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BIOMD0000000128 - Bertram2006_Endothelin

 

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Reference Publication
Publication ID: 16434725
Bertram R, Tabak J, Toporikova N, Freeman ME.
Endothelin action on pituitary lactotrophs: one receptor, many GTP-binding proteins.
Sci. STKE 2006 Jan; 2006(319): pe4
Department of Mathematics, Florida State University, Tallahassee, FL 32306, USA. bertram@math.fsu.edu  [more]
Model
Original Model: http://www.math.fsu.edu/~b...
Submitter: Enuo He
Submission ID: MODEL6509019628
Submission Date: 08 Aug 2007 07:26:50 UTC
Last Modification Date: 05 Jul 2012 16:31:29 UTC
Creation Date: 03 Aug 2007 13:17:36 UTC
Encoders:  Enuo He
set #1
bqbiol:isVersionOf Gene Ontology G-protein coupled receptor binding
Gene Ontology endothelin receptor activity
Gene Ontology adenylate cyclase-modulating G-protein coupled receptor signaling pathway
bqbiol:occursIn Taxonomy Rattus
Notes

The model is according to the paper Endothelin Action on Pituitary Lactotrophs: One Receptor, Many GTP-Binding Proteins Figure 1 has been simulated by MathSBML. The figure for the [Ca2+]i and [Ca2+]ER have been normalized in the paper.Original model comes from http://www.math.fsu.edu/~bertram/software/pituitary

The units for parameters and species are varied from one to another, so I omit the unit definition here . Conductances in pS; currents in fA; Ca concentrations in uM; time in ms


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.

Model
Publication ID: 16434725 Submission Date: 08 Aug 2007 07:26:50 UTC Last Modification Date: 05 Jul 2012 16:31:29 UTC Creation Date: 03 Aug 2007 13:17:36 UTC
Mathematical expressions
Reactions
reaction_0000001 reaction_0000002 reaction_000003  
Rules
Assignment Rule (variable: minf) Assignment Rule (variable: ninf) Assignment Rule (variable: hinf) Assignment Rule (variable: ica)
Assignment Rule (variable: igirk) Assignment Rule (variable: ik) Assignment Rule (variable: ainf) Assignment Rule (variable: hinfer)
Assignment Rule (variable: jerp) Assignment Rule (variable: binf) Assignment Rule (variable: o) Assignment Rule (variable: jmemtot)
Assignment Rule (variable: jerleak) Assignment Rule (variable: jerip3) Assignment Rule (variable: jertot) Assignment Rule (variable: perl_inf)
Rate Rule (variable: h) Rate Rule (variable: variable for direct inhibition of secretion) Rate Rule (variable: voltage) Rate Rule (variable: delayed rectifier activation)
Events
ET-1 switch      
Physical entities
Compartments Species
cell cytosolic calcium concentration ER calcium concentration cAMP
Global parameters
vh sh tauh kserca
sigmav kc vn vk
taun gk sn vca
gca vm sm lambda
cm f fer alpha
perl dact dip3 dinh
ninf minf hinf ica
igirk ik girk IP3
ainf hinfer jerp binf
o jerleak jerip3 jertot
jmemtot ki perl_inf taudir
cAMPlow ETswitch h variable for direct inhibition of secretion
voltage delayed rectifier activation    
Reactions (3)
 
 reaction_0000001  → [cytosolic calcium concentration];  
 
 reaction_0000002  → [ER calcium concentration];  
 
 reaction_000003  → [cAMP];  
 
Rules (20)
 
 Assignment Rule (name: minf) minf = 1/(1+exp((vm-V)/sm))
 
 Assignment Rule (name: ninf) ninf = 1/(1+exp((vn-V)/sn))
 
 Assignment Rule (name: hinf) hinf = 1/(1+exp((vh-V)/sh))
 
 Assignment Rule (name: ica) ica = gca*minf*(V-vca)
 
 Assignment Rule (name: igirk) igirk = girk*h*(V-vk)
 
 Assignment Rule (name: ik) ik = gk*n*(V-vk)
 
 Assignment Rule (name: ainf) ainf = 1/(1+dact/c)
 
 Assignment Rule (name: hinfer) hinfer = 1/(1+c/dinh)
 
 Assignment Rule (name: jerp) jerp = kserca*c
 
 Assignment Rule (name: binf) binf = IP3/(IP3+dip3)
 
 Assignment Rule (name: o) o = ainf^3*binf^3*hinfer^3
 
 Assignment Rule (name: jmemtot) jmemtot = -(alpha*ica+kc*c)
 
 Assignment Rule (name: jerleak) jerleak = perl*(cer-c)
 
 Assignment Rule (name: jerip3) jerip3 = o*(cer-c)
 
 Assignment Rule (name: jertot) jertot = jerleak+jerip3-jerp
 
 Assignment Rule (name: perl_inf) perl_inf = inh*cAMP*c^4/(ki^4+c^4)
 
 Rate Rule (name: h) d [ h] / d t= (hinf-h)/tauh
 
 Rate Rule (name: inh) d [ variable for direct inhibition of secretion] / d t= ETswitch*(0.2-inh)/taudir
 
 Rate Rule (name: V) d [ voltage] / d t= (-ica-ik-igirk)/cm
 
 Rate Rule (name: n) d [ delayed rectifier activation] / d t= lambda*(ninf-n)/taun
 
Events (1)
 
 ET-1 switch
IP3 = 0.3
girk = 3000
ETswitch = 1
 
  Spatial dimensions: 3.0  Compartment size: 1.0
 
 cytosolic calcium concentration
Compartment: cell
Initial concentration: 0.3
 
 ER calcium concentration
Compartment: cell
Initial concentration: 260.0
 
 cAMP
Compartment: cell
Initial concentration: 1.0
 
Global Parameters (50)
 
   vh
Value: -20.0
Constant
 
   sh
Value: 70.0
Constant
 
   tauh
Value: 20.0
Constant
 
   kserca
Value: 0.4
Constant
 
   sigmav
Value: 10.0
Constant
 
   kc
Value: 0.15
Constant
 
   vn
Value: -16.0
Constant
 
   vk
Value: -75.0
Constant
 
   taun
Value: 20.0
Constant
 
   gk
Value: 3500.0
Constant
 
   sn
Value: 5.0
Constant
 
   vca
Value: 25.0
Constant
 
   gca
Value: 2000.0
Constant
 
   vm
Value: -20.0
Constant
 
   sm
Value: 12.0
Constant
 
   lambda
Value: 1.25
Constant
 
   cm
Value: 5300.0
Constant
 
   f
Value: 0.01
Constant
 
   fer
Value: 0.01
Constant
 
   alpha
Value: 4.5E-6
Constant
 
   perl
Value: 5.0E-4
Constant
 
   dact
Value: 0.35
Constant
 
   dip3
Value: 0.5
Constant
 
   dinh
Value: 0.4
Constant
 
   ninf
Value: NaN
 
   minf
Value: NaN
 
   hinf
Value: NaN
 
   ica
Value: NaN
 
   igirk
Value: NaN
 
   ik
Value: NaN
 
   girk
Value: 1000.0
 
   IP3  
 
   ainf
Value: NaN
 
   hinfer
Value: NaN
 
   jerp
Value: NaN
 
   binf
Value: NaN
 
   o
Value: NaN
 
   jerleak
Value: NaN
 
   jerip3
Value: NaN
 
   jertot
Value: NaN
 
   jmemtot
Value: NaN
 
   ki
Value: 0.5
Constant
 
   perl_inf
Value: NaN
 
   taudir
Value: 20000.0
Constant
 
 cAMPlow
Value: 0.2
Constant
 
   ETswitch  
 
   h  
 
   variable for direct inhibition of secretion
Value: 1.0
 
   voltage
Value: -60.0
 
   delayed rectifier activation  
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000128

Curator's comment: (updated: 10 Aug 2007 18:07:01 BST)

Figure 1 has been simulated by MathSBML.

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