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Molecule Parameter List for Ca-PSD

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-PSD participated asMoleculeSum total ofEnzymeSubstrate of an enzymeProduct of an enzymeSubstrate in ReactionProduct in Reaction
No. of occurrences1000031

Accession and Pathway Details
Accession NameAccession No.Accession TypePathway Link
  • AMPAR_CaMKII_
    strong_coupling
  • 64Network
    Shared_Object_AMPAR_CaMKII_strong_coupling CaMKII CaM 
    PP1 AMPAR_memb PP2B 
    PKA AC PP1_PSD 
    AMPAR 
    This is a model of tight coupling between the AMPAR trafficking bistability, and the CaMKII autophosphorylation bistability. In this model, the CaMKII activity is self sustaining only when AMPAR is turned on. Further, CaMKII turns on when AMPAR is turned on.

    Ca-PSD acting as a Molecule in  
    AMPAR_CaMKII_strong_coupling Network
    NameAccession NamePathway NameInitial Conc.
    (uM)
    Volume
    (fL)
    Buffered
    Ca-PSD
  • AMPAR_CaMKII_
    strong_coupling

    Accession No. : 64
  • Shared_Object_
    AMPAR_CaMKII_
    strong_coupling

    Pathway No. : 271
  • 0.080.01No

    Ca-PSD acting as a Substrate in a reaction in  
    AMPAR_CaMKII_strong_coupling 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
    1
  • CaM-TR2-bind-Ca-
    PSD
  • AMPAR_CaMKII_
    strong_coupling

    Accession No. : 64
  • CaM
    Pathway No. : 273
    72
    (uM^-2 s^-1)
    72
    (s^-1)
    Kd(af) = 1(uM)-Substrate
    Ca-PSD
    Ca-PSD
    CaM-PSD

    Product
    CaM-TR2-Ca2-PSD
      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 !)....
    2
  • CaM-TR2-Ca2-bind
    -Ca-PSD
  • AMPAR_CaMKII_
    strong_coupling

    Accession No. : 64
  • CaM
    Pathway No. : 273
    3.6
    (uM^-1 s^-1)
    10
    (s^-1)
    Kd(bf) = 2.7778(uM)-Substrate
    Ca-PSD
    CaM-TR2-Ca2-PSD

    Product
    CaM-Ca3-PSD
      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
    3
  • CaM-Ca3-bind-Ca-
    PSD
  • AMPAR_CaMKII_
    strong_coupling

    Accession No. : 64
  • CaM
    Pathway No. : 273
    0.465
    (uM^-1 s^-1)
    10
    (s^-1)
    Kd(bf) = 21.5048(uM)-Substrate
    Ca-PSD
    CaM-Ca3-PSD

    Product
    CaM-Ca4-PSD
      Use K3 = 21.5 uM here from Stemmer and Klee table 3. kb/kf =21.5 * 6e5 so kf = 7.75e-7, kb = 10

    Ca-PSD acting as a Product in a reaction in  
    AMPAR_CaMKII_strong_coupling 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_PSD
  • AMPAR_CaMKII_
    strong_coupling

    Accession No. : 64
  • Shared_Object_
    AMPAR_CaMKII_
    strong_coupling

    Pathway No. : 271
  • 100
    (s^-1)
    100
    (s^-1)
    Keq = 1(uM)0.005secSubstrate
    Ca_control_PSD

    Product
    Ca-PSD



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