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Molecule Parameter List for GAP

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
GAP participated asMoleculeSum total ofEnzymeSubstrate of an enzymeProduct of an enzymeSubstrate in ReactionProduct in Reaction
No. of occurrences1011001

Accession and Pathway Details
Accession NameAccession No.Accession TypePathway Link
  • MAPK-bistability
    -fig1c
  • 35Network
    Shared_Object_MAPK-bistability-fig1c Sos PKC 
    MAPK PLA2 Ras 
    PDGFR 
    Model for figure 1c in Bhalla US et al. Science (2002) 297(5583):1018-23.
    The demo for this figure is available here. This synaptic signaling model is without the MKP-1 feedback, so it is bistable and remains so over long periods.

    GAP acting as a Molecule in  
    MAPK-bistability-fig1c Network
    NameAccession NamePathway NameInitial Conc.
    (uM)
    Volume
    (fL)
    Buffered
    GAP
  • MAPK-bistability
    -fig1c

    Accession No. : 35
  • Ras
    Pathway No. : 184
    0.0021000No
    GTPase-activating proteins. See Boguski and McCormick 1993 Nature 366:643-654 Turn off Ras by helping to hydrolyze bound GTP. This one is probably NF1, ie., Neurofibromin as it is inhibited by AA and lipids, and expressed in neural cells. p120-GAP is also a possible candidate, but is less regulated. Both may exist at similar levels. See Eccleston et al JBC 268(36) pp27012-19 Level=.002

    GAP acting as an Enzyme in  
    MAPK-bistability-fig1c Network
    Enzyme Molecule /
    Enzyme Activity
    Accession NamePathway NameKm (uM)kcat (s^-1)RatioEnzyme TypeReagents
    GAP /
    GAP-inact-ras
  • MAPK-bistability
    -fig1c

    Accession No. : 35
  • Ras
    Pathway No. : 184
    1.010410100explicit E-S complexSubstrate
    GTP-Ras

    Product
    GDP-Ras
    From Eccleston et al JBC 268(36)pp27012-19 get Kd < 2uM, kcat - 10/sec From Martin et al Cell 63 843-849 1990 get Kd ~ 250 nM, kcat = 20/min I will go with the Eccleston figures as there are good error bars (10%). The two sets of values are reasonably close. k1 = 1.666e-3/sec, k2 = 1000/sec, k3 = 10/sec (note k3 is rate-limiting) This is one of the rare cases where we have direct info on the k3 being rate-limiting. Hence the ratio I use for the k2:k3 rates is 100 rather than the usual 4.

    GAP acting as a Substrate for an Enzyme in  
    MAPK-bistability-fig1c Network
    Enzyme Molecule /
    Enzyme Activity
    Accession NamePathway NameKm (uM)kcat (s^-1)RatioEnzyme TypeReagents
    PKC-active  /
    PKC-inact-GAP
  • MAPK-bistability
    -fig1c

    Accession No. : 35
  • Shared_Object_
    MAPK-bistability
    -fig1c

    Pathway No. : 179
  • 66.6667254explicit E-S complexSubstrate
    GAP

    Product
    GAP*
    Rate consts are PKC generic rates. This reaction inactivates GAP. The reaction is from the Boguski and McCormick 1993 review in Nature 366:643-654 The phosphorylation Vmax is 6x higher to account for balance of GDP-Ras:GDP-Ras.

    GAP acting as a Product in a reaction in  
    MAPK-bistability-fig1c 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
    dephosph-GAP
  • MAPK-bistability
    -fig1c

    Accession No. : 35
  • Ras
    Pathway No. : 184
    0.1
    (s^-1)
    0
    (s^-1)
    --Substrate
    GAP*

    Product
    GAP
    Assume a reasonably good rate for dephosphorylating it, 0.1/sec. This fits well with resting levels of active kinase and the degree of activation as well as time-course of turnoff of Ras activation, but data is quite indirect.



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