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Molecule List for pathway CaRegulation (Pathway Number 149) in Accession NonOsc_Ca_IP3metabolism (Accession Number 31)

Default ordering is done according to Pathway Number. Table headers can be used for changing the default ordering.
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The entries are grouped according to Pathway Number and are alternately color coded using  and  color.
  NameAccession
Type
Initial
Conc.

(uM)
Volume
(fL)
BufferedSum Total Of
1 CaNetwork0.081000No
    This pool represents intracellular calcium. Resting levels are around 80 nM, but this is subject to all sorts of influxes and pumps.
2 Ca-extNetwork4000100000Yes
    Extracell Ca conc = 4 mM Extracell vol assumed 100 X cell vol. It is anyway kept buffered for the purposes of the model, so the concentration won't change.
3 
  • Ca-leak-from-ext
    racell
  • Network0.00081000No
        This represents the pool of Ca leak channels. The conc gradient is so large that this pool needs only a small number of molecules. For an equilibrium at 0.1 uM we need flow of 36e3/sec. With a permeability of 0.01 and a conc gradient of 4mM->0.1 uM (4e4) we get flux = N * perm * grad => N = 36e3 / (1e-2 * 4e3) = 900 if flux = 20e3, N =500, which is what we use. This works out to a concentration of 0.83 nM.
    4 
  • Ca-leak-to-cytop
    lasm
  • Network0.0241000Yes
        represents the channels that leak Ca into the cytoplasm. Effects of membrane potential are not considered. The amount and total flux are constrained by the need to balance Ca flux and keep basal Ca around 80 nM.
    5 Ca-sequesterNetwork5.796160No
        Sequestered Ca pool The vol is 0.16 * the vol of the cell as a whole.
    6 Ca10-CalNetwork0160No
        Calsequestrin with 10 Ca molecules bound
    7 Ca15-CalNetwork0160No
        Calsequestrin with 15 Ca molecules bound
    8 Ca20-CalNetwork0160No
        Calsequestrin with 20 Ca molecules bound
    9 Ca25-CalNetwork0160No
        Calsequestrin with 25 Ca molecules bound
    10 Ca30-CalNetwork0160No
        Calsequestrin with 30 Ca molecules bound
    11 Ca35-CalNetwork0160No
        Calsequestrin with 35 Ca molecules bound
    12 Ca40-CalNetwork0160No
        Calsequestrin with 40 Ca molecules bound
    13 Ca5-CalNetwork0160No
        Calsequestrin with 5 Ca molecules bound
    14 CaEPumpNetwork0.0051000No
        The calcium electrogenic pump: Mc Burney and Neering, TINS 10(4), 1987, 164-169. We treat the pump as a simple Michaelis-Menten enzyme. Levels are constrained tightly by the need to keep resting Ca levels at 80 nM.
    15 CalseqNetwork9.09160No
        This is Calsequestrin or the calcium buffer in the ER. from Cala & Jones, JBC 258(19), 1983: 11932-36 Calseq is present as 4mg/g of membrane protein; membrane protein = 2% of cell mass = 0.02 * 1g/cc * (1e-9)cc = (2e-11) g Hence Calseq = 8e-14/55000 moles per (1.6e-13)l = 9.091uM As per Guidebook to the calcium-binding proteins by Celio; and Mitchell et al, JBC 263, 1988: 1376-81; 1 mol of Calsequestrin binds 40 mol of Ca. This is the stoichiometry we use. System limitations do not allow us to create a 40th order reaction. Hence Calseq binding to Ca has been modeled in eight consecutive steps of 5th order each. The affinity of Calsequestrin for Ca in our model is constrained by the levels of free Ca in the stores (Ca-sequester). We use a Kd such that Ca-sequester levels remain similar to levels in the CaRegulation model without Ca buffering.
    16 
  • capacitive_Ca_
    entry*
  • Network0.011000No
        This mechanism has taken a while to be more tightly confirmed as probably being the TRP channel. In this model the channel is implemented to match experimental observations about capacitative Ca entry. Levels are set by two constraints: the resting Ca levels, and the height of the response to IP3.
    17 CaTranspNetwork0.241000No
        The calcium transporter levels are constrained by the resting levels of Ca in the cell. The rate of Ca sequestration depends on the amount of this pool.
    18 CaTransp-2CaNetwork01000No
        equivalent to the enzyme-substrate complex. 2 Ca are bound to the transporter. ATP is ignored.
    19 inact_cap_entryNetwork01000No
        represents the portion of the capacitative-Ca entry channel which is blocked when there is lots of Ca sequestered in the stores
    20 IP3Network01000No IP3(145)
        Inositol(145)trisphosphate

     
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    Database compilation and code copyright (C) 2005, Upinder S. Bhalla and NCBS/TIFR
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