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BIOMD0000000599 - Coggins2014 - CXCL12 dependent recruitment of beta arrestin

 

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Reference Publication
Publication ID: 24896823
Coggins NL, Trakimas D, Chang SL, Ehrlich A, Ray P, Luker KE, Linderman JJ, Luker GD.
CXCR7 controls competition for recruitment of β-arrestin 2 in cells expressing both CXCR4 and CXCR7.
PLoS ONE 2014; 9(6): e98328
Center for Molecular Imaging, Department of Radiology, Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America.  [more]
Model
Original Model: BIOMD0000000599.origin
Submitter: Jennifer Linderman
Submission ID: MODEL1408060000
Submission Date: 06 Aug 2014 13:11:40 UTC
Last Modification Date: 18 Apr 2016 14:58:25 UTC
Creation Date: 18 Apr 2016 11:39:25 UTC
Encoders:  Nick Juty
   Vijayalakshmi Chelliah
   Jennifer Linderman
   Ryan Gutenkunst
   Timothy Leach
   Syeda Kazmi
   Alexander McNeish
   David Byrne
set #1
bqbiol:isVersionOf Gene Ontology CXCL12-activated CXCR4 signaling pathway
Gene Ontology chemokine (C-X-C motif) ligand 12 signaling pathway
set #2
bqbiol:hasTaxon Taxonomy Homo sapiens
Notes
Model
Publication ID: 24896823 Submission Date: 06 Aug 2014 13:11:40 UTC Last Modification Date: 18 Apr 2016 14:58:25 UTC Creation Date: 18 Apr 2016 11:39:25 UTC
Mathematical expressions
Reactions
Be binding R4 Bp binding R4 Be binding C4 Bp binding C4
Be binding R7 Bp binding R7 Be binding C7 Bp binding C7
Internalization of R4Be Internalization of R4Bp Internalization of C4Be Internalization of C4Bp
Internalization of R7Be Internalization of R7Bp Internalization of C7Be Internalization of C7Bp
Dissocation of Be from C4Bei Dissociation of Bp from C4Bpi Dissociation of Be from R7Bei Dissociation of Bp from R7Bpi
Trafficking of C7Bei to late endosomes Trafficking of C7Bpi to late endosomes Recycling of R4Bei Recycling of R4Bpi
Recycling of R7Beii Recycling of R7Bpii Recycling of C7Beii Recycling of C7Bpii
Degradation of C4Beii Degradation of C4Bpii Degradation of L12i L12 binding R4
L12 binding R7 L12 binding R4Be L12 binding R4Bp L12 binding R7Be
L12 binding R7Bp      
Rules
Assignment Rule (variable: Total4) Assignment Rule (variable: Total7) Assignment Rule (variable: %Beta) Assignment Rule (variable: %CXCR4)
Assignment Rule (variable: %CXCR7)      
Physical entities
Compartments Species
Intracellular Be Bp C4
C4Be C4Beii C4Bp
C4Bpi C7 C7Bei
C7Beii C7Bp C7Bpi
L12i R4 R4Be
C7Bpii R7Bpii R7Bp
R7 C4Bpii C4Bei
R4Bpi R4Bp R7Be
R7Bei R7Beii C7Be
R4Bei R7Bpi L12
Global parameters
kf,L12,4 kf,L12,7 kf,B,4 kf,B,7
KD,R4,L12 KD,R7,L12 KD,C4,B KD,C7,B
ke,R4B ke,R7B ke,C7Bi koff,B,4
koff,B,7 krec,R4Bi krec,R7Bii krec,C7Bii
kdeg,C4Bii kdeg,L12i KD,R4,B KD,R7,B
ke,C4B ke,C7B n4 n7
n47 Nav Vwell Vcell
nmol_to_mol Total4 Total7 %Beta
%CXCR4 %CXCR7 Initial for Be Initial for Bp
Initial for C4 Initial for C7 Initial for R4 Initial for R7
Reactions (37)
 
 Be binding R4 [Be] + [R4] ↔ [R4Be];   {R4} , {R4Be} , {Be}
 
 Bp binding R4 [Bp] + [R4] ↔ [R4Bp];   {R4} , {R4Bp} , {Bp}
 
 Be binding C4 [Be] + [C4] ↔ [C4Be];   {Be} , {C4} , {C4Be}
 
 Bp binding C4 [Bp] + [C4] ↔ [C4Bp];   {Bp} , {C4} , {C4Bp}
 
 Be binding R7 [Be] + [R7] ↔ [R7Be];   {Be} , {R7} , {R7Be}
 
 Bp binding R7 [Bp] + [R7] ↔ [R7Bp];   {R7Bp} , {R7} , {Bp}
 
 Be binding C7 [Be] + [C7] ↔ [C7Be];   {Be} , {C7Be} , {C7}
 
 Bp binding C7 [Bp] + [C7] ↔ [C7Bp];   {C7Bp} , {Bp} , {C7}
 
 Internalization of R4Be [R4Be] → [R4Bei] + [Be];   {R4Be}
 
 Internalization of R4Bp [R4Bp] → [R4Bpi] + [Bp];   {R4Bp}
 
 Internalization of C4Be [C4Be] → [C4Bei] + [L12i];   {C4Be}
 
 Internalization of C4Bp [C4Bp] → [C4Bpi] + [L12i];   {C4Bp}
 
 Internalization of R7Be [R7Be] → [R7Bei];   {R7Be}
 
 Internalization of R7Bp [R7Bp] → [R7Bpi];   {R7Bp}
 
 Internalization of C7Be [C7Be] → [C7Bei] + [L12i];   {C7Be}
 
 Internalization of C7Bp [C7Bp] → [C7Bpi] + [L12i];   {C7Bp}
 
 Dissocation of Be from C4Bei [C4Bei] → [C4Beii] + [Be];   {C4Bei}
 
 Dissociation of Bp from C4Bpi [C4Bpi] → [C4Bpii] + [Bp];   {C4Bpi}
 
 Dissociation of Be from R7Bei [R7Bei] → [R7Beii] + [Be];   {R7Bei}
 
 Dissociation of Bp from R7Bpi [R7Bpi] → [R7Bpii] + [Bp];   {R7Bpi}
 
 Trafficking of C7Bei to late endosomes [C7Bei] → [C7Beii];   {C7Bei}
 
 Trafficking of C7Bpi to late endosomes [C7Bpi] → [C7Bpii];   {C7Bpi}
 
 Recycling of R4Bei [R4Bei] → [R4];   {R4Bei}
 
 Recycling of R4Bpi [R4Bpi] → [R4];   {R4Bpi}
 
 Recycling of R7Beii [R7Beii] → [R7];   {R7Beii}
 
 Recycling of R7Bpii [R7Bpii] → [R7];   {R7Bpii}
 
 Recycling of C7Beii [C7Beii] → [R7] + [Be];   {C7Beii}
 
 Recycling of C7Bpii [C7Bpii] → [R7] + [Bp];   {C7Bpii}
 
 Degradation of C4Beii [C4Beii] → ;   {C4Beii}
 
 Degradation of C4Bpii [C4Bpii] → ;   {C4Bpii}
 
 Degradation of L12i [L12i] → ;   {L12i}
 
 L12 binding R4 [L12] + [R4] ↔ [C4];   {L12} , {R4} , {C4}
 
 L12 binding R7 [L12] + [R7] ↔ [C7];   {L12} , {R7} , {C7}
 
 L12 binding R4Be [L12] + [R4Be] ↔ [C4Be];   {L12} , {R4Be} , {C4Be}
 
 L12 binding R4Bp [L12] + [R4Bp] ↔ [C4Bp];   {L12} , {R4Bp} , {C4Bp}
 
 L12 binding R7Be [L12] + [R7Be] ↔ [C7Be];   {L12} , {R7Be} , {C7Be}
 
 L12 binding R7Bp [L12] + [R7Bp] ↔ [C7Bp];   {L12} , {C7Bp} , {R7Bp}
 
Rules (5)
 
 Assignment Rule (name: Total4) Total4 = species_7+species_8+species_24
 
 Assignment Rule (name: Total7) Total7 = species_12+species_13+species_17+species_19+species_30
 
 Assignment Rule (name: _Beta) %Beta = (species_2+species_3)/(Metabolite_1+Metabolite_3)*100
 
 Assignment Rule (name: _CXCR4) %CXCR4 = (species_4+species_15)/(Metabolite_5+Metabolite_27)*100
 
 Assignment Rule (name: _CXCR7) %CXCR7 = (species_9+species_20)/(Metabolite_15+Metabolite_37)*100
 
Functions (14)
 
 Mass action (reversible with KD)_12_1 lambda(parameter_22, parameter_4, species_19, species_20, species_3, parameter_4*(species_3*species_20-parameter_22*species_19))
 
 Mass action (reversible with KD)_10 lambda(parameter_22, parameter_4, species_2, species_20, species_25, parameter_4*(species_2*species_20-parameter_22*species_25))
 
 Mass action (reversible with KD)_5_4 lambda(parameter_10, parameter_2, parameter_22, parameter_28, parameter_30, parameter_6, parameter_7, species_1, species_12, species_19, parameter_2*parameter_7/(parameter_28*parameter_30)*(species_1*species_19-parameter_6*parameter_10*parameter_28*parameter_30/parameter_7/parameter_22*species_12))
 
 Mass action (reversible with KD)_5_3 lambda(parameter_10, parameter_2, parameter_22, parameter_28, parameter_30, parameter_6, parameter_7, species_1, species_25, species_28, parameter_2*parameter_7/(parameter_28*parameter_30)*(species_1*species_25-parameter_6*parameter_10*parameter_28*parameter_30/parameter_7/parameter_22*species_28))
 
 Mass action (reversible with KD)_1_1 lambda(parameter_1, parameter_28, parameter_30, parameter_5, parameter_7, species_1, species_15, species_4, parameter_1*parameter_7/(parameter_28*parameter_30)*(species_15*species_1-parameter_5*parameter_28*parameter_30/parameter_7*species_4))
 
 Mass action (reversible with KD)_5_1 lambda(parameter_1, parameter_21, parameter_28, parameter_30, parameter_5, parameter_7, parameter_9, species_1, species_16, species_5, parameter_1*parameter_7/(parameter_28*parameter_30)*(species_1*species_16-parameter_5*parameter_9*parameter_28*parameter_30/parameter_7/parameter_21*species_5))
 
 Mass action (reversible with KD)_9 lambda(parameter_3, parameter_9, species_3, species_4, species_7, parameter_3*(species_3*species_4-parameter_9*species_7))
 
 Mass action (reversible with KD)_7 lambda(parameter_21, parameter_3, species_15, species_24, species_3, parameter_3*(species_3*species_15-parameter_21*species_24))
 
 Mass action (reversible with KD)_6 lambda(parameter_21, parameter_3, species_15, species_16, species_2, parameter_3*(species_2*species_15-parameter_21*species_16))
 
 Mass action (reversible with KD)_1_2 lambda(parameter_2, parameter_28, parameter_30, parameter_6, parameter_7, species_1, species_20, species_9, parameter_2*parameter_7/(parameter_28*parameter_30)*(species_20*species_1-parameter_6*parameter_28*parameter_30/parameter_7*species_9))
 
 Mass action (reversible with KD)_12 lambda(parameter_10, parameter_4, species_2, species_28, species_9, parameter_4*(species_2*species_9-parameter_10*species_28))
 
 Mass action (reversible with KD)_8 lambda(parameter_3, parameter_9, species_2, species_4, species_5, parameter_3*(species_2*species_4-parameter_9*species_5))
 
 Mass action (reversible with KD)_5_2 lambda(parameter_1, parameter_21, parameter_28, parameter_30, parameter_5, parameter_7, parameter_9, species_1, species_24, species_7, parameter_1*parameter_7/(parameter_28*parameter_30)*(species_1*species_24-parameter_5*parameter_9*parameter_28*parameter_30/parameter_7/parameter_21*species_7))
 
 Mass action (reversible with KD)_13 lambda(parameter_10, parameter_4, species_12, species_3, species_9, parameter_4*(species_3*species_9-parameter_10*species_12))
 
 Intracellular Spatial dimensions: 3.0  Compartment size: 1.0
 
 Be
Compartment: Intracellular
Initial concentration: 328437.241399281
 
 Bp
Compartment: Intracellular
Initial concentration: 492655.862098776
 
 C4
Compartment: Intracellular
Initial concentration: 0.0
 
 C4Be
Compartment: Intracellular
Initial concentration: 0.0
 
 C4Beii
Compartment: Intracellular
Initial concentration: 0.0
 
 C4Bp
Compartment: Intracellular
Initial concentration: 0.0
 
 C4Bpi
Compartment: Intracellular
Initial concentration: 0.0
 
 C7
Compartment: Intracellular
Initial concentration: 0.0
 
 C7Bei
Compartment: Intracellular
Initial concentration: 0.0
 
 C7Beii
Compartment: Intracellular
Initial concentration: 0.0
 
 C7Bp
Compartment: Intracellular
Initial concentration: 0.0
 
 C7Bpi
Compartment: Intracellular
Initial concentration: 0.0
 
 L12i
Compartment: Intracellular
Initial concentration: 0.0
 
 R4
Compartment: Intracellular
Initial concentration: 133539.963932179
 
 R4Be
Compartment: Intracellular
Initial concentration: 5434.48582568463
 
 C7Bpii
Compartment: Intracellular
Initial concentration: 0.0
 
 R7Bpii
Compartment: Intracellular
Initial concentration: 345117.328033337
 
 R7Bp
Compartment: Intracellular
Initial concentration: 97340.7848290227
 
 R7
Compartment: Intracellular
Initial concentration: 509483.771339917
 
 C4Bpii
Compartment: Intracellular
Initial concentration: 0.0
 
 C4Bei
Compartment: Intracellular
Initial concentration: 0.0
 
 R4Bpi
Compartment: Intracellular
Initial concentration: 271724.292902136
 
 R4Bp
Compartment: Intracellular
Initial concentration: 8151.72873852455
 
 R7Be
Compartment: Intracellular
Initial concentration: 64893.856552701
 
 R7Bei
Compartment: Intracellular
Initial concentration: 101234.416222443
 
 R7Beii
Compartment: Intracellular
Initial concentration: 230078.21868896
 
 C7Be
Compartment: Intracellular
Initial concentration: 0.0
 
 R4Bei
Compartment: Intracellular
Initial concentration: 181149.528601477
 
 R7Bpi
Compartment: Intracellular
Initial concentration: 151851.62433362
 
 L12
Compartment: Intracellular
Initial concentration: 1.16E8
 
Global Parameters (40)
 
 kf,L12,4
Value: 0.0021
Constant
 
 kf,L12,7
Value: 0.0014
Constant
 
 kf,B,4
Value: 8.5E-9
Constant
 
 kf,B,7
Value: 1.4E-8
Constant
 
 KD,R4,L12
Value: 40.0
Constant
 
 KD,R7,L12
Value: 0.84
Constant
 
 KD,C4,B
Value: 5100000.0
Constant
 
 KD,C7,B
Value: 650000.0
Constant
 
 ke,R4B
Value: 0.0023
Constant
 
 ke,R7B
Value: 0.0039
Constant
 
 ke,C7Bi
Value: 5.5E-4
Constant
 
 koff,B,4
Value: 7.4E-4
Constant
 
 koff,B,7
Value: 0.0025
Constant
 
 krec,R4Bi
Value: 6.9E-5
Constant
 
 krec,R7Bii
Value: 0.0011
Constant
 
 krec,C7Bii
Value: 2.8E-4
Constant
 
 kdeg,C4Bii
Value: 1.0E-4
Constant
 
 kdeg,L12i
Value: 1.0E-4
Constant
 
 KD,R4,B
Value: 7800000.0
Constant
 
 KD,R7,B
Value: 2300000.0
Constant
 
 ke,C4B
Value: 0.0047
Constant
 
 ke,C7B
Value: 0.0021
Constant
 
 n4
Value: 40000.0
Constant
 
 n7
Value: 40000.0
Constant
 
 n47
Value: 40000.0
Constant
 
 Nav
Value: 6.02E23
Constant
 
 Vwell
Value: 7.0E-5
Constant
 
 Vcell
Value: 8.4E-12
Constant
 
 nmol_to_mol
Value: 1.0E9
Constant
 
  Total4
Value: 8151.72873852455
 
  Total7
Value: 249192.409162643
 
  %Beta
Value: 100.0
 
  %CXCR4
Value: 100.0
 
  %CXCR7
Value: 100.0
 
 Initial for Be
Value: 328437.241399281
Constant
 
 Initial for Bp
Value: 492655.862098776
Constant
 
 Initial for C4
Constant
 
 Initial for C7
Constant
 
 Initial for R4
Value: 133539.963932179
Constant
 
 Initial for R7
Value: 509483.771339917
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000599

Curator's comment: (updated: 18 Apr 2016 12:44:35 BST)

The results from Figure 4 for CXCR4+-CXCR7+ cells were reproduced, as were panels C and D of Supplementary Figure B. Note that FigSB panel C is reproduced qualitatively, but there are some slight quantitative differences from the reference figure. The curation simulations were performed in Copasi, with figures combined in OmniGraffle. The reference publication simulations used Matlab.

Additional file(s)
  • COPASI file with simulation settings:
    The COPASI file reproduces all plots described in the curation tab.
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