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BIOMD0000000601 - Rosas2015 - Caffeine-induced luminal SR calcium changes

 

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Reference Publication
Publication ID: 26390403
Perez-Rosas NC, Gomez-Viquez NL, Dagnino-Acosta A, Santillan M, Guerrero-Hernandez A.
Kinetics on Demand Is a Simple Mathematical Solution that Fits Recorded Caffeine-Induced Luminal SR Ca2+ Changes in Smooth Muscle Cells.
PLoS ONE 2015; 10(9): e0138195
Unidad Monterrey, Cinvestav, Apodaca, Nuevo Leon, Mexico.  [more]
Model
Original Model: BIOMD0000000601.origin
Submitter: Norma Citlalcue Perez-Rosas
Submission ID: MODEL1406180001
Submission Date: 18 Jun 2014 18:11:30 UTC
Last Modification Date: 18 Apr 2016 14:54:42 UTC
Creation Date: 18 Apr 2016 13:46:09 UTC
Encoders:  Nick Juty
   Vijayalakshmi Chelliah
   Norma Citlalcue Perez-Rosas
   Ryan Gutenkunst
   Daniel Macias
   Emmet Andrews
   Ryan Mammana
   Sara Carey
   Emily Merritt
   Julie McGrath
   Joshua Kochanowsky
set #1
bqbiol:isVersionOf Gene Ontology release of sequestered calcium ion into cytosol by sarcoplasmic reticulum
set #2
bqbiol:hasTaxon Taxonomy Cavia porcellus
set #3
bqbiol:occursIn Brenda Tissue Ontology urinary bladder smooth muscle
Notes
This SBML model reproduced the calcium release from SR by application of 20 mM or 2mM caffeine, described in the paper. 

* Ca_i_Total and Ca_SR_Total respectively represent the total calcium concentration in the sarcoplasm and in the sarcoplasmic reticulum. 

* Ca_i  and Ca_SR respectively represent the free calcium concentration in the sarcoplasm and  the sarcoplasmic reticulum.

* J1 is the calcium  flux due to all mechanisms (except SERCA pumps) that remove the excess of calcium from the sarcoplasm.

* J2 is the calcium flux from the reticulum to the sarcoplasm via the ryanodine receptors (RyR) present in the reticulum membrane.

* J3 is the calcium flux from the sarcoplasm to the reticulum by the SERCA pumps located in the reticulum membrane.

*The parameters are a,  b, B c, Ca_i_basal, Ca_SR_basal, caff, csq,  gamma, KC, kf, KR, Ks, nf, ns and nv.

* The value of KC for the model were calculated for J2=J3, after substituting Ca_i=Ca_i_basal, Ca_SR=Ca_SR_basal and caff=0. 

* Po represents the RyR open probability based on CICR. 

* Caffeine (caff)** increases the calcium affinity of smooth muscle's RyR so they open even when calcium is at basal level.

** Due to caffeine-induced calcium release, a 5 seconds  pulse of caffeine (20 mM) was applied (event called Caff_ON) at 10 seconds after the simulation starts. The event called Caff_OFF starts when the pulse of caffeine finished (caff=0).

* PE denotes the concentration of calcium binding sites. 

* Xi=Ca_SR_Total+PE+KR

*In order to reproduce the dynamics of calcium following the application of 2 mM of caffeine, the value of some parameters needs to be change: b=35, Ca_i_basal=9.257e-6, gamma=7.45, caff=0.002 and the initial condition for Ca_i_Total=9.257e-6.

*The unit of the calcium concentration is mol/L.

* The unit of time is second. 

*The original SBML code was exported from COPASI 4.12 (Build 81).
Model
Publication ID: 26390403 Submission Date: 18 Jun 2014 18:11:30 UTC Last Modification Date: 18 Apr 2016 14:54:42 UTC Creation Date: 18 Apr 2016 13:46:09 UTC
Mathematical expressions
Reactions
J3 J2 J1  
Rules
Assignment Rule (variable: PE) Assignment Rule (variable: Xi) Assignment Rule (variable: Ca_i) Assignment Rule (variable: Ca_SR)
Assignment Rule (variable: KC) Assignment Rule (variable: Po)    
Events
Caff_ON Caff_OFF    
Physical entities
Compartments Species
SR Ca_SR_Total Ca_SR  
cytoplasm Ca_i_Total Ca_i caff
Global parameters
a b c Ca_i_basal
gamma nv Ks ns
B nf kf KR
csq KC Po PE
Ca_SR_basal Xi    
Reactions (3)
 
 J3 [Ca_i_Total] + [Ca_i] → [Ca_SR_Total] + [Ca_i];  
 
 J2 [Ca_SR_Total] + [Ca_SR] + [Ca_i] → [Ca_i_Total] + [Ca_SR] + [Ca_i];  
 
 J1 [Ca_i_Total] + [Ca_i] → [Ca_i];  
 
Rules (6)
 
 Assignment Rule (name: parameter_24) PE = parameter_15*(parameter_14-parameter_25)
 
 Assignment Rule (name: parameter_26) Xi = mwd805cc43_4a96_472f_a894_c119a6aa895f+parameter_24+parameter_14
 
 Assignment Rule (name: mwe1a0a651_d2d5_4f75_8d45_9336c60eb9a6) Ca_i = mw40a96ef6_32da_46d1_9712_4f53f60bad43/parameter_9
 
 Assignment Rule (name: mw447078ee_8bc8_4358_abcd_ade10dba93b0) Ca_SR = (parameter_26-(parameter_26^2-4*mwd805cc43_4a96_472f_a894_c119a6aa895f*parameter_14)^(1/2))/2
 
 Assignment Rule (name: parameter_22) KC = (parameter_2*parameter_5^parameter_6*(parameter_4/parameter_9)^parameter_10*(parameter_25-parameter_4/parameter_9)*((parameter_4/parameter_9)^parameter_8+parameter_7^parameter_8)/(parameter_3*(parameter_4/parameter_9)^parameter_8)-(parameter_4/parameter_9)^parameter_10)^(1/parameter_10)
 
 Assignment Rule (name: parameter_23) Po = (mwe1a0a651_d2d5_4f75_8d45_9336c60eb9a6*(1+parameter_11*mw168e0d8a_b9f7_4d4c_b437_a81206c5d381))^parameter_10/(parameter_22^parameter_10+(mwe1a0a651_d2d5_4f75_8d45_9336c60eb9a6*(1+parameter_11*mw168e0d8a_b9f7_4d4c_b437_a81206c5d381))^parameter_10)
 
Events (2)
 
 Caff_ON
caff = 0.02
 
 Caff_OFF
caff = 0
 
 SR Spatial dimensions: 3.0  Compartment size: 0.052
 
 Ca_SR_Total
Compartment: SR
Initial amount: 0.00165
 
  Ca_SR
Compartment: SR
Initial amount: 7.8E-6
 
 cytoplasm Spatial dimensions: 3.0  Compartment size: 1.0
 
 Ca_i_Total
Compartment: cytoplasm
Initial amount: 7.5E-6
 
  Ca_i
Compartment: cytoplasm
Initial amount: 7.5E-8
 
 caff
Compartment: cytoplasm
Initial amount: 0.0
 
Global Parameters (18)
 
 a
Value: 35.0
Constant
 
 b
Value: 65.0
Constant
 
 c
Value: 1.125E-5
Constant
 
 Ca_i_basal
Value: 7.5E-6
Constant
 
 gamma
Value: 0.052
Constant
 
 nv
Value: 1.7
Constant
 
 Ks
Value: 3.0E-7
Constant
 
 ns
Value: 2.0
Constant
 
 B
Value: 100.0
Constant
 
 nf
Value: 1.8
Constant
 
 kf
Value: 4000.0
Constant
 
 KR
Value: 1.515E-4
Constant
 
 csq
Value: 10.0
Constant
 
  KC
Value: 9.45128810336575E-7
 
  Po
Value: 0.0103445237903673
 
  PE
Value: 1.50000000000001E-5
 
 Ca_SR_basal
Value: 1.5E-4
Constant
 
  Xi
Value: 0.0018165
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000601

Curator's comment: (updated: 18 Apr 2016 15:31:49 BST)

Figure 2C of the reference publication has been reproduced. Simulations were
performed using SimBiology in Matlab R2015a and results were plotted using matplotlib. Quantitatively similar results were found using Copasi.

Additional file(s)
  • Matlab SBproj file:
    The original submitted SBML file represented all variables as parameters and used rate rules to directly specify the dynamics. The model has been transformed to semantically use species, compartments, and reactions.
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