MODEL0912160005
type: SBMLModel
parameter: metaid_0000006
parameter: metaid_0000021
parameter: metaid_0000009
parameter: metaid_0000022
substance units: 608838
rule: metaid_0000029
parameter: metaid_0000012
notes: This a model from the article: NFAT functions as a working memory of Ca2+ signals in decoding Ca2+ oscillation. Tomida T, Hirose K, Takizawa A, Shibasaki F, Iino M. EMBO J 2003 Aug 1;22(15):3825-32 12881417 , Abstract: Transcription by the nuclear factor of activated T cells (NFAT) is regulated by the frequency of Ca(2+) oscillation. However, why and how Ca(2+) oscillation regulates NFAT activity remain elusive. NFAT is dephosphorylated by Ca(2+)-dependent phosphatase calcineurin and translocates from the cytoplasm to the nucleus to initiate transcription. We analyzed the kinetics of dephosphorylation and translocation of NFAT. We show that Ca(2+)-dependent dephosphorylation proceeds rapidly, while the rephosphorylation and nuclear transport of NFAT proceed slowly. Therefore, after brief Ca(2+) stimulation, dephosphorylated NFAT has a lifetime of several minutes in the cytoplasm. Thus, Ca(2+) oscillation induces a build-up of dephosphorylated NFAT in the cytoplasm, allowing effective nuclear translocation, provided that the oscillation interval is shorter than the lifetime of dephosphorylated NFAT. We also show that Ca(2+) oscillation is more cost-effective in inducing the translocation of NFAT than continuous Ca(2+) signaling. Thus, the lifetime of dephosphorylated NFAT functions as a working memory of Ca(2+) signals and enables the control of NFAT nuclear translocation by the frequency of Ca(2+) oscillation at a reduced cost of Ca(2+) signaling. This model was taken from the CellML repository and automatically converted to SBML. The original model was: Tomida T, Hirose K, Takizawa A, Shibasaki F, Iino M. (2003) - version01 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. To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer …
rule: metaid_0000026
rule: metaid_0000036
parameter: metaid_0000014
parameter: metaid_0000015
parameter: metaid_0000005
rule: metaid_0000033
time units: 659290
parameter: metaid_0000020
rule: metaid_0000030
parameter: metaid_0000018
parameter: metaid_0000019
parameter: metaid_0000010
curated: false
parameter: metaid_0000011
name: Tomida2003_NFATfunctions_CalciumOscillation
rule: metaid_0000027
parameter: metaid_0000013
parameter: metaid_0000003
parameter: metaid_0000004
rule: metaid_0000034
rule: metaid_0000031
parameter: metaid_0000017
parameter: metaid_0000007
parameter: metaid_0000008
parameter: metaid_0000023
volume units: 970346
length unit: 027038
rule: metaid_0000028
compartment: metaid_0000024
is described by: http://identifiers.org/pubmed/12881417
rule: metaid_0000025
rule: metaid_0000035
parameter: metaid_0000016
area units: area
rule: metaid_0000032

metaid_0000006
type: Parameter
constant: false
value: 0.0
name: NFAT_nuc

metaid_0000021
type: Parameter
constant: false
value: NaN
name: percentage_NFAT_cyt

metaid_0000009
type: Parameter
constant: true
value: 0.359
name: k1_stim

metaid_0000022
type: Parameter
constant: false
value: NaN
name: percentage_NFATP_cyt

metaid_0000012
type: Parameter
constant: true
value: 0.06
name: k3

metaid_0000014
type: Parameter
constant: true
value: 3.0
name: stim_wavelength

metaid_0000015
type: Parameter
constant: true
value: 0.5
name: stim_duration

metaid_0000005
type: Parameter
constant: false
value: 0.0
name: NFAT_cyt

metaid_0000020
type: Parameter
constant: false
value: NaN
name: Jexport

metaid_0000018
type: Parameter
constant: false
value: NaN
name: Jdephosphorylation

metaid_0000019
type: Parameter
constant: false
value: NaN
name: Jtranslocate

metaid_0000010
type: Parameter
constant: false
value: NaN
name: k1

metaid_0000011
type: Parameter
constant: true
value: 0.147
name: k2

metaid_0000013
type: Parameter
constant: true
value: 0.035
name: k4

metaid_0000003
type: Parameter
constant: true
value: NaN
name: time

metaid_0000004
type: Parameter
constant: false
value: 5000.0
name: NFATP_cyt

metaid_0000017
type: Parameter
constant: true
value: 1.0
name: time_before_stim

metaid_0000007
type: Parameter
constant: false
value: NaN
name: NFAT_tot

metaid_0000008
type: Parameter
constant: true
value: 0.0
name: k1_unstim

metaid_0000023
type: Parameter
constant: false
value: NaN
name: percentage_NFAT_nuc

metaid_0000024
type: Compartment
constant: true
size: 1.0
spatial dimensions: 3.0

metaid_0000016
type: Parameter
constant: false
value: NaN
name: stim_on