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Molecule Parameter List for CaM-Ca4-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-Ca4-PSD participated asMoleculeSum total ofEnzymeSubstrate of an enzymeProduct of an enzymeSubstrate in ReactionProduct in Reaction
No. of occurrences1000032

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-Ca4-PSD acting as a Molecule in  
CaMKII_model3 Network
NameAccession NamePathway NameInitial Conc.
(uM)
Volume
(fL)
Buffered
CaM-Ca4-PSDCaMKII_model3
Accession No. : 63
  • Shared_Object_
    CaMKII_model3

    Pathway No. : 263
  • 00.01No

    CaM-Ca4-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
    1
  • CaMKII-bind-CaM-
    PSD
  • CaMKII_model3
    Accession No. : 63
  • Shared_Object_
    CaMKII_model3

    Pathway No. : 263
  • 49.9998
    (uM^-1 s^-1)
    0
    (s^-1)
    --Substrate
    CaM-Ca4-PSD
    CaMKII-PSD

    Product
    CaMKII-CaM-PSD
    2
  • CaMKII-thr286-bi
    nd-CaM-PSD
  • CaMKII_model3
    Accession No. : 63
  • Shared_Object_
    CaMKII_model3

    Pathway No. : 263
  • 1000.02
    (uM^-1 s^-1)
    0.1
    (s^-1)
    Kd(bf) = 0.0001(uM)-Substrate
    CaM-Ca4-PSD
  • CaMKII-thr286-PS
    D


    Product
  • CaMKII-thr286-Ca
    M-PSD

  •   Same values as for the main compartment Can the main compartment pool of Ca/CaM be used?
    3equilibCaMKII_model3
    Accession No. : 63
  • Shared_Object_
    CaMKII_model3

    Pathway No. : 263
  • 540
    (s^-1)
    60
    (s^-1)
    Not applicable**-Substrate
    CaM-Ca4-PSD

    Product
    CaM-Ca4
      Diffusional equilibrium between PSD- and cytosolic compartment. According to D. Bary in Cell Movements 2nd ed 2001 D for proteins is 5e-7 cm^2/s giving 10 ms for a translocation of 1 um.
    ** This is a trasport reation between compartments of different volumes. Therefore Kd is not applicable. Please Note Kf, Kb units are in number of molecules instead of concentration

    CaM-Ca4-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
    1
  • 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
    2CaMKII-diss-CaMCaMKII_model3
    Accession No. : 63
  • Shared_Object_
    CaMKII_model3

    Pathway No. : 263
  • 5
    (s^-1)
    0
    (uM^-1 s^-1)
    --Substrate
    CaMKII-CaM-PSD

    Product
    CaM-Ca4-PSD
    CaMKII-PSD



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