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Molecule Parameter List for CaM-TR2-Ca2-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
CaM-TR2-Ca2-PSD participated asMoleculeSum total ofEnzymeSubstrate of an enzymeProduct of an enzymeSubstrate in ReactionProduct in Reaction
No. of occurrences1000011

Accession and Pathway Details
Accession NameAccession No.Accession TypePathway Link
  • AMPAR_traff_
    model0
  • 59Network
    Shared_Object_AMPAR_traff_model0 CaMKII CaM 
    PP1 PP2B PP1_PSD 
    PKA AC AMPAR 
    AMPAR_memb 
    This is model 0 from Hayer and Bhalla, PLoS Comput Biol 2005. It has a bistable model of AMPAR traffick, plus a non-bistable model of CaMKII. This differs from the reference model (model 1) in that model0 lacks degradation and turno ver reactions for AMPAR.

    CaM-TR2-Ca2-PSD acting as a Molecule in  
    AMPAR_traff_model0 Network
    NameAccession NamePathway NameInitial Conc.
    (uM)
    Volume
    (fL)
    Buffered
    CaM-TR2-Ca2-PSD
  • AMPAR_traff_
    model0

    Accession No. : 59
  • CaM
    Pathway No. : 236
    00.01No
    This is the intermediate where the TR2 end (the high-affinity end) has bound the Ca but the TR1 end has not.

    CaM-TR2-Ca2-PSD acting as a Substrate in a reaction in  
    AMPAR_traff_model0 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-TR2-Ca2-bind
    -Ca-PSD
  • AMPAR_traff_
    model0

    Accession No. : 59
  • CaM
    Pathway No. : 236
    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

    CaM-TR2-Ca2-PSD acting as a Product in a reaction in  
    AMPAR_traff_model0 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-TR2-bind-Ca-
    PSD
  • AMPAR_traff_
    model0

    Accession No. : 59
  • CaM
    Pathway No. : 236
    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 !)....



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