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Molecule Parameter List for CaM-Ca4

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
CaM-Ca4 participated asMoleculeSum total ofEnzymeSubstrate of an enzymeProduct of an enzymeSubstrate in ReactionProduct in Reaction
No. of occurrences1000061

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.

    CaM-Ca4 acting as a Molecule in  
    Ajay_Bhalla_2004_PKM_Tuning Network
    NameAccession NamePathway NameInitial Conc.
    (uM)
    Volume
    (fL)
    Buffered
    CaM-Ca4
  • Ajay_Bhalla_
    2004_PKM_Tuning

    Accession No. : 76
  • Shared_Object_
    Ajay_Bhalla_
    2004_PKM_tuning

    Pathway No. : 312
  • 01.5No

    CaM-Ca4 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
    1CaM-bind-GEF
  • Ajay_Bhalla_
    2004_PKM_Tuning

    Accession No. : 76
  • Ras
    Pathway No. : 318
    199.998
    (uM^-1 s^-1)
    1
    (s^-1)
    Kd(bf) = 0.005(uM)-Substrate
    CaM-Ca4
    inact-GEF

    Product
    CaM-GEF
      We have no numbers for this. It is probably between the two extremes represented by the CaMKII phosph states, and I have used guesses based on this. kf=1e-4 kb=1 The reaction is based on Farnsworth et al Nature 376 524-527 1995
    2CaMKII-bind-CaM
  • Ajay_Bhalla_
    2004_PKM_Tuning

    Accession No. : 76
  • CaMKII
    Pathway No. : 322
    49.9995
    (uM^-1 s^-1)
    5
    (s^-1)
    Kd(bf) = 0.1(uM)-Substrate
    CaM-Ca4
    CaMKII

    Product
    CaMKII-CaM
      This is tricky. There is some cooperativity here arising from interactions between the subunits of the CAMKII holoenzyme. However, the stoichiometry is 1. Kb/Kf = 6e4 #/cell. Rate is fast (see Hanson et al Neuron 12 943-956 1994) so lets say kb = 10. This gives kf = 1.6667e-4 H&S AnnRev Biochem 92 give tau for dissoc as 0.2 sec at low Ca, 0.4 at high. Low Ca = 100 nM = physiol.
    3
  • CaMK-thr286-bind
    -CaM
  • Ajay_Bhalla_
    2004_PKM_Tuning

    Accession No. : 76
  • CaMKII
    Pathway No. : 322
    1000.17
    (uM^-1 s^-1)
    0.1
    (s^-1)
    Kd(bf) = 0.0001(uM)-Substrate
    CaM-Ca4
    CaMKII-thr286

    Product
  • CaMKII-thr286*-C
    aM

  •   Affinity is up 1000X. Time to release is about 20 sec, so the kb is OK at 0.1 This makes Kf around 1.6666e-3
    4
  • CaMCa4-bind-CaNA
    B
  • Ajay_Bhalla_
    2004_PKM_Tuning

    Accession No. : 76
  • PP2B
    Pathway No. : 325
    600.003
    (uM^-1 s^-1)
    1
    (s^-1)
    Kd(bf) = 0.0017(uM)-Substrate
    CaM-Ca4
    CaNAB-Ca4

    Product
    CaMCa4-CaNAB
    5CaM-bind-AC1
  • Ajay_Bhalla_
    2004_PKM_Tuning

    Accession No. : 76
  • AC
    Pathway No. : 327
    49.9995
    (uM^-1 s^-1)
    1
    (s^-1)
    Kd(bf) = 0.02(uM)-Substrate
    AC1
    CaM-Ca4

    Product
    AC1-CaM
      Half-max at 20 nM CaM (Tang et al JBC 266:13 8595-8603 1991 kb/kf = 20 nM = 12000 #/cell so kf = kb/12000 = kb * 8.333e-5
    6CaM_bind_PDE1
  • Ajay_Bhalla_
    2004_PKM_Tuning

    Accession No. : 76
  • AC
    Pathway No. : 327
    720
    (uM^-1 s^-1)
    5
    (s^-1)
    Kd(bf) = 0.0069(uM)-Substrate
    CaM-Ca4
    PDE1

    Product
    CaM.PDE1
      For olf epi PDE1, affinity is 7 nM. Assume same for brain. Reaction should be pretty fast. Assume kb = 5/sec. Then kf = 5 / (0.007 * 6e5) = 1.2e-3

    CaM-Ca4 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
    CaM-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



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