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Molecule Parameter List for AA

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
AA participated asMoleculeSum total ofEnzymeSubstrate of an enzymeProduct of an enzymeSubstrate in ReactionProduct in Reaction
No. of occurrences1000540

Accession and Pathway Details
Accession NameAccession No.Accession TypePathway Link
  • Ajay_Bhalla_
    2004_Feedback_
    Tuning
  • 78Network
    Shared_Object_Ajay_Bhalla_2004_Feedback_Tuning PKC PLA2 
    PLCbeta Gq MAPK 
    Ras EGFR Sos 
    PLC_g CaMKII CaM 
    PP1 PP2B PKA 
    AC 
    This model is taken from Ajay SM, Bhalla US. Eur J Neurosci. 2004 Nov;20(10):2671-80. This is the feedback model from Figure 8a.

    AA acting as a Molecule in  
    Ajay_Bhalla_2004_Feedback_Tuning Network
    NameAccession NamePathway NameInitial Conc.
    (uM)
    Volume
    (fL)
    Buffered
    AA
  • Ajay_Bhalla_
    2004_Feedback_
    Tuning

    Accession No. : 78
  • Shared_Object_
    Ajay_Bhalla_
    2004_Feedback_
    Tuning

    Pathway No. : 347
  • 01.5No

    AA acting as a Product of an Enzyme in  
    Ajay_Bhalla_2004_Feedback_Tuning Network
     Enzyme Molecule /
    Enzyme Activity
    Accession NamePathway NameKm (uM)kcat (s^-1)RatioEnzyme TypeReagents
    1PLA2-Ca*  /
    kenz
  • Ajay_Bhalla_
    2004_Feedback_
    Tuning

    Accession No. : 78
  • PLA2
    Pathway No. : 349
    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_Feedback_
    Tuning

    Accession No. : 78
  • PLA2
    Pathway No. : 349
    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_Feedback_
    Tuning

    Accession No. : 78
  • PLA2
    Pathway No. : 349
    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_Feedback_
    Tuning

    Accession No. : 78
  • PLA2
    Pathway No. : 349
    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_Feedback_
    Tuning

    Accession No. : 78
  • PLA2
    Pathway No. : 349
    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

    AA acting as a Substrate in a reaction in  
    Ajay_Bhalla_2004_Feedback_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
    1
  • PKC-act-by-Ca-AA
  • Ajay_Bhalla_
    2004_Feedback_
    Tuning

    Accession No. : 78
  • PKC
    Pathway No. : 348
    0.0012
    (uM^-1 s^-1)
    0.1
    (s^-1)
    Kd(bf) = 83.3354(uM)-Substrate
    AA
    PKC-Ca

    Product
    PKC-Ca-AA*
      Schaechter and Benowitz We have to increase Kf for conc scaling Changed kf to 2e-9 on Sept 19, 94. This gives better match.
    2PKC-act-by-AA
  • Ajay_Bhalla_
    2004_Feedback_
    Tuning

    Accession No. : 78
  • PKC
    Pathway No. : 348
    0.0001
    (uM^-1 s^-1)
    0.1
    (s^-1)
    Kd(bf) = 833.3542(uM)-Substrate
    AA
    PKC-cytosolic

    Product
    PKC-AA*
      Raise kf from 1.667e-10 to 2e-10 to get better match to data.
    3PKC-n-DAG-AA
  • Ajay_Bhalla_
    2004_Feedback_
    Tuning

    Accession No. : 78
  • PKC
    Pathway No. : 348
    0.018
    (uM^-1 s^-1)
    2
    (s^-1)
    Kd(bf) = 111.1111(uM)-Substrate
    AA
    PKC-DAG

    Product
    PKC-DAG-AA
      Reduced kf to 0.66X to match Shinomura et al data. Initial: kf = 3.3333e-9 New: 2e-9 Newer: 2e-8 kb was 0.2 now 2.
    4Degrade-AA
  • Ajay_Bhalla_
    2004_Feedback_
    Tuning

    Accession No. : 78
  • PLA2
    Pathway No. : 349
    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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