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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 occurrences11000120

Accession and Pathway Details
Accession NameAccession No.Accession TypePathway Link
  • Synaptic_
    Network
    		• 16Network
    Shared_Object_Synaptic_Network,  PKC,  PLA2,  
    PLCbeta,  Gq,  MAPK,  
    Ras,  EGFR,  Sos,  
    PLC_g,  CaMKII,  CaM,  
    PP1,  PP2B,  PKA,  
    AC,  CaRegulation 
    This model is an annotated version of the synaptic signaling network.
    The primary reference is Bhalla US and Iyengar R. Science (1999) 283(5400):381-7 but several of the model pathways have been updated.
    Bhalla US Biophys J. 2002 Aug;83(2):740-52
    Bhalla US J Comput Neurosci. 2002 Jul-Aug;13(1):49-62

    Ca acting as a Molecule in      Synaptic_Network Network
    NameAccession NamePathway NameInitial Conc.
    (uM)    		Volume
    (fL)    		Buffered
    Ca
  • Synaptic_
    Network
    Accession No. : 16
  • Shared_Object_
    Synaptic_
    Network
    Pathway No. : 70
    		• 0.081000No
    This calcium pool is treated as being buffered to a steady 0.08 uM, which is the resting level.

    Ca acting as a Summed Molecule in      Synaptic_Network Network
    Accession NamePathway NameTargetInput
  • Synaptic_
    Network
    Accession No. : 16
  • Shared_Object_
    Synaptic_
    Network
    Pathway No. : 70
    		• CaCa_stim
    Ca_intracell
    This calcium pool is treated as being buffered to a steady 0.08 uM, which is the resting level.

    Ca acting as a Substrate in a reaction in      Synaptic_Network 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
  • Synaptic_
    Network
    Accession No. : 16
    		• PKC
    Pathway No. : 71    		0.6
    (uM^-1 s^-1)    		0.5
    (s^-1)    		Kd(bf) = 0.8333(uM)-Substrate
    Ca
    PKC-cytosolic

    Product
    PKC-Ca
      This Kd is a straightforward result from the Schaechter and Benowitz 1993 J Neurosci 13(10):4361 curves. The time-course is based on the known rapid activation of PKC and also the fact that Ca association with proteins is typically quite fast. My guess is that this tau of 2 sec is quite conservative and the actualy rate may be much faster. The parameter is quite insensitive for most stimuli.
    2PLA2-Ca-act
  • Synaptic_
    Network
    Accession No. : 16
    		• PLA2
    Pathway No. : 72    		1
    (uM^-1 s^-1)    		0.1
    (s^-1)    		Kd(bf) = 0.1(uM)-Substrate
    Ca
    PLA2-cytosolic

    Product
    PLA2-Ca*
      Direct activation of PLA2 by Ca. From Leslie and Channon BBA 1045 (1990) 261-270 fig6 pp267.
    3PLA2*-Ca-act
  • Synaptic_
    Network
    Accession No. : 16
    		• PLA2
    Pathway No. : 72    		6
    (uM^-1 s^-1)    		0.1
    (s^-1)    		Kd(bf) = 0.0167(uM)-Substrate
    Ca
    PLA2*

    Product
    PLA2*-Ca
      Nemenoff et al 1993 JBC 268:1960 report a 2X to 4x activation of PLA2 by MAPK, which seems dependent on Ca as well. This reaction represents this activation. Rates are scaled to give appropriate fold activation.
    4Act-PLC-Ca
  • Synaptic_
    Network
    Accession No. : 16
    		• PLCbeta
    Pathway No. : 73    		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 Assigned affinity to a Kd of 0.333 to maintain detailed balance.
    5PLC-Gq-bind-Ca
  • Synaptic_
    Network
    Accession No. : 16
    		• PLCbeta
    Pathway No. : 73    		30
    (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 of 0.1 uM for Ca, from Smrcka et al 1991 Science 251:804-807 so kf /kb = 1/6e4 = 1.666e-5:1. See the Act-PLC-by-Gq reaction. Raised kf to 5e-5 based on match to conc-eff curves from Smrcka et al.
    6Ca_act_PLC_g
  • Synaptic_
    Network
    Accession No. : 16
    		• PLC_g
    Pathway No. : 79    		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*
  • Synaptic_
    Network
    Accession No. : 16
    		• PLC_g
    Pathway No. : 79    		12
    (uM^-1 s^-1)    		10
    (s^-1)    		Kd(bf) = 0.8333(uM)-Substrate
    Ca
    PLC_G*

    Product
    Ca.PLC_g*
      Again, we refer to Homma et al and Wahl et al, for preference using Wahl et al JBC 267(15):10447-10456 1992. Half-Max of the phosph form is at 316 nM. Use kb of 10 as this is likely to be pretty fast. As we are phosphorylating the Ca-bound form, equils have shifted. kf should now be 2e-5 (Kf = 12) to match the reported half-max.
    8CaM-TR2-bind-Ca
  • Synaptic_
    Network
    Accession No. : 16
    		• CaM
    Pathway No. : 81    		72
    (uM^-2 s^-1)    		72
    (s^-1)    		Kd(af) = 1(uM)-Substrate
    Ca
    Ca
    CaM

    Product
    CaM-TR2-Ca2
      We use the Martin et al 1985 Eur J Biochem 151(3):543-550 rates here, plus the Drabikowski and Brzeska 1982 JBC 257(19):11584-11590 binding consts. All are scaled by 3X to cell temperature. kf = 2e-10 kb = 72 Stemmer & Klee 1994 Biochem 33:6859-6866 have values of : K1=.9, K2=1.1. Assume 1.0uM for both
    9
  • CaM-TR2-Ca2-bind
    -Ca
  • Synaptic_
    Network
    Accession No. : 16
    		• CaM
    Pathway No. : 81    		3.6
    (uM^-1 s^-1)    		10
    (s^-1)    		Kd(bf) = 2.7778(uM)-Substrate
    Ca
    CaM-TR2-Ca2

    Product
    CaM-Ca3
      Stemmer and Klee 1994 Biochem 33:6859-6866 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
  • Synaptic_
    Network
    Accession No. : 16
    		• CaM
    Pathway No. : 81    		0.465
    (uM^-1 s^-1)    		10
    (s^-1)    		Kd(bf) = 21.5054(uM)-Substrate
    Ca
    CaM-Ca3

    Product
    CaM-Ca4
      Use K3 = 21.5 uM here from Stemmer and Klee table 3. Stemmer and Klee 1994 Biochem 33:6859-6866 kb/kf =21.5 * 6e5 so kf = 7.75e-7, kb = 10
    11
  • Ca-bind-CaNAB-Ca
    2
  • Synaptic_
    Network
    Accession No. : 16
    		• PP2B
    Pathway No. : 83    		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 1994 Biochem 33:6859-6866, this specific parm on pg 6863, the Kact is 0.5 uM. Assume binding is fast, 1 sec.
    12Ca-bind-CaNAB
  • Synaptic_
    Network
    Accession No. : 16
    		• PP2B
    Pathway No. : 83    		10008
    (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. This doesn't really matter much because it will always be bound at physiological Ca.