units: per_min)
Constant
 
deg_bin (1)
 
   r5
Value: 0.12   (Units: per_min)
Constant
 
deg_bi (1)
 
   r2
Value: 0.024   (Units: per_min)
Constant
 
deg_bn (1)
 
   deg5_c
Value: 6.0E-5   (Units: per_min)
Constant
 
deg_bn_n (1)
 
   deg5_n
Value: 6.0E-5   (Units: per_min)
Constant
 
deg_b_n (1)
 
   deg2_n
Value: 0.18   (Units: per_min)
Constant
 
deg_b (1)
 
   deg2_c
Value: 0.18   (Units: per_min)
Constant
 
int_2bin (2)
 
   a5_3
Value: 30.0   (Units: per_uM_per_min)
Constant
 
   d5_3
Value: 6.0E-5   (Units: per_min)
Constant
 
int_2bni (2)
 
   a8
Value: 2.88   (Units: per_uM_per_min)
Constant
 
   d2_2
Value: 0.105   (Units: per_min)
Constant
 
int_bn_n (2)
 
   a5_2
Value: 30.0   (Units: per_uM_per_min)
Constant
 
   d5_2
Value: 6.0E-5   (Units: per_min)
Constant
 
int_bn (2)
 
   a5_1
Value: 30.0   (Units: per_uM_per_min)
Constant
 
   d5_1
Value: 6.0E-5   (Units: per_min)
Constant
 
int_bi (2)
 
   a2
Value: 0.36   (Units: per_uM_per_min)
Constant
 
   d2_1
Value: 0.105   (Units: per_min)
Constant
 
tsl_b (1)
 
   tr1b
Value: 0.2448   (Units: per_min)
Constant
 
mdeg_b (1)
 
   tr3b
Value: 0.0168   (Units: per_min)
Constant
 
txn_b (1)
 
   tr2b
Value: 4.272E-5   (Units: uM_per_min)
Constant
 
loc_n (2)
 
   k1_2
Value: 5.4   (Units: per_min)
Constant
 
   k1_1
Value: 0.0048   (Units: per_min)
Constant
 
txn_e (1)
 
   tr2e
Value: 3.048E-5   (Units: uM_per_min)
Constant
 
mdeg_e (1)
 
   tr3e
Value: 0.0168   (Units: per_min)
Constant
 
tsl_e (1)
 
   tr1e
Value: 0.2448   (Units: per_min)
Constant
 
int_ei (2)
 
   a3
Value: 0.54   (Units: per_uM_per_min)
Constant
 
   d3_1
Value: 0.105   (Units: per_min)
Constant
 
int_en (2)
 
   a6_1
Value: 30.0   (Units: per_uM_per_min)
Constant
 
   d6_1
Value: 6.0E-5   (Units: per_min)
Constant
 
int_en_n (2)
 
   a6_2
Value: 30.0   (Units: per_uM_per_min)
Constant
 
   d6_2
Value: 6.0E-5   (Units: per_min)
Constant
 
int_2eni (2)
 
   a9
Value: 4.2   (Units: per_uM_per_min)
Constant
 
   d3_2
Value: 0.105   (Units: per_min)
Constant
 
int_2ein (2)
 
   a6_3
Value: 30.0   (Units: per_uM_per_min)
Constant
 
   d6_3
Value: 6.0E-5   (Units: per_min)
Constant
 
deg_e (1)
 
   deg3_c
Value: 0.18   (Units: per_min)
Constant
 
deg_e_n (1)
 
   deg3_n
Value: 0.18   (Units: per_min)
Constant
 
deg_en_n (1)
 
   deg6_n
Value: 6.0E-5   (Units: per_min)
Constant
 
deg_en (1)
 
   deg6_c
Value: 6.0E-5   (Units: per_min)
Constant
 
deg_ei (1)
 
   r3
Value: 0.036   (Units: per_min)
Constant
 
deg_ein (1)
 
   r6
Value: 0.18   (Units: per_min)
Constant
 
loc_e (2)
 
   tp1e
Value: 0.018   (Units: per_min)
Constant
 
   tp2e
Value: 0.012   (Units: per_min)
Constant
 
loc_en (1)
 
   k2_e
Value: 0.414   (Units: per_min)
Constant
 
IKK_deg (1)
 
   IKK_deg
Constant
 
itxn_a (1)
 
   tr2a_i
Value: 1.98   (Units: per_uM_per_min)
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000147

Curator's comment: (updated: 18 Jan 2010 13:30:14 GMT)

The plots depict the total protein levels of the different IkB isoforms as shown in Figure 3A and NFkBn for wild type as shown in Fig 3B. Results obtained using Copasi 4.5.

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