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BIOMD0000000326 - DellOrco2009_phototransduction

 

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Reference Publication
Publication ID: 19756313
Dell'Orco D, Schmidt H, Mariani S, Fanelli F.
Network-level analysis of light adaptation in rod cells under normal and altered conditions.
Mol Biosyst 2009 Oct; 5(10): 1232-1246
Department of Chemistry and Dulbecco Telethon Institute, University of Modena and Reggio Emilia Via Campi 183, 41100 Modena, Italy. daniele.dellorco@gmail.com  [more]
Model
Original Model: Phototransduction cascade ...
Submitter: Daniele Dell'Orco
Submission ID: MODEL1103090000
Submission Date: 09 Mar 2011 11:17:29 UTC
Last Modification Date: 01 Apr 2014 22:23:48 UTC
Creation Date: 01 Apr 2011 12:40:49 UTC
Encoders:  Vijayalakshmi Chelliah
   Daniele Dell'Orco
set #1
bqbiol:hasProperty Mathematical Modelling Ontology MAMO_0000046
set #2
bqbiol:hasTaxon Taxonomy Mus musculus
set #3
bqmodel:isDerivedFrom PubMed 16212700
set #4
bqbiol:isVersionOf Gene Ontology phototransduction
set #5
bqbiol:occursIn FMA Rod cell
Cell Type Ontology retinal rod cell
Notes

This a model from the article:
Network-level analysis of light adaptation in rod cells under normal and altered conditions.
Dell'Orco D, Schmidt H, Mariani S, Fanelli F Mol Biosyst2009 Oct; 5(10):1232-46 19756313,
Abstract:
Photoreceptor cells finely adjust their sensitivity and electrical response according to changes in light stimuli as a direct consequence of the feedback and regulation mechanisms in the phototransduction cascade. In this study, we employed a systems biology approach to develop a dynamic model of vertebrate rod phototransduction that accounts for the details of the underlying biochemistry. Following a bottom-up strategy, we first reproduced the results of a robust model developed by Hamer et al. (Vis. Neurosci., 2005, 22(4), 417), and then added a number of additional cascade reactions including: (a) explicit reactions to simulate the interaction between the activated effector and the regulator of G-protein signalling (RGS); (b) a reaction for the reformation of the G-protein from separate subunits; (c) a reaction for rhodopsin (R) reconstitution from the association of the opsin apoprotein with the 11-cis-retinal chromophore; (d) reactions for the slow activation of the cascade by opsin. The extended network structure successfully reproduced a number of experimental conditions that were inaccessible to prior models. With a single set of parameters the model was able to predict qualitative and quantitative features of rod photoresponses to light stimuli ranging over five orders of magnitude, in normal and altered conditions, including genetic manipulations of the cascade components. In particular, the model reproduced the salient dynamic features of the rod from Rpe65(-/-) animals, a well established model for Leber congenital amaurosis and vitamin A deficiency. The results of this study suggest that a systems-level approach can help to unravel the adaptation mechanisms in normal and in disease-associated conditions on a molecular basis.


Note:

Figure 7 of the reference is reproduced here. Each plot is obtained by increasing flash strength. More details about generating the plots can be obtained from the comments in the curation figure (go to curation tab).

This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2011 The BioModels.net Team.
For more information see the terms of use.
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: 19756313 Submission Date: 09 Mar 2011 11:17:29 UTC Last Modification Date: 01 Apr 2014 22:23:48 UTC Creation Date: 01 Apr 2011 12:40:49 UTC
Mathematical expressions
Reactions
v_r1 v_r2_0 v_r2_1 v_r2_2
v_r2_3 v_r2_4 v_r2_5 v_r2_6
v_r3_0 v_r3_1 v_r3_2 v_r3_3
v_r3_4 v_r3_5 v_r4_1 v_r4_2
v_r4_3 v_r4_4 v_r4_5 v_r4_6
v_r5_1 v_r5_2 v_r5_3 v_r5_4
v_r5_5 v_r5_6 v_r6_1 v_r6_2
v_r6_3 v_r6_4 v_r6_5 v_r6_6
v_r7_0 v_r7_1 v_r7_2 v_r7_3
v_r7_4 v_r7_5 v_r7_6 v_r8
v_r9 v_r10 v_r11 v_r12
v_r13_0 v_r13_1 v_r13_2 v_r13_3
v_r13_4 v_r13_5 v_r13_6 v_r14_0
v_r14_1 v_r14_2 v_r14_3 v_r14_4
v_r14_5 v_r14_6 v_r15_0 v_r15_1
v_r15_2 v_r15_3 v_r15_4 v_r15_5
v_r15_6 v_r16_0 v_r16_1 v_r16_2
v_r16_3 v_r16_4 v_r16_5 v_r16_6
v_r17 v_r18 v_r19 v_r20
v_r21 v_r22 v_r23 v_r24
v_r25 v_r26 v_r27 v_r28
v_r29 v_r30 v_r31 v_r32
v_r33 v_r34 v_r35  
Rules
Assignment Rule (variable: background) Assignment Rule (variable: premag) Assignment Rule (variable: mag) Assignment Rule (variable: predur)
Assignment Rule (variable: dur) Assignment Rule (variable: del) Assignment Rule (variable: preflash) Assignment Rule (variable: testflash)
Assignment Rule (variable: stimulus) Assignment Rule (variable: numConcFactor) Assignment Rule (variable: kRK1_1) Assignment Rule (variable: kRK1_2)
Assignment Rule (variable: kRK1_3) Assignment Rule (variable: kRK1_4) Assignment Rule (variable: kRK1_5) Assignment Rule (variable: kRK1_6)
Assignment Rule (variable: kA1_1) Assignment Rule (variable: kA1_2) Assignment Rule (variable: kA1_3) Assignment Rule (variable: kA1_4)
Assignment Rule (variable: kA1_5) Assignment Rule (variable: kA1_6) Assignment Rule (variable: kG1_1) Assignment Rule (variable: kG1_2)
Assignment Rule (variable: kG1_3) Assignment Rule (variable: kG1_4) Assignment Rule (variable: kG1_5) Assignment Rule (variable: kG1_6)
Assignment Rule (variable: E) Assignment Rule (variable: Rec_wCa2) Assignment Rule (variable: alfamax) Assignment Rule (variable: J)
Assignment Rule (variable: deltaJ)      
Physical entities
Compartments Species
cytosol Arr Ca2_buff Ca2_free
G_GTP Ga_GDP Ga_GTP
Ga_GTP_PDE_a_Ga_GTP Ga_GTP_a_PDE_a_Ga_GTP Gbg
Gt Ops Ops_G
Ops_G_GTP Ops_Gt PDE
PDE_Ga_GTP PDE_a_Ga_GTP R
R0 R0_G R0_G_GTP
R0_Gt R0_RKpre R1
R1_Arr R1_G R1_G_GTP
R1_Gt R1_RKpost R1_RKpre
R2 R2_Arr R2_G
R2_G_GTP R2_Gt R2_RKpost
R2_RKpre R3 R3_Arr
R3_G R3_G_GTP R3_Gt
R3_RKpost R3_RKpre R4
R4_Arr R4_G R4_G_GTP
R4_Gt R4_RKpost R4_RKpre
R5 R5_Arr R5_G
R5_G_GTP R5_Gt R5_RKpost
R5_RKpre R6 R6_Arr
R6_G R6_G_GTP R6_Gt
R6_RKpost R6_RKpre RGS
RGS_Ga_GTP_a_PDE_a_Ga_GTP RGS_PDE_a_Ga_GTP RK
Rec_wCa2_RK cGMP  
Global parameters
Rtot PDEtot Gtot Rectot
RGStot ArrTot flashBG flash0Dur
flash0Mag flashDel flashDur flashMag
otherstimulus kRK1_0 omega kRK2
RKdark kRK3_ATP kRK4 omega_arr
kArr kA2 kA3 kOps
kRrecyc kG1_0 kG2 kG3
kG4_GDP kG5_GTP kG6 kG7
kGrecyc kGshutoff kP1 kP1_rev
kP2 kP3 kP4 kPDEshutoff
kRGS1 kRGS2 kRec3 kRec4
Kp w Vcyto Kc
m betadark betasub fCa
Jdark F cGMPdark ncg
gammaCa Ca2dark Ca2_0 k1
k2 eT ktherm background
premag mag predur dur
del preflash testflash stimulus
numConcFactor kRK1_1 kRK1_2 kRK1_3
kRK1_4 kRK1_5 kRK1_6 kA1_1
kA1_2 kA1_3 kA1_4 kA1_5
kA1_6 kG1_1 kG1_2 kG1_3
kG1_4 kG1_5 kG1_6 E
Rec_wCa2 alfamax J deltaJ
Reactions (91)
 
 v_r1 [R] → [R0];  
 
 v_r2_0 [R0] + [RK] ↔ [R0_RKpre];  
 
 v_r2_1 [R1] + [RK] ↔ [R1_RKpre];  
 
 v_r2_2 [R2] + [RK] ↔ [R2_RKpre];  
 
 v_r2_3 [R3] + [RK] ↔ [R3_RKpre];  
 
 v_r2_4 [R4] + [RK] ↔ [R4_RKpre];  
 
 v_r2_5 [R5] + [RK] ↔ [R5_RKpre];  
 
 v_r2_6 [R6] + [RK] ↔ [R6_RKpre];  
 
 v_r3_0 [R0_RKpre] → [R1_RKpost];  
 
 v_r3_1 [R1_RKpre] → [R2_RKpost];  
 
 v_r3_2 [R2_RKpre] → [R3_RKpost];  
 
 v_r3_3 [R3_RKpre] → [R4_RKpost];  
 
 v_r3_4 [R4_RKpre] → [R5_RKpost];  
 
 v_r3_5 [R5_RKpre] → [R6_RKpost];  
 
 v_r4_1 [R1_RKpost] → [R1] + [RK];  
 
 v_r4_2 [R2_RKpost] → [R2] + [RK];  
 
 v_r4_3 [R3_RKpost] → [R3] + [RK];  
 
 v_r4_4 [R4_RKpost] → [R4] + [RK];  
 
 v_r4_5 [R5_RKpost] → [R5] + [RK];  
 
 v_r4_6 [R6_RKpost] → [R6] + [RK];  
 
 v_r5_1 [Arr] + [R1] ↔ [R1_Arr];  
 
 v_r5_2 [Arr] + [R2] ↔ [R2_Arr];  
 
 v_r5_3 [Arr] + [R3] ↔ [R3_Arr];  
 
 v_r5_4 [Arr] + [R4] ↔ [R4_Arr];  
 
 v_r5_5 [Arr] + [R5] ↔ [R5_Arr];  
 
 v_r5_6 [Arr] + [R6] ↔ [R6_Arr];  
 
 v_r6_1 [R1_Arr] → [Arr] + [Ops];  
 
 v_r6_2 [R2_Arr] → [Arr] + [Ops];  
 
 v_r6_3 [R3_Arr] → [Arr] + [Ops];  
 
 v_r6_4 [R4_Arr] → [Arr] + [Ops];  
 
 v_r6_5 [R5_Arr] → [Arr] + [Ops];  
 
 v_r6_6 [R6_Arr] → [Arr] + [Ops];  
 
 v_r7_0 [R0] → [Ops];  
 
 v_r7_1 [R1] → [Ops];  
 
 v_r7_2 [R2] → [Ops];  
 
 v_r7_3 [R3] → [Ops];  
 
 v_r7_4 [R4] → [Ops];  
 
 v_r7_5 [R5] → [Ops];  
 
 v_r7_6 [R6] → [Ops];  
 
 v_r8 [Gt] + [Ops] ↔ [Ops_Gt];  
 
 v_r9 [Ops_Gt] ↔ [Ops_G];  
 
 v_r10 [Ops_G] → [Ops_G_GTP];  
 
 v_r11 [Ops_G_GTP] → [G_GTP] + [Ops];  
 
 v_r12 [Ops] → [R];  
 
 v_r13_0 [Gt] + [R0] ↔ [R0_Gt];  
 
 v_r13_1 [Gt] + [R1] ↔ [R1_Gt];  
 
 v_r13_2 [Gt] + [R2] ↔ [R2_Gt];  
 
 v_r13_3 [Gt] + [R3] ↔ [R3_Gt];  
 
 v_r13_4 [Gt] + [R4] ↔ [R4_Gt];  
 
 v_r13_5 [Gt] + [R5] ↔ [R5_Gt];  
 
 v_r13_6 [Gt] + [R6] ↔ [R6_Gt];  
 
 v_r14_0 [R0_Gt] ↔ [R0_G];  
 
 v_r14_1 [R1_Gt] ↔ [R1_G];  
 
 v_r14_2 [R2_Gt] ↔ [R2_G];  
 
 v_r14_3 [R3_Gt] ↔ [R3_G];  
 
 v_r14_4 [R4_Gt] ↔ [R4_G];  
 
 v_r14_5 [R5_Gt] ↔ [R5_G];  
 
 v_r14_6 [R6_Gt] ↔ [R6_G];  
 
 v_r15_0 [R0_G] → [R0_G_GTP];  
 
 v_r15_1 [R1_G] → [R1_G_GTP];  
 
 v_r15_2 [R2_G] → [R2_G_GTP];  
 
 v_r15_3 [R3_G] → [R3_G_GTP];  
 
 v_r15_4 [R4_G] → [R4_G_GTP];  
 
 v_r15_5 [R5_G] → [R5_G_GTP];  
 
 v_r15_6 [R6_G] → [R6_G_GTP];  
 
 v_r16_0 [R0_G_GTP] → [G_GTP] + [R0];  
 
 v_r16_1 [R1_G_GTP] → [G_GTP] + [R1];  
 
 v_r16_2 [R2_G_GTP] → [G_GTP] + [R2];  
 
 v_r16_3 [R3_G_GTP] → [G_GTP] + [R3];  
 
 v_r16_4 [R4_G_GTP] → [G_GTP] + [R4];  
 
 v_r16_5 [R5_G_GTP] → [G_GTP] + [R5];  
 
 v_r16_6 [R6_G_GTP] → [G_GTP] + [R6];  
 
 v_r17 [G_GTP] → [Ga_GTP] + [Gbg];  
 
 v_r18 [Ga_GTP] + [PDE] ↔ [PDE_Ga_GTP];  
 
 v_r19 [PDE_Ga_GTP] → [PDE_a_Ga_GTP];  
 
 v_r20 [Ga_GTP] + [PDE_a_Ga_GTP] → [Ga_GTP_PDE_a_Ga_GTP];  
 
 v_r21 [Ga_GTP_PDE_a_Ga_GTP] → [Ga_GTP_a_PDE_a_Ga_GTP];  
 
 v_r22 [Ga_GTP_a_PDE_a_Ga_GTP] + [RGS] → [RGS_Ga_GTP_a_PDE_a_Ga_GTP];  
 
 v_r23 [RGS_Ga_GTP_a_PDE_a_Ga_GTP] → [Ga_GDP] + [PDE_a_Ga_GTP] + [RGS];  
 
 v_r24 [PDE_a_Ga_GTP] + [RGS] → [RGS_PDE_a_Ga_GTP];  
 
 v_r25 [RGS_PDE_a_Ga_GTP] → [Ga_GDP] + [PDE] + [RGS];  
 
 v_r26 [PDE_a_Ga_GTP] → [Ga_GDP] + [PDE];  
 
 v_r27 [Ga_GTP_a_PDE_a_Ga_GTP] → [Ga_GDP] + [PDE_a_Ga_GTP];  
 
 v_r28 [Ga_GTP] → [Ga_GDP];  
 
 v_r29 [Ga_GDP] + [Gbg] → [Gt];  
 
 v_r30 [RK] ↔ [Rec_wCa2_RK];   {Ca2_free}
 
 v_r31 [Ca2_free] ↔ [Ca2_buff];  
 
 v_r32 [Ca2_free] → ;  
 
 v_r33  → [Ca2_free];   {cGMP}
 
 v_r34  → [cGMP];   {Ca2_free}
 
 v_r35 [cGMP] → ;   {Ga_GTP_a_PDE_a_Ga_GTP} , {PDE_a_Ga_GTP}
 
Rules (33)
 
 Assignment Rule (name: background) background = flashBG
 
 Assignment Rule (name: premag) premag = flash0Mag/flash0Dur
 
 Assignment Rule (name: mag) mag = flashMag/flashDur
 
 Assignment Rule (name: predur) predur = flash0Dur
 
 Assignment Rule (name: dur) dur = flashDur
 
 Assignment Rule (name: del) del = flashDel
 
 Assignment Rule (name: preflash) preflash = piecewise(premag, (time <= predur), 0)
 
 Assignment Rule (name: testflash) testflash = piecewise(mag, ((time >= del)) && ((time <= (del+dur))), 0)
 
 Assignment Rule (name: stimulus) stimulus = background+preflash+testflash+otherstimulus
 
 Assignment Rule (name: numConcFactor) numConcFactor = 1/(6.022E5*Vcyto)
 
 Assignment Rule (name: kRK1_1) kRK1_1 = kRK1_0*exp(-omega)
 
 Assignment Rule (name: kRK1_2) kRK1_2 = kRK1_0*exp((-omega)*2)
 
 Assignment Rule (name: kRK1_3) kRK1_3 = kRK1_0*exp((-omega)*3)
 
 Assignment Rule (name: kRK1_4) kRK1_4 = kRK1_0*exp((-omega)*4)
 
 Assignment Rule (name: kRK1_5) kRK1_5 = kRK1_0*exp((-omega)*5)
 
 Assignment Rule (name: kRK1_6) kRK1_6 = 0
 
 Assignment Rule (name: kA1_1) kA1_1 = kArr*exp(omega_arr)
 
 Assignment Rule (name: kA1_2) kA1_2 = kArr*exp(omega_arr*2)
 
 Assignment Rule (name: kA1_3) kA1_3 = kArr*exp(omega_arr*3)
 
 Assignment Rule (name: kA1_4) kA1_4 = kArr*exp(omega_arr*4)
 
 Assignment Rule (name: kA1_5) kA1_5 = kArr*exp(omega_arr*5)
 
 Assignment Rule (name: kA1_6) kA1_6 = kArr*exp(omega_arr*6)
 
 Assignment Rule (name: kG1_1) kG1_1 = kG1_0*exp(-omega)
 
 Assignment Rule (name: kG1_2) kG1_2 = kG1_0*exp((-omega)*2)
 
 Assignment Rule (name: kG1_3) kG1_3 = kG1_0*exp((-omega)*3)
 
 Assignment Rule (name: kG1_4) kG1_4 = kG1_0*exp((-omega)*4)
 
 Assignment Rule (name: kG1_5) kG1_5 = kG1_0*exp((-omega)*5)
 
 Assignment Rule (name: kG1_6) kG1_6 = kG1_0*exp((-omega)*6)
 
 Assignment Rule (name: E) E = PDE_a_Ga_GTP+2*Ga_GTP_a_PDE_a_Ga_GTP
 
 Assignment Rule (name: Rec_wCa2) Rec_wCa2 = (Rectot-Rec_wCa2_RK*numConcFactor)/(1+(Kp/Ca2_free)^w)
 
 Assignment Rule (name: alfamax) alfamax = betadark*cGMPdark*(1+(Ca2dark/Kc)^m)
 
 Assignment Rule (name: J) J = 2/(2+fCa)*(cGMP/cGMPdark)^ncg*Jdark+fCa/(fCa+2)*(Ca2_free-Ca2_0)/(Ca2dark-Ca2_0)*Jdark
 
 Assignment Rule (name: deltaJ) deltaJ = Jdark-J
 
 cytosol Spatial dimensions: 3.0  Compartment size: 1.0
 
 Arr
Compartment: cytosol
Initial concentration: 3.13E7
 
 Ca2_buff
Compartment: cytosol
Initial concentration: 42.857
 
 Ca2_free
Compartment: cytosol
Initial concentration: 0.6
 
 G_GTP
Compartment: cytosol
Initial concentration: 0.0
 
 Ga_GDP
Compartment: cytosol
Initial concentration: 0.0
 
 Ga_GTP
Compartment: cytosol
Initial concentration: 0.0
 
 Ga_GTP_PDE_a_Ga_GTP
Compartment: cytosol
Initial concentration: 0.0
 
 Ga_GTP_a_PDE_a_Ga_GTP
Compartment: cytosol
Initial concentration: 0.0
 
 Gbg
Compartment: cytosol
Initial concentration: 0.0
 
 Gt
Compartment: cytosol
Initial concentration: 3.6E8
 
 Ops
Compartment: cytosol
Initial concentration: 0.0
 
 Ops_G
Compartment: cytosol
Initial concentration: 0.0
 
 Ops_G_GTP
Compartment: cytosol
Initial concentration: 0.0
 
 Ops_Gt
Compartment: cytosol
Initial concentration: 0.0
 
 PDE
Compartment: cytosol
Initial concentration: 1.335E7
 
 PDE_Ga_GTP
Compartment: cytosol
Initial concentration: 0.0
 
 PDE_a_Ga_GTP
Compartment: cytosol
Initial concentration: 0.0
 
 R
Compartment: cytosol
Initial concentration: 3.6E9
 
 R0
Compartment: cytosol
Initial concentration: 0.0
 
 R0_G
Compartment: cytosol
Initial concentration: 0.0
 
 R0_G_GTP
Compartment: cytosol
Initial concentration: 0.0
 
 R0_Gt
Compartment: cytosol
Initial concentration: 0.0
 
 R0_RKpre
Compartment: cytosol
Initial concentration: 0.0
 
 R1
Compartment: cytosol
Initial concentration: 0.0
 
 R1_Arr
Compartment: cytosol
Initial concentration: 0.0
 
 R1_G
Compartment: cytosol
Initial concentration: 0.0
 
 R1_G_GTP
Compartment: cytosol
Initial concentration: 0.0
 
 R1_Gt
Compartment: cytosol
Initial concentration: 0.0
 
 R1_RKpost
Compartment: cytosol
Initial concentration: 0.0
 
 R1_RKpre
Compartment: cytosol
Initial concentration: 0.0
 
 R2
Compartment: cytosol
Initial concentration: 0.0
 
 R2_Arr
Compartment: cytosol
Initial concentration: 0.0
 
 R2_G
Compartment: cytosol
Initial concentration: 0.0
 
 R2_G_GTP
Compartment: cytosol
Initial concentration: 0.0
 
 R2_Gt
Compartment: cytosol
Initial concentration: 0.0
 
 R2_RKpost
Compartment: cytosol
Initial concentration: 0.0
 
 R2_RKpre
Compartment: cytosol
Initial concentration: 0.0
 
 R3
Compartment: cytosol
Initial concentration: 0.0
 
 R3_Arr
Compartment: cytosol
Initial concentration: 0.0
 
 R3_G
Compartment: cytosol
Initial concentration: 0.0
 
 R3_G_GTP
Compartment: cytosol
Initial concentration: 0.0
 
 R3_Gt
Compartment: cytosol
Initial concentration: 0.0
 
 R3_RKpost
Compartment: cytosol
Initial concentration: 0.0
 
 R3_RKpre
Compartment: cytosol
Initial concentration: 0.0
 
 R4
Compartment: cytosol
Initial concentration: 0.0
 
 R4_Arr
Compartment: cytosol
Initial concentration: 0.0
 
 R4_G
Compartment: cytosol
Initial concentration: 0.0
 
 R4_G_GTP
Compartment: cytosol
Initial concentration: 0.0
 
 R4_Gt
Compartment: cytosol
Initial concentration: 0.0
 
 R4_RKpost
Compartment: cytosol
Initial concentration: 0.0
 
 R4_RKpre
Compartment: cytosol
Initial concentration: 0.0
 
 R5
Compartment: cytosol
Initial concentration: 0.0
 
 R5_Arr
Compartment: cytosol
Initial concentration: 0.0
 
 R5_G
Compartment: cytosol
Initial concentration: 0.0
 
 R5_G_GTP
Compartment: cytosol
Initial concentration: 0.0
 
 R5_Gt
Compartment: cytosol
Initial concentration: 0.0
 
 R5_RKpost
Compartment: cytosol
Initial concentration: 0.0
 
 R5_RKpre
Compartment: cytosol
Initial concentration: 0.0
 
 R6
Compartment: cytosol
Initial concentration: 0.0
 
 R6_Arr
Compartment: cytosol
Initial concentration: 0.0
 
 R6_G
Compartment: cytosol
Initial concentration: 0.0
 
 R6_G_GTP
Compartment: cytosol
Initial concentration: 0.0
 
 R6_Gt
Compartment: cytosol
Initial concentration: 0.0
 
 R6_RKpost
Compartment: cytosol
Initial concentration: 0.0
 
 R6_RKpre
Compartment: cytosol
Initial concentration: 0.0
 
 RGS
Compartment: cytosol
Initial concentration: 3000000.0
 
 RGS_Ga_GTP_a_PDE_a_Ga_GTP
Compartment: cytosol
Initial concentration: 0.0
 
 RGS_PDE_a_Ga_GTP
Compartment: cytosol
Initial concentration: 0.0
 
 RK
Compartment: cytosol
Initial concentration: 10838.0
 
 Rec_wCa2_RK
Compartment: cytosol
Initial concentration: 4204560.0
 
 cGMP
Compartment: cytosol
Initial concentration: 4.0
 
Global Parameters (96)
 
   Rtot
Value: 3.6E9
Constant
 
   PDEtot
Value: 1.335E7
Constant
 
   Gtot
Value: 3.6E8
Constant
 
   Rectot
Value: 35.0
Constant
 
   RGStot
Value: 3000000.0
Constant
 
   ArrTot
Value: 3.13E7
Constant
 
   flashBG
Constant
 
   flash0Dur
Value: 0.001
Constant
 
   flash0Mag
Constant
 
   flashDel
Constant
 
   flashDur
Value: 0.001
Constant
 
   flashMag
Constant
 
   otherstimulus
Constant
 
   kRK1_0
Value: 0.0076429599557114
Constant
 
   omega
Value: 0.6
Constant
 
   kRK2
Value: 250.0
Constant
 
   RKdark
Value: 10838.0
Constant
 
   kRK3_ATP
Value: 400.0
Constant
 
   kRK4
Value: 20.0
Constant
 
   omega_arr
Value: 0.81323
Constant
 
   kArr
Value: 6.0918E-10
Constant
 
   kA2
Value: 0.00323198
Constant
 
   kA3
Value: 0.0445091
Constant
 
   kOps
Value: 6.1172E-13
Constant
 
   kRrecyc
Value: 7.0E-4
Constant
 
   kG1_0
Value: 3.0586111111E-5
Constant
 
   kG2
Value: 2250.34
Constant
 
   kG3
Value: 2000.0
Constant
 
   kG4_GDP
Value: 600.0
Constant
 
   kG5_GTP
Value: 750.0
Constant
 
   kG6
Value: 2000.0
Constant
 
   kG7
Value: 200.0
Constant
 
   kGrecyc
Value: 2.0
Constant
 
   kGshutoff
Value: 0.05
Constant
 
   kP1
Value: 0.0549715
Constant
 
   kP1_rev
Constant
 
   kP2
Value: 940.706
Constant
 
   kP3
Value: 1.49834E-9
Constant
 
   kP4
Value: 21.0881
Constant
 
   kPDEshutoff
Value: 0.033
Constant
 
   kRGS1
Value: 1.57E-7
Constant
 
   kRGS2
Value: 256.07
Constant
 
   kRec3
Value: 9.68777
Constant
 
   kRec4
Value: 0.610084
Constant
 
   Kp
Value: 0.425272
Constant
 
   w
Value: 2.0
Constant
 
   Vcyto
Value: 1.0
Constant
 
   Kc
Value: 0.17
Constant
 
   m
Value: 2.5
Constant
 
   betadark
Value: 1.2
Constant
 
   betasub
Value: 4.3E-4
Constant
 
   fCa
Value: 0.2
Constant
 
   Jdark
Value: 29.7778
Constant
 
   F
Value: 96485.3415
Constant
 
   cGMPdark
Value: 4.0
Constant
 
   ncg
Value: 3.0
Constant
 
   gammaCa
Value: 47.554
Constant
 
   Ca2dark
Value: 0.6
Constant
 
   Ca2_0
Value: 0.01
Constant
 
   k1
Value: 0.381529
Constant
 
   k2
Value: 1.9094
Constant
 
   eT
Value: 400.0
Constant
 
   ktherm
Value: 0.0238
Constant
 
   background  
 
   premag  
 
   mag  
 
   predur  
 
   dur  
 
   del  
 
   preflash  
 
   testflash  
 
   stimulus  
 
   numConcFactor  
 
   kRK1_1  
 
   kRK1_2  
 
   kRK1_3  
 
   kRK1_4  
 
   kRK1_5  
 
   kRK1_6  
 
   kA1_1  
 
   kA1_2  
 
   kA1_3  
 
   kA1_4  
 
   kA1_5  
 
   kA1_6  
 
   kG1_1  
 
   kG1_2  
 
   kG1_3  
 
   kG1_4  
 
   kG1_5  
 
   kG1_6  
 
   E  
 
   Rec_wCa2  
 
   alfamax  
 
   J  
 
   deltaJ  
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000326

Curator's comment: (updated: 01 Apr 2011 14:09:59 BST)

Figures 7D, 7E and 7F of the reference publication has been reproduced here.The plot shows the photoresponses from rods stimulated by flashes of increasing strength (by varying flash0Mag). In order to obtain figure 7, the following parameters need to altered.
Flash intensity: flash0Mag = 1.54, 12.5, 45.8, 184, 800, 2000; other parameters: flashBG = 0; flash0Dur = flashDur = 0.024; flashDel = 0; flashMag = 0;
In addition to the above changes, to obtain 1) figure 7E, set Rec_wCa2_RK(0) = 1.0091e+07; RK(0) = 26011; RKdark = 26011; and 2) figure 7F, set RGS(0) = 6.9e+06.

The model was integrated and simulated using Copasi v4.6 (Build 32).

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