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Molecule Parameter List for GEF-Gprot-bg

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
GEF-Gprot-bg participated asMoleculeSum total ofEnzymeSubstrate of an enzymeProduct of an enzymeSubstrate in ReactionProduct in Reaction
No. of occurrences1010001

Accession and Pathway Details
Accession NameAccession No.Accession TypePathway Link
  • Ajay_Bhalla_
    2004_PKM_Tuning
  • 76Network
    PKC Shared_Object_Ajay_Bhalla_2004_PKM_tuning PLA2 
    PLCbeta Gq MAPK 
    Ras EGFR Sos 
    PLC_g CaMKII CaM 
    PP1 PP2B PKA 
    AC PKM 
    This model is taken from the Ajay SM, Bhalla US. Eur J Neurosci. 2004 Nov;20(10):2671-80. This is the reference feedforward model from Figure 8a.

    GEF-Gprot-bg acting as a Molecule in  
    Ajay_Bhalla_2004_PKM_Tuning Network
    NameAccession NamePathway NameInitial Conc.
    (uM)
    Volume
    (fL)
    Buffered
    GEF-Gprot-bg
  • Ajay_Bhalla_
    2004_PKM_Tuning

    Accession No. : 76
  • Ras
    Pathway No. : 318
    01.5No
    Guanine nucleotide exchange factor. This activates raf by exchanging bound GDP with GTP. I have left the GDP/GTP out of this reaction, it would be trivial to put them in. See Boguski & McCormick. Possible candidate molecules: RasGRF, smgGDS, Vav (in dispute). rasGRF: Kcat= 1.2/min Km = 680 nM smgGDS: Kcat: 0.37 /min, Km = 220 nM. vav: Turnover up over baseline by 10X,

    GEF-Gprot-bg acting as an Enzyme in  
    Ajay_Bhalla_2004_PKM_Tuning Network
    Enzyme Molecule /
    Enzyme Activity
    Accession NamePathway NameKm (uM)kcat (s^-1)RatioEnzyme TypeReagents
    GEF-Gprot-bg /
    GEF-bg_act-ras
  • Ajay_Bhalla_
    2004_PKM_Tuning

    Accession No. : 76
  • Ras
    Pathway No. : 318
    0.5050510.024explicit E-S complexSubstrate
    GDP-Ras

    Product
    GTP-Ras
    Kinetics based on the activation of Gq by the receptor complex in the Gq model (in turn based on the Mahama and Linderman model) k1 = 2e-5, k2 = 1e-10, k3 = 10 (I do not know why they even bother with k2). Lets put k1 at 2e-6 to get a reasonable equilibrium More specific values from, eg.g: Orita et al JBC 268(34) 25542-25546 from rasGRF and smgGDS: k1=3.3e-7; k2 = 0.08, k3 = 0.02

    GEF-Gprot-bg acting as a Product in a reaction in  
    Ajay_Bhalla_2004_PKM_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
    bg-act-GEF
  • Ajay_Bhalla_
    2004_PKM_Tuning

    Accession No. : 76
  • Ras
    Pathway No. : 318
    6
    (uM^-1 s^-1)
    1
    (s^-1)
    Kd(bf) = 0.1667(uM)-Substrate
    BetaGamma
    inact-GEF

    Product
    GEF-Gprot-bg
    SoS/GEF is present at 50 nM ie 3e4/cell. BetaGamma maxes out at 9e4. Assume we have 1/3 of the GEF active when the BetaGamma is 1.5e4. so 1e4 * kb = 2e4 * 1.5e4 * kf, so kf/kb = 3e-5. The rate of this equil should be reasonably fast, say 1/sec



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