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Molecule Parameter List for Ca

The statistics table lists the distribution of a molecule acting either as a substrate, product, enzyme or as a molecule within the network.
The text color of a molecule is highlighted by color.
Statistics
Ca participated asMoleculeSum total ofEnzymeSubstrate of an enzymeProduct of an enzymeSubstrate in ReactionProduct in Reaction
No. of occurrences10000131

Accession and Pathway Details
Accession NameAccession No.Accession TypePathway Link
  • Ajay_Bhalla_
    2004_PKM_Tuning
  • 76Network
    PKC Shared_Object_Ajay_Bhalla_2004_PKM_tuning PLA2 
    PLCbeta Gq MAPK 
    Ras EGFR Sos 
    PLC_g CaMKII CaM 
    PP1 PP2B PKA 
    AC PKM 
    This model is taken from the Ajay SM, Bhalla US. Eur J Neurosci. 2004 Nov;20(10):2671-80. This is the reference feedforward model from Figure 8a.

    Ca acting as a Molecule in  
    Ajay_Bhalla_2004_PKM_Tuning Network
    NameAccession NamePathway NameInitial Conc.
    (uM)
    Volume
    (fL)
    Buffered
    Ca
  • Ajay_Bhalla_
    2004_PKM_Tuning

    Accession No. : 76
  • Shared_Object_
    Ajay_Bhalla_
    2004_PKM_tuning

    Pathway No. : 312
  • 0.081.5No

    Ca acting as a Substrate in a reaction in  
    Ajay_Bhalla_2004_PKM_Tuning Network
    Kd is calculated only for second order reactions, like nA+nB <->nC or nA<->nC+nD, where n is number and A,B,C,D are molecules, where as for first order reactions Keq is calculated. Kd for higher order reaction are not consider.
     NameAccession NamePathway NameKfKbKdtauReagents
    1PKC-act-by-Ca
  • Ajay_Bhalla_
    2004_PKM_Tuning

    Accession No. : 76
  • PKC
    Pathway No. : 313
    0.6
    (uM^-1 s^-1)
    0.5
    (s^-1)
    Kd(bf) = 0.8333(uM)-Substrate
    Ca
    PKC-cytosolic

    Product
    PKC-Ca
      Need est of rate of assoc of Ca and PKC. Assume it is fast The original parameter-searched kf of 439.4 has been scaled by 1/6e8 to account for change of units to n. Kf now 8.16e-7, kb=.6085 Raised kf to 1e-6 to match Ca curve, kb to .5
    2PLA2-Ca-act
  • Ajay_Bhalla_
    2004_PKM_Tuning

    Accession No. : 76
  • PLA2
    Pathway No. : 314
    1
    (uM^-1 s^-1)
    0.1
    (s^-1)
    Kd(bf) = 0.1(uM)-Substrate
    Ca
    PLA2-cytosolic

    Product
    PLA2-Ca*
      Leslie and Channon BBA 1045 (1990) 261-270 fig6 pp267.
    3PLA2*-Ca-act
  • Ajay_Bhalla_
    2004_PKM_Tuning

    Accession No. : 76
  • PLA2
    Pathway No. : 314
    6
    (uM^-1 s^-1)
    0.1
    (s^-1)
    Kd(bf) = 0.0167(uM)-Substrate
    Ca
    PLA2*

    Product
    PLA2*-Ca
      To start off, same kinetics as the PLA2-Ca-act direct pathway. Oops ! Missed out the Ca input to this pathway first time round. Let's raise the forward rate about 3x to 5e-6. This will let us reduce the rather high rates we have used for the kenz on PLA2*-Ca. In fact, it may be that the rates are not that different, just that this pathway for getting the PLA2 to the memb is more efficien....
    4Act-PLC-Ca
  • Ajay_Bhalla_
    2004_PKM_Tuning

    Accession No. : 76
  • PLCbeta
    Pathway No. : 315
    3
    (uM^-1 s^-1)
    1
    (s^-1)
    Kd(bf) = 0.3333(uM)-Substrate
    Ca
    PLC

    Product
    PLC-Ca
      Affinity for Ca = 1uM without AlF, 0.1 with: from Smrcka et al science 251 pp 804-807 1991 so [Ca].kf = kb so kb/kf = 1 * 6e5 = 1/1.66e-6 11 June 1996: Raised affinity to 5e-6 to maintain balance. See notes.
    5PLC-Gq-bind-Ca
  • Ajay_Bhalla_
    2004_PKM_Tuning

    Accession No. : 76
  • PLCbeta
    Pathway No. : 315
    29.9997
    (uM^-1 s^-1)
    1
    (s^-1)
    Kd(bf) = 0.0333(uM)-Substrate
    Ca
    PLC-Gq

    Product
    PLC-Ca-Gq
      this step has a high affinity for Ca, from Smrcka et al. 0.1uM so kf /kb = 1/6e4 = 1.666e-5:1. See the Act-PLC-by-Gq reac. 11 Jun 1996: Raised kf to 5e-5 based on match to conc-eff curves from Smrcka et al.
    6Ca_act_PLC_g
  • Ajay_Bhalla_
    2004_PKM_Tuning

    Accession No. : 76
  • PLC_g
    Pathway No. : 321
    180
    (uM^-1 s^-1)
    10
    (s^-1)
    Kd(bf) = 0.0556(uM)-Substrate
    Ca
    PLC_g

    Product
    Ca.PLC_g
      Nice curves from Homma et al JBC 263:14 6592-6598 1988 Fig 5c. The activity falls above 10 uM, but that is too high to reach physiologically anyway, so we'll ignore the higher pts and match the lower ones only. Half-max at 1 uM. But Wahl et al JBC 267:15 10447-10456 1992 have half-max at 56 nM which is what I'll use.
    7Ca_act_PLC_g*
  • Ajay_Bhalla_
    2004_PKM_Tuning

    Accession No. : 76
  • PLC_g
    Pathway No. : 321
    11.9997
    (uM^-1 s^-1)
    10
    (s^-1)
    Kd(bf) = 0.8334(uM)-Substrate
    Ca
    PLC_G*

    Product
    Ca.PLC_g*
      Again, we refer to Homma et al and Wahl et al, for preference using Wahl. Half-Max of the phosph form is at 316 nM. Use kb of 10 as this is likely to be pretty fast. Did some curve comparisons, and instead of 316 nM giving a kf of 5.27e-5, we will use 8e-5 for kf. 16 Sep 97. As we are now phosphorylating the Ca-bound form, equils have shifted. kf should now be 2e-5 to match the curves.
    8CaM-TR2-bind-Ca
  • Ajay_Bhalla_
    2004_PKM_Tuning

    Accession No. : 76
  • CaM
    Pathway No. : 323
    72.0001
    (uM^-2 s^-1)
    72
    (s^-1)
    Kd(af) = 1(uM)-Substrate
    Ca
    Ca
    CaM

    Product
    CaM-TR2-Ca2
      Lets use the fast rate consts here. Since the rates are so different, I am not sure whether the order is relevant. These correspond to the TR2C fragment. We use the Martin et al rates here, plus the Drabicowski binding consts. All are scaled by 3X to cell temp. kf = 2e-10 kb = 72 Stemmer & Klee: K1=.9, K2=1.1. Assume 1.0uM for both. kb/kf=3.6e11. If kb=72, kf = 2e-10 (Exactly the same !)....
    9
  • CaM-TR2-Ca2-bind
    -Ca
  • Ajay_Bhalla_
    2004_PKM_Tuning

    Accession No. : 76
  • CaM
    Pathway No. : 323
    3.6
    (uM^-1 s^-1)
    10
    (s^-1)
    Kd(bf) = 2.7778(uM)-Substrate
    Ca
    CaM-TR2-Ca2

    Product
    CaM-Ca3
      K3 = 21.5, K4 = 2.8. Assuming that the K4 step happens first, we get kb/kf = 2.8 uM = 1.68e6 so kf =6e-6 assuming kb = 10
    10CaM-Ca3-bind-Ca
  • Ajay_Bhalla_
    2004_PKM_Tuning

    Accession No. : 76
  • CaM
    Pathway No. : 323
    0.465
    (uM^-1 s^-1)
    10
    (s^-1)
    Kd(bf) = 21.5052(uM)-Substrate
    Ca
    CaM-Ca3

    Product
    CaM-Ca4
      Use K3 = 21.5 uM here from Stemmer and Klee table 3. kb/kf =21.5 * 6e5 so kf = 7.75e-7, kb = 10
    11
  • Ca-bind-CaNAB-Ca
    2
  • Ajay_Bhalla_
    2004_PKM_Tuning

    Accession No. : 76
  • PP2B
    Pathway No. : 325
    3.6
    (uM^-2 s^-1)
    1
    (s^-1)
    Kd(af) = 0.527(uM)-Substrate
    Ca
    Ca
    CaNAB-Ca2

    Product
    CaNAB-Ca4
      This process is probably much more complicated and involves CaM. However, as I can't find detailed info I am bundling this into a single step. Based on Steemer and Klee pg 6863, the Kact is 0.5 uM. kf/kb = 1/(0.5 * 6e5)^2 = 1.11e-11
    12Ca-bind-CaNAB
  • Ajay_Bhalla_
    2004_PKM_Tuning

    Accession No. : 76
  • PP2B
    Pathway No. : 325
    10008.4
    (uM^-2 s^-1)
    1
    (s^-1)
    Kd(af) = 0.01(uM)-Substrate
    Ca
    Ca
    CaNAB

    Product
    CaNAB-Ca2
      going on the experience with CaM, we put the fast (high affinity) sites first. We only know (Stemmer and Klee) that the affinity is < 70 nM. Assuming 10 nM at first, we get kf = 2.78e-8, kb = 1. Try 20 nM. kf = 7e-9, kb = 1 
    13trigger_PKM
  • Ajay_Bhalla_
    2004_PKM_Tuning

    Accession No. : 76
  • PKM
    Pathway No. : 328
    0.1
    (uM^-2 s^-1)
    0.4
    (s^-1)
    Kd(af) = 2(uM)-Substrate
    Ca
    Ca
    Ca_detector

    Product
  • Ca.detector_
    complex


  • Ca acting as a Product in a reaction in  
    Ajay_Bhalla_2004_PKM_Tuning Network
    Kd is calculated only for second order reactions, like nA+nB <->nC or nA<->nC+nD, where n is number and A,B,C,D are molecules, where as for first order reactions Keq is calculated. Kd for higher order reaction are not consider.
    NameAccession NamePathway NameKfKbKdtauReagents
    Ca_stoch
  • Ajay_Bhalla_
    2004_PKM_Tuning

    Accession No. : 76
  • Shared_Object_
    Ajay_Bhalla_
    2004_PKM_tuning

    Pathway No. : 312
  • 100
    (s^-1)
    100
    (s^-1)
    Keq = 1(uM)0.005secSubstrate
    Ca_input

    Product
    Ca



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