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Molecule Parameter List for GTP-Ras

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
GTP-Ras participated asMoleculeSum total ofEnzymeSubstrate of an enzymeProduct of an enzymeSubstrate in ReactionProduct in Reaction
No. of occurrences1001230

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.

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

    Accession No. : 35
  • Ras
    Pathway No. : 184
    01000No
    Only a very small fraction (7% unstim, 15% stim) of ras is GTP-bound. Gibbs et al JBC 265(33) 20437

    GTP-Ras 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
    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.

    GTP-Ras acting as a Product of an Enzyme in  
    MAPK-bistability-fig1c Network
     Enzyme Molecule /
    Enzyme Activity
    Accession NamePathway NameKm (uM)kcat (s^-1)RatioEnzyme TypeReagents
    1Shc*.Sos.Grb2  /
    Sos.Ras_GEF
  • MAPK-bistability
    -fig1c

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

    Pathway No. : 179
  • 0.5050510.024explicit E-S complexSubstrate
    GDP-Ras

    Product
    GTP-Ras
        Rates from Orita et al JBC 268(34):25542-25546
    2GEF*  /
    GEF*-act-ras
  • MAPK-bistability
    -fig1c

    Accession No. : 35
  • Ras
    Pathway No. : 184
    0.5050510.024explicit E-S complexSubstrate
    GDP-Ras

    Product
    GTP-Ras
        Kinetics from Orita et al JBC 268(34):25542-25546. Note that the Vmax is slow, but it does match the slow GTP hydrolysis rates.

    GTP-Ras acting as a Substrate 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
    1
  • Ras-intrinsic-GT
    Pase
  • MAPK-bistability
    -fig1c

    Accession No. : 35
  • Ras
    Pathway No. : 184
    0.0001
    (s^-1)
    0
    (s^-1)
    --Substrate
    GTP-Ras

    Product
    GDP-Ras
      This is extremely slow (kf = 1e-4), but it is significant as so little GAP actually gets complexed with it that the total GTP turnover rises only by 2-3 X (see Gibbs et al, JBC 265(33) 20437-20422) and Eccleston et al JBC 268(36) 27012-27019 There is no back reaction as we assume this to be a regular irreversible Michaelis-Menten zeroth order hydrolysis.
    2Ras-act-craf
  • MAPK-bistability
    -fig1c

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

    Pathway No. : 179
  • 60
    (uM^-1 s^-1)
    0.5
    (s^-1)
    Kd(bf) = 0.0083(uM)-Substrate
    GTP-Ras
    craf-1*

    Product
    Raf*-GTP-Ras
      Assume binding is fast and limited only by available Ras*. So kf = kb/[craf-1] If kb is 1/sec, then kf = 1/0.2 uM = 1/(0.2 * 6e5) = 8.3e-6 Later: Raise it by 10 X to about 1e-4, giving a Kf of 60 for Kb of 0.5 and a tau of approx 2 sec. Based on: Hallberg et al JBC 269:6 3913-3916 1994, 3% of cellular Raf is complexed with Ras. This step needed to memb-anchor and activate Raf: Leevers et al Nature 369 411-414. Also see Koide et al 1993 PNAS USA 90(18):8683-8686
    3
  • Ras-act-unphosph
    -raf
  • MAPK-bistability
    -fig1c

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

    Pathway No. : 179
  • 6
    (uM^-1 s^-1)
    1
    (s^-1)
    Kd(bf) = 0.1667(uM)-Substrate
    GTP-Ras
    craf-1

    Product
    RGR
      Based on rates of Ras-act-craf which has Kf=60, Kb= 0.5. This reaction was introduced to account for the PKC-independent activation of MAPK. This reac should have less affinity but similar tau as compared to the Ras-cat-craf, since the phosphorylated Raf form has a greater effect on MAPK.



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