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Molecule Parameter List for PKA-active

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
PKA-active participated asMoleculeSum total ofEnzymeSubstrate of an enzymeProduct of an enzymeSubstrate in ReactionProduct in Reaction
No. of occurrences1030012

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.

PKA-active acting as a Molecule in  
CaMKII_model3 Network
NameAccession NamePathway NameInitial Conc.
(uM)
Volume
(fL)
Buffered
PKA-activeCaMKII_model3
Accession No. : 63
  • Shared_Object_
    CaMKII_model3

    Pathway No. : 263
  • 00.09No

    PKA-active acting as an Enzyme in  
    CaMKII_model3 Network
     Enzyme Molecule /
    Enzyme Activity
    Accession NamePathway NameKm (uM)kcat (s^-1)RatioEnzyme TypeReagents
    1PKA-active /
    PKA-phosph-I1
    CaMKII_model3
    Accession No. : 63
  • Shared_Object_
    CaMKII_model3

    Pathway No. : 263
  • 7.5000894explicit E-S complexSubstrate
    I1

    Product
    I1*
        #s from Bramson et al CRC crit rev Biochem 15:2 93-124. They have a huge list of peptide substrates and I have chosen high-ish rates. These consts give too much PKA activity, so lower Vmax 1/3. Now, k1 = 3e-5, k2 = 36, k3 = 9 (still pretty fast). Also lower Km 1/3 so k1 = 1e-5 Cohen et al FEBS Lett 76:182-86 1977 say rate =30% PKA act on phosphokinase beta.
    2PKA-active /
  • PKA-phosph-I1_
    PSD
  • CaMKII_model3
    Accession No. : 63
  • Shared_Object_
    CaMKII_model3

    Pathway No. : 263
  • 7.5000894explicit E-S complexSubstrate
    I1

    Product
    I1*
    3PKA-active /
    phosph-PDE
    CaMKII_model3
    Accession No. : 63
  • Shared_Object_
    CaMKII_model3

    Pathway No. : 263
  • 7.5000894explicit E-S complexSubstrate
    cAMP-PDE

    Product
    cAMP-PDE*
        Same rates as PKA-phosph-I1

    PKA-active 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
    inhib-PKACaMKII_model3
    Accession No. : 63
    PKA
    Pathway No. : 270
    59.9994
    (uM^-1 s^-1)
    1
    (s^-1)
    Kd(bf) = 0.0167(uM)-Substrate
    PKA-active
    PKA-inhibitor

    Product
    inhibited-PKA
    This has to be set to zero for matching the expts in vitro. In vivo we need to consider the inhibition though. kf = 1e-5 kb = 1

    PKA-active 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
    1Release-C1CaMKII_model3
    Accession No. : 63
    PKA
    Pathway No. : 270
    60
    (s^-1)
    17.9998
    (uM^-1 s^-1)
    Kd(cb) = 0.3(uM)-Substrate
    R2C2-cAMP4

    Product
    PKA-active
    R2C-cAMP4
      This has to be fast, as the activation of PKA by cAMP is also fast. kf was 10
    2Release-C2CaMKII_model3
    Accession No. : 63
    PKA
    Pathway No. : 270
    60
    (s^-1)
    17.9998
    (uM^-1 s^-1)
    Kd(cb) = 0.3(uM)-Substrate
    R2C-cAMP4

    Product
    PKA-active
    R2-cAMP4



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