NCBS Home page
Accession List
Pathway List
Search
Authorized Users
Help
News archives

Enter a Search String

Special character and space not allowed in the query term. Search string should be at least 2 characters long.
Search in: Search for Match By

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
3d_fold_model8Network
Shared_Object_3d_fold_model PKC MAPK 
PLA2 Ras 
This model is an annotated version of the synaptic signaling network.
The primary reference is Bhalla US and Iyengar R. Science (1999) 283(5400):381-7 but several of the model pathways have been updated Bhalla US, Ram PT, Iyengar R. Science. 2002 Aug 9;297(5583):1018-23.

AA acting as a Molecule in  
3d_fold_model Network
NameAccession NamePathway NameInitial Conc.
(uM)
Volume
(fL)
Buffered
AA3d_fold_model
Accession No. : 8
  • Shared_Object_
    3d_fold_model

    Pathway No. : 54
  • 01000No

    AA acting as a Product of an Enzyme in  
    3d_fold_model Network
     Enzyme Molecule /
    Enzyme Activity
    Accession NamePathway NameKm (uM)kcat (s^-1)RatioEnzyme TypeReagents
    1PLA2-Ca*  /
    kenz
    3d_fold_model
    Accession No. : 8
    PLA2
    Pathway No. : 57
    205.44explicit E-S complexSubstrate
    APC

    Product
    AA
        10 x raise oct22 12 x oct 24, set k2 = 4 * k3
    2PIP2-PLA2*  /
    kenz
    3d_fold_model
    Accession No. : 8
    PLA2
    Pathway No. : 57
    2011.044explicit 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
    3d_fold_model
    Accession No. : 8
    PLA2
    Pathway No. : 57
    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
    3d_fold_model
    Accession No. : 8
    PLA2
    Pathway No. : 57
    20604explicit E-S complexSubstrate
    APC

    Product
    AA
        10 X raise oct 22 12 X raise oct 24 + conversion to k2 =4 * k3
    5PLA2*-Ca  /
    kenz
    3d_fold_model
    Accession No. : 8
    PLA2
    Pathway No. : 57
    201204explicit 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  
    3d_fold_model 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
  • 3d_fold_model
    Accession No. : 8
    PKC
    Pathway No. : 55
    0.0012
    (uM^-1 s^-1)
    0.1
    (s^-1)
    Kd(bf) = 83.3333(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-AA3d_fold_model
    Accession No. : 8
    PKC
    Pathway No. : 55
    0.0001
    (uM^-1 s^-1)
    0.1
    (s^-1)
    Kd(bf) = 833.3333(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-AA3d_fold_model
    Accession No. : 8
    PKC
    Pathway No. : 55
    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-AA3d_fold_model
    Accession No. : 8
    PLA2
    Pathway No. : 57
    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
    This Copyright is applied to ensure that the contents of this database remain freely available. Please see FAQ for details.