Figure4 and Figure5 can be simulated by Copasi. Figure4 can be simulated in MathSBML as well. There are some typos in the paper:K29=234, is it should k_29; Table2, reaction17, is there are "slash" missing in between the rate equation; reaction 33,"Akt-PI-PP" in the last term of denominator instead of "AktPI-P" . For plotting figure4, we create another extra parameter *_percent, and use assignment rule calculate percentage of each species.
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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.
- A computational model on the modulation of mitogen-activated protein kinase (MAPK) and Akt pathways in heregulin-induced ErbB signalling.
- Hatakeyama M, Kimura S, Naka T, Kawasaki T, Yumoto N, Ichikawa M, Kim JH, Saito K, Saeki M, Shirouzu M, Yokoyama S, Konagaya A
- The Biochemical journal , 7/ 2003 , Volume 373 , pages: 451-463 , PubMed ID: 12691603
- RIKEN Genomic Sciences Center, 1-7-22 Suehirocho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan. email@example.com
- ErbB tyrosine kinase receptors mediate mitogenic signal cascade by binding a variety of ligands and recruiting the different cassettes of adaptor proteins. In the present study, we examined heregulin (HRG)-induced signal transduction of ErbB4 receptor and found that the phosphatidylinositol 3'-kinase (PI3K)-Akt pathway negatively regulated the extracellular signal-regulated kinase (ERK) cascade by phosphorylating Raf-1 on Ser(259). As the time-course kinetics of Akt and ERK activities seemed to be transient and complex, we constructed a mathematical simulation model for HRG-induced ErbB4 receptor signalling to explain the dynamics of the regulation mechanism in this signal transduction cascade. The model reflected well the experimental results observed in HRG-induced ErbB4 cells and in other modes of growth hormone-induced cell signalling that involve Raf-Akt cross-talk. The model suggested that HRG signalling is regulated by protein phosphatase 2A as well as Raf-Akt cross-talk, and protein phosphatase 2A modulates the kinase activity in both the PI3K-Akt and MAPK (mitogen-activated protein kinase) pathways.
|BIOMD0000000146_url.xml||SBML L2V1 representation of Hatakeyama2003_MAPK||87.92 KB||Preview | Download|
|BIOMD0000000146.xpp||Auto-generated XPP file||14.26 KB||Preview | Download|
|BIOMD0000000146-biopax2.owl||Auto-generated BioPAX (Level 2)||62.68 KB||Preview | Download|
|BIOMD0000000146.vcml||Auto-generated VCML file||120.08 KB||Preview | Download|
|BIOMD0000000146.svg||Auto-generated Reaction graph (SVG)||100.55 KB||Preview | Download|
|BIOMD0000000146.pdf||Auto-generated PDF file||311.61 KB||Preview | Download|
|BIOMD0000000146-biopax3.owl||Auto-generated BioPAX (Level 3)||97.95 KB||Preview | Download|
|BIOMD0000000146_urn.xml||Auto-generated SBML file with URNs||85.98 KB||Preview | Download|
|BIOMD0000000146.m||Auto-generated Octave file||19.67 KB||Preview | Download|
|BIOMD0000000146.sci||Auto-generated Scilab file||14.56 KB||Preview | Download|
|BIOMD0000000146.png||Auto-generated Reaction graph (PNG)||446.34 KB||Preview | Download|
- Model originally submitted by : Enuo He
- Submitted: Sep 6, 2007 9:06:00 AM
- Last Modified: May 27, 2014 12:17:39 AM
- Submitted on: May 27, 2014 12:17:39 AM
- Submitted by: Enuo He
- With comment: Current version of Hatakeyama2003_MAPK
- Submitted on: Sep 6, 2007 9:06:00 AM
- Submitted by: Enuo He
- With comment: Original import of Hatakeyama2003_MAPK
(*) You might be seeing discontinuous revisions as only public revisions are displayed here. Any private revisions of this model will only be shown to the submitter and their collaborators.
: Variable used inside SBML models
1-phosphatidyl-1D-myo-inositol 3,4,5-trisphosphate ; IPR015744
phosphatidylinositol 3-phosphate ; IPR015744
1-phosphatidyl-1D-myo-inositol 3,4-bisphosphate ; IPR015744
IPR003527; IPR008349; IPR008350
phosphate(3-) ; IPR008349; phosphate(3-) ; IPR008350
diphosphate(4-) ; IPR008349; diphosphate(4-) ; IPR008350
|PIP3 => P_I||compartment_0000001*V28*PIP3/(K28+PIP3)||V28 = 17000.0; K28 = 9.02|
|P_I => PIP3; PI3Kstar||compartment_0000001*k27*PI3Kstar*P_I/(K27+P_I)||K27 = 39.1; k27 = 16.9|
|PIP3 + Akt => AktPIP3||compartment_0000001*(k29*PIP3*Akt-k_29*AktPIP3)||k29 = 507.0; k_29 = 234.0|
|AktPIP3 => AktPIP||compartment_0000001*V30*AktPIP3/(K30*(1+AktPIP/K32)+AktPIP3)||V30 = 20000.0; K30 = 80000.0; K32 = 80000.0|
|AktPIP => AktPIP3; MEKP, MEKPP, AktPIPP, PP2A||compartment_0000001*k31*PP2A*AktPIP/(K31*(1+MEKP/K16+MEKPP/K18+AktPIPP/K33)+AktPIP)||K16 = 2200.0; K33 = 12.0; K18 = 60.0; k31 = 0.107; K31 = 4.35|
|AktPIP => AktPIPP; AktPIP3||compartment_0000001*V32*AktPIP/(K32*(1+AktPIP3/K30)+AktPIP)||K30 = 80000.0; K32 = 80000.0; V32 = 20000.0|
|AktPIPP => AktPIP; MEKP, MEKPP, PP2A||compartment_0000001*k33*PP2A*AktPIPP/(K33*(1+MEKP/K16+MEKPP/K18+AktPIP/K31)+AktPIPP)||K33 = 12.0; K16 = 2200.0; K18 = 60.0; K31 = 4.35; k33 = 0.211|
|ERK => ERKP; MEKPP||compartment_0000001*k19*MEKPP*ERK/(K19*(1+ERKP/K21)+ERK)||K19 = 146000.0; K21 = 146000.0; k19 = 9.5|
|ERKP => ERK; ERKPP, MKP3||compartment_0000001*k20*MKP3*ERKP/(K20*(1+ERKPP/K22)+ERKP)||K22 = 60.0; K20 = 160.0; k20 = 0.3|
|ERKPP => ERKP; MKP3||compartment_0000001*k22*MKP3*ERKPP/(K22*(1+ERKP/K20)+ERKPP)||K22 = 60.0; K20 = 160.0; k22 = 0.27|
|RShP + GS => RShGS||compartment_0000001*(k7*RShP*GS-k_7*RShGS)||k_7 = 546.0; k7 = 60.0|
(added: 28 Aug 2007, 00:16:43, updated: 28 Aug 2007, 00:16:43)