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Molecule Parameter List for CaM-Ca3-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-Ca3-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
CaMKII_model363Network
Shared_Object_CaMKII_model3 CaMKII CaM 
PP1 PP2B PP1_PSD 
AC PKA 
This is the complete model of CaMKII bistability, model 3. It exhibits bistability in CaMKII activation due to autophosphorylation at the PSD and local saturation of PP1. This version of model 3 includes PKA regulatory input. This has little effect on the deterministic calculations, but the PKA pathway introduces a lot of noise which causes a difference in stochastic runs.

CaM-Ca3-PSD acting as a Molecule in  
CaMKII_model3 Network
NameAccession NamePathway NameInitial Conc.
(uM)
Volume
(fL)
Buffered
CaM-Ca3-PSDCaMKII_model3
Accession No. : 63
  • Shared_Object_
    CaMKII_model3

    Pathway No. : 263
  • 0.00250.01No

    CaM-Ca3-PSD acting as a Substrate in a reaction in  
    CaMKII_model3 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-
    PSD
  • CaMKII_model3
    Accession No. : 63
    CaM
    Pathway No. : 265
    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

    CaM-Ca3-PSD acting as a Product in a reaction in  
    CaMKII_model3 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
  • CaMKII_model3
    Accession No. : 63
    CaM
    Pathway No. : 265
    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



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