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BIOMD0000000124 - Wu2006_K+Channel

 

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Reference Publication
Publication ID: 16375866
Wu SN, Chang HD.
Diethyl pyrocarbonate, a histidine-modifying agent, directly stimulates activity of ATP-sensitive potassium channels in pituitary GH(3) cells.
Biochem. Pharmacol. 2006 Feb; 71(5): 615-623
Department of Physiology, National Cheng Kung University Medical College, No 1, University Road, Tainan 70101, Taiwan. snwu@mail.ncku.edu.tw  [more]
Model
Original Model: http://senselab.med.yale.e...
Submitter: Enuo He
Submission ID: MODEL2981976537
Submission Date: 05 Jul 2007 08:16:33 UTC
Last Modification Date: 28 Feb 2014 16:06:07 UTC
Creation Date: 25 Jun 2007 16:36:46 UTC
Encoders:  Enuo He
set #1
bqmodel:isDerivedFrom PubMed 15294427
PubMed 6305437
set #2
bqbiol:isVersionOf Gene Ontology histone modification
Gene Ontology neuronal action potential
Gene Ontology ATP-activated inward rectifier potassium channel activity
set #3
bqbiol:hasTaxon Taxonomy Rattus
Notes

The model is described in the paper by Wu and Chang (2006). Diethyl pyrocarbonate, a histidine-modifying agent, directly stimulates activity of ATP-sensitive potassium channels in pituitary GH3 cells. Biochem Pharmacol. 71(5): 615-23.

The unit of time is ms, and the simulation time is 80 s, that is 8e4 ms. Therfore, you probably need to increase the maximum steps for your simulator.

The figure 7 has been reproduced by MathSBML. Application of DEPC as indicated at horizontal bar was mimicked by an increase of maximal conductance of Katp-channels from 500 to 530 ps at t=30 s.


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: 16375866 Submission Date: 05 Jul 2007 08:16:33 UTC Last Modification Date: 28 Feb 2014 16:06:07 UTC Creation Date: 25 Jun 2007 16:36:46 UTC
Mathematical expressions
Reactions
cytosolic free Ca2+ concentration ER Ca2+ concentration    
Rules
Assignment Rule (variable: alphaIRn) Assignment Rule (variable: betaIRn) Assignment Rule (variable: nIRinf) Assignment Rule (variable: tauIRn)
Assignment Rule (variable: alphaIRr) Assignment Rule (variable: betaIRr) Assignment Rule (variable: rIRinf) Assignment Rule (variable: tauIRr)
Assignment Rule (variable: minf) Assignment Rule (variable: delayed rectifier k current) Assignment Rule (variable: w) Assignment Rule (variable: nucleotide sensitive k current)
Assignment Rule (variable: calcium current) Assignment Rule (variable: ninf) Assignment Rule (variable: ainf) Assignment Rule (variable: ca dependent k current)
Assignment Rule (variable: jmem) Assignment Rule (variable: jserca) Assignment Rule (variable: jleak) Assignment Rule (variable: oinf)
Assignment Rule (variable: jip3) Assignment Rule (variable: jer) Rate Rule (variable: nIR) Rate Rule (variable: rIR)
Assignment Rule (variable: erg like k current) Rate Rule (variable: n) Rate Rule (variable: a) Rate Rule (variable: V)
Events
event_0000001      
Physical entities
Compartments Species
GH3 cell cytosolic free ca concentration ER ca concentration  
Global parameters
ca current conductance ca activated k conductance k current conductance erg k current conductance
ca reversal potential k reversal potential vir membrane capacitance
taun alpha fcyt kpmca
kd vn vm sn
sm kserca dact dinact
fer pleak dip3 vcytver
ip3 sa r taua
gkatp alphaIRn betaIRn nIRinf
tauIRn alphaIRr betaIRr rIRinf
tauIRr calcium current delayed rectifier k current ca dependent k current
nucleotide sensitive k current erg like k current minf ninf
ainf w jmem jserca
jleak jip3 oinf jer
V n a nIR
rIR      
Reactions (2)
 
 cytosolic free Ca2+ concentration  → [cytosolic free ca concentration];  
 
 ER Ca2+ concentration  → [ER ca concentration];  
 
Rules (28)
 
 Assignment Rule (name: alphaIRn) alphaIRn = 0.09/(1+exp(0.11*(V+100)))
 
 Assignment Rule (name: betaIRn) betaIRn = 0.00035*exp(0.07*(V+25))
 
 Assignment Rule (name: nIRinf) nIRinf = 1/(1+betaIRn/alphaIRn)
 
 Assignment Rule (name: tauIRn) tauIRn = 1/(alphaIRn+betaIRn)
 
 Assignment Rule (name: alphaIRr) alphaIRr = 30/(1+exp(0.04*(V+230)))
 
 Assignment Rule (name: betaIRr) betaIRr = 0.15/(1+exp((-0.05)*(V+120)))
 
 Assignment Rule (name: rIRinf) rIRinf = 1/(1+betaIRr/alphaIRr)
 
 Assignment Rule (name: tauIRr) tauIRr = 1/(alphaIRr+betaIRr)
 
 Assignment Rule (name: minf) minf = 1/(1+exp((vm-V)/sm))
 
 Assignment Rule (name: ik) delayed rectifier k current = gk*n*(V-vk)
 
 Assignment Rule (name: w) w = c^5/(c^5+kd^5)
 
 Assignment Rule (name: ikatp) nucleotide sensitive k current = gkatp*a*(V-vk)
 
 Assignment Rule (name: ica) calcium current = gca*minf*(V-vca)
 
 Assignment Rule (name: ninf) ninf = 1/(1+exp((vn-V)/sn))
 
 Assignment Rule (name: ainf) ainf = 1/(1+exp((r-c)/sa))
 
 Assignment Rule (name: ikca) ca dependent k current = gkca*w*(V-vk)
 
 Assignment Rule (name: jmem) jmem = -(alpha*ica+kpmca*c)
 
 Assignment Rule (name: jserca) jserca = kserca*c
 
 Assignment Rule (name: jleak) jleak = pleak*(cer-c)
 
 Assignment Rule (name: oinf) oinf = c/(dact+c)*ip3/(dip3+ip3)*dinact/(dinact+c)
 
 Assignment Rule (name: jip3) jip3 = oinf*(cer-c)
 
 Assignment Rule (name: jer) jer = jleak+jip3-jserca
 
 Rate Rule (name: nIR) d [ nIR] / d t= (nIRinf-nIR)/tauIRn
 
 Rate Rule (name: rIR) d [ rIR] / d t= (rIRinf-rIR)/tauIRr
 
 Assignment Rule (name: iir) erg like k current = gir*nIR*rIR*(V-vir)
 
 Rate Rule (name: n) d [ n] / d t= (ninf-n)/taun
 
 Rate Rule (name: a) d [ a] / d t= (ainf-a)/taua
 
 Rate Rule (name: V) d [ V] / d t= (-(ica+ik+ikca+ikatp+iir))/cm
 
Events (1)
 
 event_0000001
gkatp = 530
 
 GH3 cell Spatial dimensions: 3.0  Compartment size: 1.0
 
 cytosolic free ca concentration
Compartment: GH3 cell
Initial concentration: 0.1
 
 ER ca concentration
Compartment: GH3 cell
Initial concentration: 100.0
 
Global Parameters (57)
 
   ca current conductance
Value: 1000.0
Constant
 
   ca activated k conductance
Value: 900.0
Constant
 
   k current conductance
Value: 1400.0
Constant
 
   erg k current conductance
Value: 5.0
Constant
 
   ca reversal potential
Value: 50.0
Constant
 
   k reversal potential
Value: -75.0
Constant
 
   vir
Value: -75.0
Constant
 
   membrane capacitance
Value: 5300.0
Constant
 
   taun
Value: 16.0
Constant
 
   alpha
Value: 4.5E-6
Constant
 
   fcyt
Value: 0.01
Constant
 
   kpmca
Value: 0.2
Constant
 
   kd
Value: 0.3
Constant
 
   vn
Value: -16.0
Constant
 
   vm
Value: -20.0
Constant
 
   sn
Value: 5.0
Constant
 
   sm
Value: 12.0
Constant
 
   kserca
Value: 0.4
Constant
 
   dact
Value: 0.35
Constant
 
   dinact
Value: 0.4
Constant
 
   fer
Value: 0.01
Constant
 
   pleak
Value: 5.0E-4
Constant
 
   dip3
Value: 0.5
Constant
 
   vcytver
Value: 5.0
Constant
 
   ip3
Constant
 
   sa
Value: 0.1
Constant
 
   r
Value: 0.14
Constant
 
   taua
Value: 300000.0
Constant
 
 gkatp
Value: 500.0
 
   alphaIRn
Value: NaN
 
   betaIRn
Value: NaN
 
   nIRinf
Value: NaN
 
   tauIRn
Value: NaN
 
   alphaIRr
Value: NaN
 
   betaIRr
Value: NaN
 
   rIRinf
Value: NaN
 
   tauIRr
Value: NaN
 
   calcium current
Value: NaN
 
   delayed rectifier k current
Value: NaN
 
   ca dependent k current
Value: NaN
 
   nucleotide sensitive k current
Value: NaN
 
   erg like k current
Value: NaN
 
   minf
Value: NaN
 
   ninf
Value: NaN
 
   ainf
Value: NaN
 
   w
Value: NaN
 
   jmem
Value: NaN
 
   jserca
Value: NaN
 
   jleak
Value: NaN
 
   jip3
Value: NaN
 
   oinf
Value: NaN
 
   jer
Value: NaN
 
   V
Value: -60.0
 
   n
Value: 0.01
 
   a
Value: 0.46
 
   nIR
Value: 0.0080
 
   rIR
Value: 0.282
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000124

Curator's comment: (updated: 10 Aug 2007 18:26:09 BST)

Figure7A in the paper reproduced by MathSBML.

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