Physiology

Reaction Diagram

reactionDiagram

Cross-References

Annotations

Reactions

Reactions
Name
Structure
Kinetics
Depiction
CaRNE1CaIn leakRNE RNEmem MassAction
CaInCaRNE1 SPCA RNEmem GeneralKinetics
CaIn CatSper Cytosole GeneralKinetics
IP3 PLCd m0 GeneralKinetics
IP3 IP3K Cytosole GeneralKinetics
CaIn LeakPP m0 GeneralLumpedKinetics
CaIn+CaPrCaBuf CalMod Cytosole MassAction
CaRNE1+CaReticCaReticCal CaRetFast RNE MassAction
CaRNE1+CaRet_SlowCaRetSlow_Calcium CaRetSlow RNE MassAction
CaIn PMCA m0 GeneralKinetics
CaIn+caMSlowCaMSlowCa CaM_slow Cytosole MassAction

leakRNE Universal ID's

leakRNE Text Annotations

SPCA Universal ID's

SPCA Text Annotations

CatSper Universal ID's

CatSper Text Annotations

PLCd Universal ID's

PLCd Text Annotations

IP3K Universal ID's

IP3K Text Annotations

LeakPP Universal ID's

LeakPP Text Annotations

CalMod Universal ID's

CalMod Text Annotations

CaRetFast Universal ID's

CaRetFast Text Annotations

CaRetSlow Universal ID's

CaRetSlow Text Annotations

PMCA Universal ID's

PMCA Text Annotations

CaM_slow Universal ID's

CaM_slow Text Annotations

Expressions for leakRNE

reaction rate

J

((Kf * CaRNE1) - (Kr * CaIn)) [molecules.um-2.s-1]

inward current density

I

0.0 [pA.um-2]

net charge valence

netValence

1.0 [1]

forward rate constant

Kf

(((kleakrne * RNE) / RNEmem) * 602.0) [molecules.um-2.s-1.uM-1]

global

kleakrne

0.1 [tbd]

reverse rate constant

Kr

0.0 [molecules.um-2.s-1.uM-1]

Expressions for SPCA

reaction rate

J

(602.0 * Vspca * (CaIn ^ 2.0) * Cytosole / RNEmem / ((Kspca ^ 2.0) + (CaIn ^ 2.0))) [molecules.um-2.s-1]

global

Vspca

0.93 [tbd]

inward current density

I

0.0 [pA.um-2]

net charge valence

netValence

1.0 [1]

local

Kspca

0.27 [tbd]

Expressions for CatSper

reaction rate

J

((((Vcatsper * (t > 25.0)) * (t < 700.0)) + (Vcatsper / p_k * (t > 700.0))) * (x < 28.0)) [uM.s-1]

global

p_k

1.8 [1]

local

Vcatsper

0.7 [uM.s-1]

Expressions for PLCd

reaction rate

J

(((1.7 * 1800.0 * (CaIn * (x > 28.0) / (Kplc + CaIn))) * HeadMembaneToAllMembraneRatio) / m0) [molecules.um-2.s-1]

inward current density

I

0.0 [pA.um-2]

net charge valence

netValence

1.0 [1]

local

HeadMembaneToAllMembraneRatio

3.0 [molecules.s-1]

local

Kplc

0.7 [uM]

Expressions for IP3K

reaction rate

J

((IP3 * 7.6) / (IP3 + 3.0)) [uM.s-1]

Expressions for LeakPP

lumped current

LumpedI

0.0 [pA]

lumped reaction rate

LumpedJ

((leakparam * Cytosole * 602.0) * leakmax) [molecules.s-1]

global

leakparam

((x < 28.0) * (t < 700.0)) [tbd]

net charge valence

netValence

1.0 [1]

local

leakmax

0.15 [tbd]

Expressions for CalMod

reaction rate

J

(((Kf * CaIn) * CaPr) - (Kr * CaBuf)) [uM.s-1]

forward rate constant

Kf

10.0 [s-1.uM-1]

reverse rate constant

Kr

(Kf * Kd_CalModfast) [s-1]

local

Kd_CalModfast

1.0 [uM]

Expressions for CaRetFast

reaction rate

J

(((Kf * CaRNE1) * CaRetic) - (Kr * CaReticCal)) [uM.s-1]

forward rate constant

Kf

0.01 [s-1.uM-1]

reverse rate constant

Kr

(Kf * Kd_CaRetic_slow) [s-1]

global

Kd_CaRetic_slow

1.0 [uM]

Expressions for CaRetSlow

reaction rate

J

(((Kf * CaRNE1) * CaRet_Slow) - (Kr * CaRetSlow_Calcium)) [uM.s-1]

forward rate constant

Kf

0.1 [s-1.uM-1]

reverse rate constant

Kr

(Kf * 2000.0) [s-1]

Expressions for PMCA

reaction rate

J

(Vpmca * ((602.0 * (CaIn ^ 2.0) * Cytosole * (x < 28.0) / m0 / ((Kpmca ^ 2.0) + (CaIn ^ 2.0))) * PP_membrane_to_all_membr_ratio)) [molecules.um-2.s-1]

inward current density

I

0.0 [pA.um-2]

net charge valence

netValence

1.0 [1]

local

Vpmca

1.0 [tbd]

local

Kpmca

0.2 [tbd]

local

PP_membrane_to_all_membr_ratio

1.55 [tbd]

Expressions for CaM_slow

reaction rate

J

(((Kf * CaIn) * caMSlow) - (Kr * CaMSlowCa)) [uM.s-1]

forward rate constant

Kf

100.0 [s-1.uM-1]

reverse rate constant

Kr

260.0 [s-1]

Structures

Name
Type
Electrical
m0 Membrane Cytosole(+)   outside(-)
RNEmem Membrane RNE(+)   Cytosole(-)
RNE Compartment (+)   (-)
outside Compartment (+)   (-)
Cytosole Compartment (+)   (-)

m0 Universal ID's

m0 Text Annotations

RNEmem Universal ID's

RNEmem Text Annotations

RNE Universal ID's

RNE Text Annotations

outside Universal ID's

outside Text Annotations

Cytosole Universal ID's

Cytosole Text Annotations

Species

Name
Structure
BioNetGen Definition
Depiction
CaIn Cytosole Cytosole
CaRNE1 RNE RNE
IP3 Cytosole Cytosole
Ip3buf Cytosole Cytosole
CaPr Cytosole Cytosole
CaBuf Cytosole Cytosole
CaRetic RNE RNE
CaReticCal RNE RNE
CaRet_Slow RNE RNE
CaRetSlow_Calcium RNE RNE
caMSlow Cytosole Cytosole
CaMSlowCa Cytosole Cytosole

CaIn Universal ID's

CaIn Text Annotations

CaRNE1 Universal ID's

CaRNE1 Text Annotations

IP3 Universal ID's

IP3 Text Annotations

Ip3buf Universal ID's

Ip3buf Text Annotations

CaPr Universal ID's

CaPr Text Annotations

CaBuf Universal ID's

CaBuf Text Annotations

CaRetic Universal ID's

CaRetic Text Annotations

CaReticCal Universal ID's

CaReticCal Text Annotations

CaRet_Slow Universal ID's

CaRet_Slow Text Annotations

CaRetSlow_Calcium Universal ID's

CaRetSlow_Calcium Text Annotations

caMSlow Universal ID's

caMSlow Text Annotations

CaMSlowCa Universal ID's

CaMSlowCa Text Annotations

Molecules

Name
BioNetGen Definition
DEPICTION

Observables

Name
Structure
Count
BNGL Definition
Sequence Type
DEPICTION

Applications

Name
Properties Math Type
Annotation
Application0 Specs - Species
Specs - Reaction
Simulations 		Deterministic (ODE) Spatial (3D)

Application0 Universal ID's

Application0 Text Annotations

Specifications (Species) - Application0 go to Simulations

Species
Initial Condition
Diffusion Constant
Structure
CaRNE1 1000.0 [uM] 20.0 [um2/s] RNE
CaRetic ((3000.0 * 18.0 / 602.0 / RNE) * 1.0) [uM] 20.0 [um2/s] RNE
CaReticCal 0.0 [uM] 20.0 [um2/s] RNE
CaRet_Slow ((3000.0 * 18.0 / 602.0 / RNE) * 18.0) [uM] 20.0 [um2/s] RNE
CaRetSlow_Calcium 0.0 [uM] 20.0 [um2/s] RNE
CaIn 0.1 [uM] Diffusion [um2/s] Cytosole
IP3 0.0 [uM] 8.0 [um2/s] Cytosole
Ip3buf 0.0 [uM] 0.0 [um2/s] Cytosole
CaPr ((1000.0 * 2.0) * 18.0 / 602.0 / Cytosole) [uM] Diffusion [um2/s] Cytosole
CaBuf 0.0 [uM] Diffusion [um2/s] Cytosole
caMSlow ((1000.0 * 2.0) * 18.0 / 602.0 / Cytosole) [uM] Diffusion [um2/s] Cytosole
CaMSlowCa 0.0 [uM] Diffusion [um2/s] Cytosole

Specifications (Reaction) - Application0 go to Simulations

Name
Enabled?
leakRNE included
SPCA included
CatSper included
PLCd included
IP3K included
LeakPP included
CalMod included
CaRetFast included
CaRetSlow included
PMCA included
CaM_slow included
IP3R included

Simulations - Application0 go to Specifications

Name
End Time
Output Options
Calcium diffusionvariationosc 1000.0

OutputTimeStep 1.0

Application0 Universal ID's

Application0 Text Annotations

Assignments

Name Variable Assignment Function Expression

Events

Name Trigger Type Variable Assignment

Geometry Geometry1120118915

(Origin: -12.5, 3.0, 3.9; Extent: 50.0, 3.5, 2.5 [um])

Dimension Type Subdomain Adjacent Subvolumes Size Mapped Compartment
Volume Analytical subdomain2 0.12512500000000001 [um3] RNE
Volume Analytical subdomain1 18.032437500000004 [um3] Cytosole
Volume Analytical subdomain0 419.3424375000001 [um3] outside
Surface subdomain0_subdomain1_membrane subdomain0 | subdomain1 96.30630517752202 [um2] m0
Surface subdomain1_subdomain2_membrane subdomain1 | subdomain2 1.033529612708134 [um2] RNEmem

Events

Name Variable Rate Expression

Global Parameters

Name
Expression
kcatABHD 3.0[tbd]
Vabhd 0.0[tbd]
KmABHD 66.0[tbd]
CatSper_0 0.0[tbd]
CatSper0 0.0[tbd]
IC50AG 0.35[tbd]
K_abhdProgf 0.0[tbd]
K_abhdProgb 0.0[tbd]
K_CatSperf 0.0[tbd]
Popen 0.0[tbd]
K2 30.0[tbd]
K3 0.005[tbd]
K5 0.25[tbd]
Z (1.0 + (CaIn * K3 / (K1 * K2)) + (CaIn / K5) + ((CaIn ^ 2.0) * K3 / (K5 * K1 * K2)) + (IP3 / K1) + (IP3 * CaIn / (K1 * K2)) + (IP3 * CaIn / (K1 * K5)) + (IP3 * CaIn * CaIn / (K1 * K2 * K5))) [tbd]
w11 (IP3 * CaIn * 1.0 / (K1 * K5 * Z))[tbd]
K1 0.13[tbd]
DOLYA (CaIn / (CaIn + 0.7))[tbd]
NIP3R 1850.0[tbd]
Kserca 0.27[tbd]
Vserca 0.92[tbd]
kleakrne 0.1[tbd]
g0 0.0[tbd]
leakparam ((x < 28.0) * (t < 700.0))[tbd]
Vcatsperfake 0.7[tbd]
Diffusion 4.0[tbd]
Kd_CaRetic_slow 1.0[uM]
Vspca 0.93[tbd]
p_k 1.8[1]

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Downloads

Model Format
Model Downloads
Virtual Cell Markup Language VCML File
PDF Report Report
COMBINE Archive OMEX File
SEDML SEDML File
File Format
Application Downloads
BNGL Application0.bngl
SBML Application0.sbml
Matlab Application0.m
NFSim XML Application0.xml