BioModelsapplication/xmlhttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000202?filename=BIOMD0000000202.pdfhttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000202?filename=BIOMD0000000202-biopax3.owlhttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000202?filename=BIOMD0000000202-biopax2.owlhttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000202?filename=BIOMD0000000202_url.xmlhttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000202?filename=BIOMD0000000202_urn.xmlhttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000202?filename=BIOMD0000000202.xpphttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000202?filename=BIOMD0000000202.pnghttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000202?filename=BIOMD0000000202.scihttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000202?filename=BIOMD0000000202.mhttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000202?filename=BIOMD0000000202.vcmlprimaryOK200Harish DharuriManually curatedL2V3https://www.ebi.ac.uk/biomodels/BIOMD000000020218538916falseBioModelsSBMLModelsChenXF2008 CICR2008MODEL7519277765Chen XF, Li CX, Wang PY, Li M, Wang WCChen XF18538916,
A mathematical model is proposed to illustrate the activation of STIM1 (stromal interaction molecule 1) protein, the assembly and activation of calcium-release activated calcium (CRAC) channels in T cells. In combination with De Young-Keizer-Li-Rinzel model, we successfully reproduce a sustained Ca(2+) oscillation in cytoplasm. Our results reveal that Ca(2+) oscillation dynamics in cytoplasm can be significantly affected by the way how the Orai1 CRAC channel are assembled and activated. A low sustained Ca(2+) influx is observed through the CRAC channels across the plasma membrane. In particular, our model shows that a tetrameric channel complex can effectively regulate the total quantity of the channels and the ratio of the active channels to the total channels, and a period of Ca(2+) oscillation about 29 s is in agreement with published experimental data. The bifurcation analyses illustrate the different dynamic properties between our mixed Ca(2+) feedback model and the single positive or negative feedback models.. null, 136.
Laboratory of Soft Matter Physics, Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100080, China.hdharuri@cds.caltech.eduCalifornia Institute of TechnologyBIOMD0000000202Relying on quantitative measurements of Ca2+ activation and inhibition of the inositol 1,4,5-trisphosphate (IP3) receptor in the endoplasmic reticulum, we construct a simplified kinetic model to describe the properties of this channel. Selecting rate constants to fit key kinetic and equilibrium data, we find that the model reproduces a variety of in vivo and in vitro experiments. In combination with Ca(2+)-ATPase activity for Ca2+ uptake into the endoplasmic reticulum, the model leads to cytoplasmic oscillations in Ca2+ concentration at fixed IP3 concentration and only a single pool of releasable Ca2+, the endoplasmic reticulum. Incorporation of a positive-feedback mechanism of Ca2+ on IP3 production by phospholipase C enriches the properties of the oscillations and leads to oscillations in Ca2+ concentration accompanied by oscillations in IP3 concentration. We discuss the possible significance of these results for the interpretation of experiments.A mathematical model is proposed to illustrate the activation of STIM1 (stromal interaction molecule 1) protein, the assembly and activation of calcium-release activated calcium (CRAC) channels in T cells. In combination with De Young-Keizer-Li-Rinzel model, we successfully reproduce a sustained Ca(2+) oscillation in cytoplasm. Our results reveal that Ca(2+) oscillation dynamics in cytoplasm can be significantly affected by the way how the Orai1 CRAC channel are assembled and activated. A low sustained Ca(2+) influx is observed through the CRAC channels across the plasma membrane. In particular, our model shows that a tetrameric channel complex can effectively regulate the total quantity of the channels and the ratio of the active channels to the total channels, and a period of Ca(2+) oscillation about 29 s is in agreement with published experimental data. The bifurcation analyses illustrate the different dynamic properties between our mixed Ca(2+) feedback model and the single positive or negative feedback models.Dynamic simulation of the effect of calcium-release activated calcium channel on cytoplasmic Ca2+ oscillation.A single-pool inositol 1,4,5-trisphosphate-receptor-based model for agonist-stimulated oscillations in Ca2+ concentration.Chen Xiao-fang XF, Li Cong-xin CX, Wang Peng-ye PY, Li Ming M, Wang Wei-chi WCDe Young G W GW, Keizer J JUVO Gene Mutation, Anti-HBsAb Positive, Beta Gene Mutation, H. pylori Positive, Recombinant DNA, adenosinetriphosphatase activity, Progesterone Receptor Positive, FGFBR Gene Rearrangement, ERBB2 Amplification, Positive Charge, RET/PTC Rearrangement, Hepatitis C Virus RNA Positive, p53 Mutation, calcium(2+) ion, PGR Positive, 1, HCV Antibody Positive, Nuclear Receptor Subfamily 3 Group A Member 1 Positive, Response Inhibition, 4, Erg-3 Gene Rearrangement, CD332 Gene Mutation, Ha-ras Gene Mutation, Methylated MGMT Promoter, EXPRESSED, HRas Proto-Oncogene, ERA Positive, G Protein Subunit Alpha q Gene Mutation, IDH Gene Mutation, CD324 Gene Mutation, TRT Promoter Mutation, Hepatitis B Virus Core Antibody Positive, c-KIT Positive, Flavoprotein Subunit of Complex II Positive, GAQ Gene Mutation, Met Proto-Oncogene (Hepatocyte Growth Factor Receptor) Gene Amplification, B7H1 Positive, BEK Gene Mutation, FGFR1 Gene Rearrangement, node-positive, Cadherin 1 Gene Mutation, PD-L1+, ESTRB Positive, XH2 Gene Mutation, NEU Gene Mutation, v-raf Murine Sarcoma Viral Oncogene Homolog B1 Gene Rearrangement, Mechanism Device, Catenin Beta 1 Gene Mutation, FGFR3 Gene Mutation, ER Beta Positive, SDHB Positive, K-RAS Mutation, CD331 Gene Rearrangement, Hepatitis B DNA Positive, C-HA-RAS1 Gene Mutation, Telomerase Reverse Transcriptase Gene Promoter Mutation, MET Amplification, ZNF-HX Gene Mutation, Methylated MGMT Gene Promoter, ERBB2 Gene Amplification, Beta Catenin Gene Mutation, Human Immunodeficiency Virus Positive, KGFR Gene Rearrangement, c-erbB2 Gene Amplification, B-RAF Gene Rearrangement, Anti-HBc Positive, Hepatitis B Virus Surface Antibody Positive, Estrogen Receptor Alpha Positive, Interpretation of Laboratory Test., 5-Triphosphate, Alpha 11 Gene Mutation, DmIKKgamma, CD331 Gene Mutation, ERB Positive, Channel Object, SDHIP Positive, dIKK, Cadherin, Interpretation, ER, JKT4 Gene Rearrangement, FGFR-2 Gene Rearrangement, FLT2 Gene Mutation, FGFR-1 Gene Rearrangement, RET Gene Rearrangement, CMC1 Gene Mutation, activation, Discussion, ATP phosphohydrolase activity, statistical significance, NRAS Gene Mutation, P53 Gene Mutation, ECAD Gene Mutation, Guanine Nucleotide-Binding Protein, PAX8 Gene Rearrangement, NR3A1 Positive, proportionality, IKK-gamma, SV40 T-antigen, rate, Keratinocyte Growth Factor Receptor Gene Rearrangement, Passageway, HER2 Amplification, EST2 Promoter Mutation, Present, ESR Positive, PDCD1L1 Positive, CD333 Gene Mutation, Positive Epstein-Barr Virus Test, Positive EBV Serum Test, calcium(II) cation, IDH Gene Family Mutation, FGFBR Gene Mutation, N-RAS Gene Mutation, HER2/Neu Amplification, TCS1 Promoter Mutation, KRAS Gene Mutation, in vitro, Feedbacks, Expression of PD-L1, BFGFR Gene Mutation, SDHF Positive, Nuclear Receptor Subfamily 3 Group A Member 2 Positive, BRCA1-Associated Protein 1 Gene Mutation, CDHE Gene Mutation, number, HCV RNA Positive, Succinate Dehydrogenase [Ubiquinone] Iron-Sulfur Subunit, Discuss, Inhibition, Hepatitis B Virus Surface Antigen Positive, dIKK-gamma, ER+, Receptor Tyrosine Kinase Gene Amplification, FGFR1 Gene Mutation, p55 Gene Rearrangement, FLG Gene Rearrangement, ATP monophosphatase activity, PDCD1LG1 Positive, DmIKK-gamma, G Protein Subunit Alpha 11 Gene Mutation, adenosine triphosphatase activity, Inhibiting, B7-H Positive, ETV Rearrangement, androgen receptor positive, proportion, Cadherin-Associated Protein, HBs Positive, Lecithinase C, MGMT Gene Methylation, Positive Number, Hepatitis B Core Antibody Positive, calcium(2+), 5-IP3, positive test result, v-Ki-ras2 Kirsten Rat Sarcoma Viral Oncogene Homolog Gene Mutation, GNAQ Gene Mutation, PD-L1 Positive, BEK Gene Rearrangement, RET Rearrangement, CTNNB1 Gene Mutation, Myo-Inositol 1, Possible, FGFR2 Gene Rearrangement, RAD54 Homolog Gene Mutation, ANO1 Positive, Statistically Significant, RAD54 Gene Mutation, Expression, HER-2 Gene Amplification, Variety, In Vivo, CD117 Positive, FGFR2 Gene Mutation, Positive EBV Test, SINGLE, Helicobacter pylori Positive, Acquisition Scheme, In Vitro Route of Administration, PR Positive, ESRB Positive, Hepatitis B Surface Protein Antigen Positive, Estrogen Receptor Positive, Reticulum, B-RAF1 Gene Rearrangement, IKKgamma, Positive Finding, ATRX, BRAF Gene Rearrangement, GNA11 Gene Mutation, HCO3--ATPase, 5-tris(dihydrogen phosphate), FLG Gene Mutation, PAX8 Rearrangement, Androgen Receptor Positive, HGFR Gene Amplification, Hepatocyte Growth Factor Receptor Gene Amplification, ESR1 Positive, coupled, MET Gene Amplification, c-MET Gene Amplification, ER-Alpha Positive, Single Person, phospholipase C1, Methylated MGMT, HBcAb Positive, Dmikkgamma, ERG Rearrangement, Tumor Protein p53 Gene Mutation, HBsAg Positive, IP Positive, Hepatitis B Surface Antigen Positive, CG16910, Anti-HCV Antibody Positive, TERT Gene Promoter Mutation, N-RAS Mutation, FLT-2 Gene Mutation, ETS Transcription Factor ERG Gene Rearrangement, Ret Proto-Oncogene Rearrangement, IDH Mutation, CEK Gene Mutation, 1p/19q Co-deletion, Phospholipase C, quotient, SDHA Positive, Solitary, Q Polypeptide Gene Mutation, quantitative, Alpha-11 Gene Mutation, Construct, Succinate Dehydrogenase [Ubiquinone] Flavoprotein Subunit, Chromatin Remodeler Gene Mutation, Alone, Estrogen Receptor 2 Positive, XNP Gene Mutation, O-6-Methylguanine-DNA Methyltransferase Gene Promoter Methylation, Fibroblast Growth Factor Receptor 1 Gene Mutation, ER Positive, v-Ets Erythroblastosis Virus E26 Oncogene Like Gene Rearrangement, Adverse Event Possibly Related to Intervention, Hepatitis C Viral RNA Positive, Significant, FLT-2 Gene Rearrangement, Possibly Related to Intervention, Combination, JKT4 Gene Mutation, AR+, KRAS Mutation, HRAS1 Gene Mutation, G-ALPHA-q Gene Mutation, BAP1 Gene Mutation, ESR-Beta Positive, ATP hydrolysis-dependent activity, Fibroblast Growth Factor Receptor 2 Gene Rearrangement, FGFR-3 Gene Rearrangement, Statistical Significance, Assortment, Inhibitory, 5-InsP3, KGFR Gene Mutation, v-Erb-B2 Avian Erythroblastic Leukemia Viral Oncogene Homolog 2 Gene Mutation, IKKg, TP53, Abnormal, KEY, Key, gene expression, estrogen receptor positive, INTP, D-myo-Inositol, (Ca2+ + Mg2+)-ATPase, Estrogen Receptor Beta Positive, INTERPRETATION, CALCIUM ION, statistically significant, ATPLC1, DOG1 Positive, Alpha Thalassemia/Mental Retardation Syndrome X-Linked Gene Mutation, ETV Family Gene Rearrangement, Ets Variant Family Rearrangement, FLT2 Gene Rearrangement, Rearrangement identified, FGFR3 Gene Rearrangement, c-Met Gene Amplification, ECT1 Gene Mutation, Estrogen Receptor 1 Positive, PR+, FMS-Like Tyrosine Kinase 2 Gene Rearrangement, Fibroblast Growth Factor Receptor 2 Gene Mutation, IDH Family Mutation, CD333 Gene Rearrangement, Anti-Hepatitis B Core Antibody Positive, B7 Homolog 1 Positive, Beta 1 (88kD) Gene Mutation, Anti-Hepatitis C Antibody Positive, Positive, ratio, ATRX Gene Mutation, ERG Gene Rearrangement, ATP hydrolase activity, Anti-HBs Antibody Positive, Ergastoplasm, TP53 Gene Mutation, 1p/19q co-deletion, KIT Proto-Oncogene Tyrosine Protein Kinase Positive, v-Ha-ras Harvey Rat Sarcoma Viral Oncogene Homolog Gene Mutation, HER2 Gene Mutation, CG17820, Positive Estrogen Receptor, Significance, results, doubly charged positive ion, HBsAb Positive, K-SAM Gene Mutation, Gene Expression, Succinate Dehydrogenase Complex Flavoprotein Subunit A Positive, ATPase-dependent activity, Hepatitis B Surface Antibody Positive, significant, Kenny, HIV Positive, Succinate Dehydrogenase Complex Iron Sulfur Subunit B Positive, fixed, KRAS2 Gene Mutation, HIV positive, 1p/19q Codeletion, POSITIVE, Possibly Related, Guanine Nucleotide Binding Protein (G Protein), Yes, In Vitro, Paired Domain Gene 8 Gene Rearrangement, Type C, SDH2 Positive, Programmed Cell Death 1 Ligand 1 Positive, ERBB2 Gene Mutation, Possible Attribution, ESR2 Positive, Ca(2+), in vivo, Hepatitis C RNA Positive, Type 1, calcium, Positive Laboratory Test Result, Paired Box 8 Gene Rearrangement, LCAM Gene Mutation, DmelCG16910, Expressed, ER-Beta Positive, E-Cadherin Gene Mutation, HRAS Gene Mutation, Arc-1 Gene Mutation, Harvey Rat Sarcoma Viral Oncogene Homolog Gene Mutation, N-SAM Gene Mutation, N-SAM Gene Rearrangement, CD274 Positive, Varietas, BRAF Rearrangement, CDH1 Gene Mutation, KRAS-2 Gene Mutation, Phospholipases C, ATPLC, PDL1 Positive, Anti-HBs Positive, KIT Positive, c-erbB2 Gene Activation, Anti-HBc Antibody Positive, TERT Promoter Mutation, presence, KAL2 Gene Mutation, ECT1 Gene Rearrangement, INTERPHALANGEAL JOINT 3, Myoinositol 1, Ca2+, Anoctamin-1 Positive, FGFR-3 Gene Mutation, Fp Positive, Fibroblast Growth Factor Receptor 1 Gene Rearrangement, Passage, OGD Gene Mutation, Anti-HBcAb Positive, Anti-Hepatitis B Virus Surface Antibody Positive, Hep C RNA Positive, dmIKKgamma, IKK[[gamma]], HIV test positive, CD274 Antigen Positive, Epithelial Gene Mutation, MET Proto-Oncogene, Erb-B2 Receptor Tyrosine Kinase Gene Mutation, BFGFR Gene Rearrangement, complex V (mitochondrial electron transport), SWS Gene Mutation, TAOS2 Positive, Fibroblast Growth Factor Receptor 3 Gene Mutation, Mechanism, Cadherin 1, E-Cadherin (Epithelial) Gene Mutation, HER2/neu Gene Mutation, ATPase activity, BRCA1 Associated Protein 1 Gene Mutation, v-Kit Hardy-Zuckerman 4 Feline Sarcoma Viral Oncogene Homolog Positive, Methylguanine-DNA Methyltransferase Gene Promoter Methylation, ARABIDOPSIS THALIANA PHOSPHOLIPASE C, Cytoplasmic, Neuroblastoma RAS Viral Oncogene Homolog Gene Mutation, H-ras Gene Mutation, ETV Gene Rearrangement, Positive Lymph Node, phospholipase C 1, IKK, CD332 Gene Rearrangement, C-H-RAS Gene Mutation, Ets Variant Gene Family Rearrangement, HER2 Gene Amplification, OGD Gene Rearrangement, KAL2 Gene Rearrangement, Anti-Hepatitis C Virus Antibody Positive, SDH1 Positive, CTNNB Gene Mutation, progesterone receptor positive, RASH1 Gene Mutation, 5-Trisphosphate, ER Alpha Positive, Cytoplasm, UCHL2 Gene Mutation, RAD54L Gene Mutation, Molecular Biology, data, GNA-11 Gene Mutation, MZN1_12, CEK Gene Rearrangement, MZN1.12, Anti-Hepatitis B Virus Core Antibody Positive, adenosine 5'-triphosphatase activity, Interphalangeal Joint 3, Hepatitis C Antibody Positive, Production, Loss of Chromosomes 1p/19q, Phospholipases, ESTRR Positive, K-SAM Gene Rearrangement, count in organism, DmelCG17820, uptake, Channel, Inositol 1, del(1p/19q), NR3A2 Positive, Fibroblast Growth Factor Receptor 3 Gene Rearrangement, MGMT Gene Promoter Methylation, DNA Construct, TMEM16A Positive, ESRA Positive, Catenin Beta-1 Gene Mutation, MGMT Methylation, AR Positive, ERBB2 Mutation, ETV Family Rearrangement, Hepatitis C Virus Antibody Positive, FMS-Like Tyrosine Kinase 2 Gene Mutation, Beta-Catenin Gene Mutation, GA11 Gene Mutation, HIV Positivity, Mast/Stem Cell Growth Factor Receptor Kit Positive, Paired Box Gene 8 Gene Rearrangement, TP2 Promoter Mutation, cytoplasm, ORAOV2 Positive, FGFR-2 Gene Mutation, Calcium-Dependent Adhesion Protein, BAP1 Mutation, c-K-ras Gene Mutation, Endoplasmic, PHOSPHOLIPASE C, Only, concentration, IP3, FGFR-1 Gene Mutation, HBs Antigen Positive, CD274 Molecule Positive, Single, Mitochondrial Positive, presence or absence in organism, GTPase Gene Mutationperiod, scale tissue, figures, scale, Effects, Longterm, Long Term Effects, plant peltate hair, peltate hair, Longterm Effect, scale (sensu Metazoa), Long-Term Effect, Papers., scales, Long-Term, Effect, time, Long-Term Effects, Long Term, Longterm EffectsComputer Modeling, simulation, Coagulation, Effects, Calcium 40, Activated, treatment effect, Kalzium, Therapy Effect, doubly charged positive ion, calcium(2+) ion., Released, Ca2+, Therapy Outcome, Treatment Effect, 20Ca, treatment outcome, Factor IV, Releasing, Discharge from Healthcare Facility, Release Determination, Activate, Calcium Channel, effect, activate, Effect, calcio, Calcium-40, Calcium, Discharged, Patient Discharge, Activation, CALCIUM ION, cytoplasm, calcium(2+), Ca(2+), Release, Cytoplasmic, calcium, Coagulation Factor IV, calcium(II) cation, Treatment Outcome, Outcome of Therapy, Appearance, Discharge, Mathematical Models and Simulations, Simulation, treatment_outcome, Blood Coagulation Factor IV, Ca, CytoplasmfalseChenXF2008_CICR
The model reproduces the plots in Figures 1 and 2. Note that the units of the time scale "A" are not right in the paper, it was corrected by the curator. Model successfully tested on MathSBML.
2015-02-242008-11-242008-11-24BIOMD0000000202185389161329108CHEBI:29108CHEBI:16595MODEL7519277765BIOMD0000000202GO:0032237GO:0051209GO:0048763GO:0005388GO:0051928GO:0050429C00076C01245131567Q13586Q96D31