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occurs in: GO:0005737
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name: Calcium-Cyt
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type: Species
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metaid_0000024
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name: k16
type: Parameter

metaid_0000038
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constant: false
boundary condition: false
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initial concentration: 0.0
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in compartment: metaid_0000003
name: EnzCatlysedProduct
type: Species

metaid_0000043
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value: 4.0
name: p
type: Parameter

metaid_0000129
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value: 4.5
name: K21
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metaid_0000017
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name: K9
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metaid_0000010
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name: k2
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name: k12
type: Parameter

metaid_0000014
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value: 1.18
name: K6
type: Parameter

metaid_0000004
is version of: GO:0005783
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name: ER
type: Compartment

metaid_0000030
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constant: true
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name: mitochondria
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metaid_0000023
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value: 0.16
name: K15
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metaid_0000008
in compartment: metaid_0000004
name: Calcium-ER
constant: false
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occurs in: GO:0005783
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initial amount: 10.0
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metaid_0000037
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initial concentration: 0.0
initial amount: NaN
in compartment: metaid_0000003
name: Enzyme
type: Species

metaid_0000128
is: SBO:0000009
constant: true
value: 0.81
name: k20
type: Parameter

metaid_0000044
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value: 3.0
name: k_enz
type: Parameter

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value: 5.0
name: k_act
type: Parameter

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value: 0.7
name: k10
type: Parameter

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value: 4.88
name: k5
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metaid_0000003
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name: cytoplasm
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BIOMD0000000331
name: Larsen2004_CalciumSpiking_EnzymeBinding
occurs in: http://identifiers.org/taxonomy/10116
parameter: metaid_0000022
parameter: metaid_0000127
parameter: metaid_0000040
is described by: http://identifiers.org/pubmed/14871603
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parameter: metaid_0000009
parameter: metaid_0000015
parameter: metaid_0000016
parameter: metaid_0000017
parameter: metaid_0000020
parameter: metaid_0000018
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substance units: 858204
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notes: This a model from the article: On the encoding and decoding of calcium signals in hepatocytes Ann Zahle Larsen, Lars Folke Olsen and Ursula Kummera Biophysical Chemistry Volume 107, Issue 1, 1 January 2004, Pages 83-99 14871603 , Abstract: Many different agonists use calcium as a second messenger. Despite intensive research in intracellular calcium signalling it is an unsolved riddle how the different types of information represented by the different agonists, is encoded using the universal carrier calcium. It is also still not clear how the information encoded is decoded again into the intracellular specific information at the site of enzymes and genes. After the discovery of calcium oscillations, one likely mechanism is that information is encoded in the frequency, amplitude and waveform of the oscillations. This hypothesis has received some experimental support. However, the mechanism of decoding of oscillatory signals is still not known. Here, we study a mechanistic model of calcium oscillations, which is able to reproduce both spiking and bursting calcium oscillations. We use the model to study the decoding of calcium signals on the basis of co-operativity of calcium binding to various proteins. We show that this co-operativity offers a simple way to decode different calcium dynamics into different enzyme activities. Note: This model corresponds to the improved model eqn 1-7, as described by Larsen et al., 2004 implemented to investigate how the cell can decode different oscillations. This is done by introducing 2 more variables Enzyme and Product in addition to the 5 variables G-alpha, PLC, Ca_cyt, Ca_ER and Ca_mit receptor-operated model described in the first part of the paper. The receptor-operated model is itself a modified version of the model described in Kummer 2000 (PMID: 10968983 )
is version of: GO:0019722
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length unit: length
parameter: metaid_0000126
rule: metaid_0000039
modified:
  W3 CDTF: Mon Jul 11 14:18:39 BST 2011
compartment: metaid_0000030
rule: metaid_0000036
is: MODEL1105060002
creator:
  ORG:
    orgname: EMBL-EBI
  n:
    given: Vijayalakshmi
    family: Chelliah
created:
  W3 CDTF: Thu May 05 13:59:47 BST 2011
parameter: metaid_0000044
parameter: metaid_0000013
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species: metaid_0000006
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parameter: metaid_0000012
type: SBMLModel
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curated: true
parameter: metaid_0000023
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time units: 858180
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metaid_0000041
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value: 0.62
name: KM
type: Parameter

metaid_0000127
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constant: true
value: 3.5
name: K19
type: Parameter

metaid_0000005
name: G-alpha
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is version of: Q9JID2
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metaid_0000022
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value: 153.0
name: k14
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constant: true
value: 3.0
name: K11
type: Parameter

metaid_0000009
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value: 0.01
name: k1
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metaid_0000045
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value: 3.0
name: k_rem
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name: k8
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metaid_0000012
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name: K4
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metaid_0000126
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metaid_0000042
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metaid_0000006
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boundary condition: false
type: Species
in compartment: metaid_0000003
initial concentration: NaN
name: PLC

metaid_0000021
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constant: true
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name: k13
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metaid_0000025
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constant: true
value: 0.05
name: K17
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metaid_0000015
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constant: true
value: 2.08
name: k7
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metaid_0000011
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constant: true
value: 0.64
name: k3
type: Parameter

metaid_0000031
initial amount: NaN
initial concentration: 0.001
has only substance units: false
occurs in: GO:0005739
type: Species
boundary condition: false
name: Calcium-mit
constant: false
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is: SBO:0000247