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Molecule Parameter List for APC

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
APC participated asMoleculeSum total ofEnzymeSubstrate of an enzymeProduct of an enzymeSubstrate in ReactionProduct in Reaction
No. of occurrences1005001

Accession and Pathway Details
Accession NameAccession No.Accession TypePathway Link
  • Ajay_Bhalla_
    2004_PKM_MKP3_
    Tuning
  • 77Network
    Shared_Object_Ajay_Bhalla_2004_PKM_MKP3_Tuning PKC PLA2 
    PLCbeta Ras Gq 
    MAPK EGFR Sos 
    PLC_g CaMKII CaM 
    PP1 PP2B PKA 
    AC MKP3 PKM 
    This model is based on Ajay SM, Bhalla US. Eur J Neurosci. 2004 Nov;20(10):2671-80. This is the feedforward model with MPK3 from figure 8a.

    APC acting as a Molecule in  
    Ajay_Bhalla_2004_PKM_MKP3_Tuning Network
    NameAccession NamePathway NameInitial Conc.
    (uM)
    Volume
    (fL)
    Buffered
    APC
  • Ajay_Bhalla_
    2004_PKM_MKP3_
    Tuning

    Accession No. : 77
  • PLA2
    Pathway No. : 331
    301.5Yes
    arachodonylphosphatidylcholine is the favoured substrate from Wijkander and Sundler, JBC 202 pp 873-880, 1991. Their assay used 30 uM substrate, which is what the kinetics in this model are based on. For the later model we should locate a more realistic value for APC.

    APC acting as a Substrate for an Enzyme in  
    Ajay_Bhalla_2004_PKM_MKP3_Tuning Network
     Enzyme Molecule /
    Enzyme Activity
    Accession NamePathway NameKm (uM)kcat (s^-1)RatioEnzyme TypeReagents
    1PLA2-Ca*  /
    kenz
  • Ajay_Bhalla_
    2004_PKM_MKP3_
    Tuning

    Accession No. : 77
  • PLA2
    Pathway No. : 331
    205.44explicit E-S complexSubstrate
    APC

    Product
    AA
        10 x raise oct22 12 x oct 24, set k2 = 4 * k3
    2PIP2-PLA2*  /
    kenz
  • Ajay_Bhalla_
    2004_PKM_MKP3_
    Tuning

    Accession No. : 77
  • PLA2
    Pathway No. : 331
    19.999811.044explicit E-S complexSubstrate
    APC

    Product
    AA
        10 X raise oct 22 12 X further raise oct 24 to allow for correct conc of enzyme
    3PIP2-Ca-PLA2*  /
    kenz
  • Ajay_Bhalla_
    2004_PKM_MKP3_
    Tuning

    Accession No. : 77
  • PLA2
    Pathway No. : 331
    20364explicit E-S complexSubstrate
    APC

    Product
    AA
        10 x raise oct 22 12 x and rescale for k2 = 4 * k3 convention oct 24 Increase further to get the match to expt, which was spoilt due to large accumulation of PLA2 in the enzyme complexed forms. Lets raise k3, leaving the others at k1 = 1.5e-5 and k2 = 144 since they are large already.
    4DAG-Ca-PLA2*  /
    kenz
  • Ajay_Bhalla_
    2004_PKM_MKP3_
    Tuning

    Accession No. : 77
  • PLA2
    Pathway No. : 331
    19.9996604explicit E-S complexSubstrate
    APC

    Product
    AA
        10 X raise oct 22 12 X raise oct 24 + conversion to k2 =4 * k3
    5PLA2*-Ca  /
    kenz
  • Ajay_Bhalla_
    2004_PKM_MKP3_
    Tuning

    Accession No. : 77
  • PLA2
    Pathway No. : 331
    20.00021204explicit E-S complexSubstrate
    APC

    Product
    AA
        This form should be 3 to 6 times as fast as the Ca-only form. I have scaled by 4x which seems to give a 5x rise. 10x raise Oct 22 12 x oct 24, changed k2 = 4 * k3

    APC acting as a Product in a reaction in  
    Ajay_Bhalla_2004_PKM_MKP3_Tuning 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
    Degrade-AA
  • Ajay_Bhalla_
    2004_PKM_MKP3_
    Tuning

    Accession No. : 77
  • PLA2
    Pathway No. : 331
    0.4
    (s^-1)
    0
    (s^-1)
    --Substrate
    AA

    Product
    APC
    I need to check if the AA degradation pathway really leads back to APC. Anyway, it is a convenient buffered pool to dump it back into. For the purposes of the full model we use a rate of degradation of 0.2/sec Raised decay to 0.4 : see PLA35.g notes for Feb17



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