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bertram1

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Model

bertram1

The SBML for this model was obtained from the BioModels database (BioModels ID: BIOMD0000000128) Biomodels notes: The model is according to the paper Endothelin Action on Pituitary Lactotrophs: One Receptor, Many GTP-Binding Proteins Figure 1 has been simulated by MathSBML. The figure for the [Ca2+]i and [Ca2+]ER have been normalized in the paper.Original model comes from http://www.math.fsu.edu/~bertram/software/pituitary. The units for parameters and species are varied from one to another, so I omit the unit definition here. Conductances in pS; currents in fA; Ca concentrations in uM; time in ms. JWS Online curation: This model was curated by reproducing Figure 1 c, cer and cAMP.

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Manuscript information

Endothelin action on pituitary lactotrophs: one receptor, many GTP-binding proteins.

  • Richard Bertram
  • Joel Tabak
  • Natalia Toporikova
  • Marc E Freeman
Sci. STKE 2006; 2006 (319):
Abstract
The endothelins are a family of hormones that have a biphasic action on pituitary lactotrophs. The initial effect is stimulatory, followed later by inhibition that persists long after the agonist has been removed. Recent research has uncovered several G protein pathways that mediate these effects.

Unit definitions 1

Unit definitions have no effect on the numerical analysis of the model. It remains the responsibility of the modeler to ensure the internal numerical consistency of the model. If units are provided, however, the consistency of the model units will be checked.

Name Definition
— 0.001 second

Compartments 1

Id Name Spatial dimensions Size
cell — 3.0 1.0

Species 3

Id Name Initial quantity Compartment Fixed
c cytosolic calcium concentration 0.3 cell ✘
cAMP — 1.0 cell ✘
cer ER calcium concentration 260.0 cell ✘

Initial assignments 0

Initial assignments are expressions that are evaluated at time=0. It is not recommended to create initial assignments for all model entities. Restrict the use of initial assignments to cases where a value is expressed in terms of values or sizes of other model entities. Note that it is not permitted to have both an initial assignment and an assignment rule for a single model entity.

Definition
Reactions 3
Id Name Objective coefficient Reaction Equation and Kinetic Law Flux bounds
reaction_0000001 — ∅ > c

cell * f * (jertot + jmemtot)
reaction_0000002 — ∅ > cer

-fer * sigmav * jertot * cell
reaction_000003 — ∅ > cAMP

cell * ETswitch * ((cAMPlow - cAMP) / taudir)

Parameters 0   50

Global parameters

Id Value
ETswitch 0.0
IP3 0.0
V -60.0
ainf 0.0
alpha 0.0000045
binf 0.0
cAMPlow 0.2
cm 5300.0
dact 0.35
dinh 0.4
dip3 0.5
f 0.01
fer 0.01
gca 2000.0
girk 1000.0
gk 3500.0
h 0.0
hinf 0.0
hinfer 0.0
ica 0.0
igirk 0.0
ik 0.0
inh 1.0
jerip3 0.0
jerleak 0.0
jerp 0.0
jertot 0.0
jmemtot 0.0
kc 0.15
ki 0.5
kserca 0.4
lambda 1.25
minf 0.0
n 0.0
ninf 0.0
o 0.0
perl 0.0005
perl_inf 0.0
sh 70.0
sigmav 10.0
sm 12.0
sn 5.0
taudir 20000.0
tauh 20.0
taun 20.0
vca 25.0
vh -20.0
vk -75.0
vm -20.0
vn -16.0

Local parameters

Id Value Reaction

Rules 0   4   16

Assignment rules

Definition
igirk = girk * h * (V - vk)
ica = gca * minf * (V - vca)
jerp = kserca * c
jerip3 = o * (cer - c)
hinfer = 1.0 / (1.0 + c / dinh)
ainf = 1.0 / (1.0 + dact / c)
ik = gk * n * (V - vk)
perl_inf = inh * cAMP * pow(c, 4.0) / (pow(ki, 4.0) + pow(c, 4.0))
jertot = jerleak + jerip3 - kserca * c
jerleak = perl * (cer - c)
jmemtot = -(alpha * gca * 1.0 / (1.0 + exp((vm - V) / sm)) * (V - vca) + kc * c)
o = pow(ainf, 3.0) * pow(binf, 3.0) * pow(hinfer, 3.0)
binf = IP3 / (IP3 + dip3)
hinf = 1.0 / (1.0 + exp((vh - V) / sh))
ninf = 1.0 / (1.0 + exp((vn - V) / sn))
minf = 1.0 / (1.0 + exp((vm - V) / sm))

Rate rules

Definition
h' = (hinf - h) / tauh
inh' = ETswitch * ((0.2 - inh) / taudir)
V' = (-ica - ik - igirk) / cm
n' = lambda * (ninf - n) / taun

Algebraic rules

Definition

Events 1

Trigger Assignments
gt(time, 60000) ETswitch = 1; girk = 3000; IP3 = 0.3