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BIOMD0000000121 - Clancy2001_Kchannel

 

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Reference Publication
Publication ID: 11334834
Clancy CE, Rudy Y.
Cellular consequences of HERG mutations in the long QT syndrome: precursors to sudden cardiac death.
Cardiovasc. Res. 2001 May; 50(2): 301-313
Cardiac Bioelectricity Research and Training Center, Department of Physiology and Biophysics, 509 Wickenden Building, Case Western Reserve University, Cleveland, Ohio 44106-7207, USA.  [more]
Model
Original Model: http://senselab.med.yale.e...
Submitter: Enuo He
Submission ID: MODEL2898180293
Submission Date: 05 Jul 2007 08:14:39 UTC
Last Modification Date: 27 Apr 2017 18:37:54 UTC
Creation Date: 20 Jun 2007 09:51:21 UTC
Encoders:  Enuo He
set #1
bqbiol:isVersionOf Gene Ontology heart process
Gene Ontology regulation of potassium ion transport
Gene Ontology delayed rectifier potassium channel activity
bqbiol:hasTaxon Taxonomy Cavia porcellus
bqbiol:isHomologTo OMIM POTASSIUM CHANNEL, VOLTAGE-GATED, SUBFAMILY H, MEMBER 2; KCNH2
set #2
bqbiol:hasProperty Mathematical Modelling Ontology MAMO_0000046
set #3
bqbiol:hasVersion Human Disease Ontology Andersen-Tawil syndrome
set #4
bqmodel:isDerivedFrom PubMed 10448858
PubMed 10318671
PubMed 7788872
PubMed 7514509
Notes

This model is according to the paper Cellular consequences of HEGR mutations in the long QT syndrome: precursors to sudden cardiac death. The author used Markovian model of cardiac Ikr in the paper. Figure4B in the paper has been reproduced using CellDesigner3.5.1. The cell is depolarized to the indicated test potential for 250ms (from 50ms to 300ms) from a holding potential of -40mV and then repolarized to -40mV. Change the value for vtest from -30,-20,-10,0,10,20,30,40 for each simulation in order to produce the different cureve in the paper.


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: 11334834 Submission Date: 05 Jul 2007 08:14:39 UTC Last Modification Date: 27 Apr 2017 18:37:54 UTC Creation Date: 20 Jun 2007 09:51:21 UTC
Mathematical expressions
Reactions
c3-c2 transition c2-c1 transition c1-o transition o-i transition
c1-i transition      
Rules
Assignment Rule (variable: reversal potential for k) Assignment Rule (variable: membrane_conductance) Assignment Rule (variable: a) Assignment Rule (variable: b)
Assignment Rule (variable: aa) Assignment Rule (variable: bb) Assignment Rule (variable: ai) Assignment Rule (variable: bi)
Assignment Rule (variable: u) Assignment Rule (variable: cardiac delayed rectifier current)    
Events
event_0000001 event_0000002    
Physical entities
Compartments Species
cell ClosedState_3 ClosedState_2 ClosedState_1
OpenState InactivationState cardiac delayed rectifier current
Global parameters
gas constant Faraday constant temperature extracellular K
introcellular K holding_potential test_potential reversal potential for k
membrane_conductance a b ain
bin aa bb ai
bi u membrane_potential  
Reactions (5)
 
 c3-c2 transition [ClosedState_3] ↔ [ClosedState_2];  
 
 c2-c1 transition [ClosedState_2] ↔ [ClosedState_1];  
 
 c1-o transition [ClosedState_1] ↔ [OpenState];  
 
 o-i transition [OpenState] ↔ [InactivationState];  
 
 c1-i transition [ClosedState_1] ↔ [InactivationState];  
 
Rules (10)
 
 Assignment Rule (name: vk) reversal potential for k = R*Temp/F*ln(ko/ki)
 
 Assignment Rule (name: Gk) membrane_conductance = 1.35E-2*ko^0.59
 
 Assignment Rule (name: a) a = 5.55E-2*exp(0.05547153*(v-12))
 
 Assignment Rule (name: b) b = 2.357E-3*exp((-0.036588)*v)
 
 Assignment Rule (name: aa) aa = 6.55E-2*exp(0.05547153*(v-36))
 
 Assignment Rule (name: bb) bb = 2.9357E-3*exp((-0.02158)*v)
 
 Assignment Rule (name: ai) ai = 0.439*exp((-0.02352)*(v+25))*4.5/ko
 
 Assignment Rule (name: bi) bi = 0.656*exp(0.000942*v)*(4.5/ko)^0.3
 
 Assignment Rule (name: u) u = ai*bb*aa/(aa*bi)
 
 Assignment Rule (name: ik) cardiac delayed rectifier current = Gk*o*(v-vk)
 
Events (2)
 
 event_0000001
membrane_potential = vtest
 
 event_0000002
membrane_potential = vhold
 
  Spatial dimensions: 3.0  Compartment size: 1.0
 
 ClosedState_3
Compartment: cell
Initial concentration: 1.0
 
 ClosedState_2
Compartment: cell
Initial concentration: 0.0
 
 ClosedState_1
Compartment: cell
Initial concentration: 0.0
 
 OpenState
Compartment: cell
Initial concentration: 0.06
 
 InactivationState
Compartment: cell
Initial concentration: 0.0
 
   cardiac delayed rectifier current
Compartment: cell
Initial concentration: 0.1
 
Global Parameters (19)
 
   gas constant
Value: 8.314
Constant
 
   Faraday constant
Value: 96.485
Constant
 
   temperature
Value: 310.0
Constant
 
   extracellular K
Value: 5.4
Constant
 
   introcellular K
Value: 140.0
Constant
 
   holding_potential
Value: -40.0
Constant
 
   test_potential
Constant
 
   reversal potential for k
Value: NaN
 
   membrane_conductance
Value: NaN
 
   a
Value: NaN
 
   b
Value: NaN
 
   ain
Value: 2.172
Constant
 
   bin
Value: 1.077
Constant
 
   aa
Value: NaN
 
   bb
Value: NaN
 
   ai
Value: NaN
 
   bi
Value: NaN
 
   u
Value: NaN
 
 membrane_potential
Value: -40.0
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000121

Curator's comment: (updated: 26 Jun 2007 23:52:30 BST)

Figure4B has been reproduced by Celldesigner 3.5.1

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