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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_traff_
    model1
  • 60Network
    Shared_Object_AMPAR_traff_model1 CaMKII CaM 
    PP1 PP2B PP1_PSD 
    PKA AC AMPAR 
    AMPAR_memb 
    This is the basic model of AMPAR trafficking bistability. It is based on Hayer and Bhalla, PLoS Comput. Biol. 2005. It includes the degradation and turnover of AMPARs. The CaMKII portion of the model is not bistable.

    Ca-PSD acting as a Molecule in  
    AMPAR_traff_model1 Network
    NameAccession NamePathway NameInitial Conc.
    (uM)
    Volume
    (fL)
    Buffered
    Ca-PSD
  • AMPAR_traff_
    model1

    Accession No. : 60
  • Shared_Object_
    AMPAR_traff_
    model1

    Pathway No. : 244
  • 0.080.01No

    Ca-PSD acting as a Substrate in a reaction in  
    AMPAR_traff_model1 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_traff_
    model1

    Accession No. : 60
  • CaM
    Pathway No. : 246
    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_traff_
    model1

    Accession No. : 60
  • CaM
    Pathway No. : 246
    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_traff_
    model1

    Accession No. : 60
  • CaM
    Pathway No. : 246
    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_traff_model1 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_traff_
    model1

    Accession No. : 60
  • Shared_Object_
    AMPAR_traff_
    model1

    Pathway No. : 244
  • 100
    (s^-1)
    100
    (s^-1)
    Keq = 1(uM)0.005secSubstrate
    Ca_control_PSD

    Product
    Ca-PSD



    Database compilation and code copyright (C) 2022, Upinder S. Bhalla and NCBS/TIFR
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