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BIOMD0000000202 - ChenXF2008_CICR

 

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Reference Publication
Publication ID: 18538916
Chen XF, Li CX, Wang PY, Li M, Wang WC.
Dynamic simulation of the effect of calcium-release activated calcium channel on cytoplasmic Ca2+ oscillation.
Biophys. Chem. 2008 Aug; 136(2-3): 87-95
Laboratory of Soft Matter Physics, Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100080, China.  [more]
Model
Original Model: BIOMD0000000202.origin
Submitter: Harish Dharuri
Submission ID: MODEL7519277765
Submission Date: 24 Nov 2008 18:21:10 UTC
Last Modification Date: 24 Feb 2015 20:33:32 UTC
Creation Date: 24 Nov 2008 07:12:39 UTC
Encoders:  Harish Dharuri
set #1
bqmodel:isDerivedFrom PubMed 1329108
set #2
bqbiol:hasTaxon Taxonomy cellular organisms
set #3
bqbiol:isVersionOf Gene Ontology activation of store-operated calcium channel activity
Gene Ontology release of sequestered calcium ion into cytosol
Notes

The model reproduces the plots in Figures 1 and 2. Note that the units of the time scale "A" are not right in the paper, it was corrected by the curator. Model successfully tested on MathSBML.

Model
Publication ID: 18538916 Submission Date: 24 Nov 2008 18:21:10 UTC Last Modification Date: 24 Feb 2015 20:33:32 UTC Creation Date: 24 Nov 2008 07:12:39 UTC
Mathematical expressions
Reactions
ER_Channel SERCA PM_Channel PMCA
PLC deg act_apoSTIM1_syn act_apoSTIM1_deg
apoSTIM1_oligo_syn apoSTIM1_oligo_deg close_CRAC_prod closed_CRAC_channel_deg
open_CRAC_channel_prod open_to_closed open_CRAC_channel_deg  
Rules
Assignment Rule (variable: Orai1) Assignment Rule (variable: S2) Rate Rule (variable: h)  
Physical entities
Compartments Species
Cytoplasm Ca_Cyt IP3_Cyt  
ER Ca_ER S2 S2a
S4    
PM Oc O_o Orai1
Global parameters
L P_IP3R Ki k_i
Ka V_SERCA p K_SERCA
k_soc V_PMleak Ca_ec V_PMCA
q K_PMCA V_PLC K_PLC
kdeg K_deg A Kd
K1 St k_a Vs4
K2 kd_oligo Vcp n_hill
Kc kdc kop l_hill
Ko kod kdo r_hill
h Orai1_t    
Reactions (15)
 
 ER_Channel [Ca_ER] → [Ca_Cyt];   {IP3_Cyt}
 
 SERCA [Ca_Cyt] → [Ca_ER];  
 
 PM_Channel  → [Ca_Cyt];   {O_o}
 
 PMCA [Ca_Cyt] → ;  
 
 PLC  → [IP3_Cyt];   {Ca_Cyt}
 
 deg [IP3_Cyt] → ;   {Ca_Cyt}
 
 act_apoSTIM1_syn  → [S2a];   {S2}
 
 act_apoSTIM1_deg [S2a] → ;  
 
 apoSTIM1_oligo_syn  → [S4];   {S2}
 
 apoSTIM1_oligo_deg [S4] → ;  
 
 close_CRAC_prod  → [Oc];   {Orai1}
 
 closed_CRAC_channel_deg [Oc] → ;  
 
 open_CRAC_channel_prod [Oc] → [O_o];   {S2a}
 
 open_to_closed [O_o] → [Oc];  
 
 open_CRAC_channel_deg [O_o] → ;  
 
Rules (3)
 
 Assignment Rule (name: Orai1) Orai1 = Orai1_t-(r_hill*Oc+r_hill*O_o)
 
 Assignment Rule (name: S2) S2 = K1^2/(Ca_ER^2+K1^2)*(St-S2a)
 
 Rate Rule (name: h) d [ h] / d t= A*(Kd-(Ca_Cyt+Kd)*h)
 
   Spatial dimensions: 3.0  Compartment size: 1.0
 
 Ca_Cyt
Compartment: Cytoplasm
Initial concentration: 0.0
 
 IP3_Cyt
Compartment: Cytoplasm
Initial concentration: 0.0
 
   Spatial dimensions: 3.0  Compartment size: 0.185
 
 Ca_ER
Compartment: ER
Initial concentration: 0.0
 
  S2
Compartment: ER
Initial concentration: 0.54
 
 S2a
Compartment: ER
Initial concentration: 0.06
 
 S4
Compartment: ER
Initial concentration: 0.0
 
   Spatial dimensions: 3.0  Compartment size: 1.0
 
   Oc
Compartment: PM
Initial concentration: 0.0
 
   O_o
Compartment: PM
Initial concentration: 0.0
 
  Orai1
Compartment: PM
Initial concentration: 0.001
 
Global Parameters (38)
 
   L
Value: 9.3E-4   (Units: s_1)
Constant
 
   P_IP3R
Value: 66.6   (Units: s_1)
Constant
 
   Ki
Value: 1.0   (Units: uM)
Constant
 
   k_i
Value: 6.0   (Units: s_1)
Constant
 
   Ka
Value: 0.4   (Units: uM)
Constant
 
   V_SERCA
Value: 1.0   (Units: uM_s_1)
Constant
 
   p
Value: 2.0   (Units: dimensionless)
Constant
 
   K_SERCA
Value: 0.15   (Units: uM)
Constant
 
   k_soc
Value: 2.3   (Units: uM_1_s_1)
Constant
 
   V_PMleak
Value: 5.0E-7   (Units: s_1)
Constant
 
   Ca_ec
Value: 1500.0   (Units: uM)
Constant
 
   V_PMCA
Value: 1.0   (Units: uM_s_1)
Constant
 
   q
Value: 2.0   (Units: dimensionless)
Constant
 
   K_PMCA
Value: 0.45   (Units: uM)
Constant
 
   V_PLC
Value: 0.5   (Units: uM_s_1)
Constant
 
   K_PLC
Value: 0.12   (Units: uM)
Constant
 
   kdeg
Value: 0.5   (Units: s_1)
Constant
 
   K_deg
Value: 0.1   (Units: uM)
Constant
 
   A
Value: 0.5   (Units: uM_1_s_1)
Constant
 
   Kd
Value: 0.4   (Units: uM)
Constant
 
   K1
Value: 5.0   (Units: uM)
Constant
 
   St
Value: 0.6   (Units: uM)
Constant
 
   k_a
Value: 4.0   (Units: s_1)
Constant
 
   Vs4
Value: 0.25   (Units: uM_s_1)
Constant
 
   K2
Value: 0.14   (Units: uM)
Constant
 
   kd_oligo
Value: 0.8   (Units: s_1)
Constant
 
   Vcp
Value: 1.8E-4   (Units: uM_s_1)
Constant
 
   n_hill
Value: 3.0   (Units: dimensionless)
Constant
 
   Kc
Value: 2.0E-5   (Units: uM)
Constant
 
   kdc
Value: 0.5   (Units: s_1)
Constant
 
   kop
Value: 0.5   (Units: s_1)
Constant
 
   l_hill
Value: 1.0   (Units: dimensionless)
Constant
 
   Ko
Value: 0.2   (Units: uM)
Constant
 
   kod
Value: 1.0   (Units: s_1)
Constant
 
   kdo
Value: 0.6   (Units: s_1)
Constant
 
   r_hill
Value: 4.0   (Units: dimensionless)
Constant
 
   h  
 
   Orai1_t
Value: 0.001   (Units: uM)
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000202

Curator's comment: (updated: 24 Nov 2008 18:20:45 GMT)

Plots correspond to the time profiles of cytosolic and ER Calcium and active STIM1 dimers as depicted in Figure 1 and figure 2.
Results obtained using MathSBML.

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