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Molecule Parameter List for G-GDP

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
G-GDP participated asMoleculeSum total ofEnzymeSubstrate of an enzymeProduct of an enzymeSubstrate in ReactionProduct in Reaction
No. of occurrences1000031

Accession and Pathway Details
Accession NameAccession No.Accession TypePathway Link
  • Synaptic_
    Network
  • 16Network
    Shared_Object_Synaptic_Network PKC PLA2 
    PLCbeta Gq MAPK 
    Ras EGFR Sos 
    PLC_g CaMKII CaM 
    PP1 PP2B PKA 
    AC CaRegulation 
    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 Biophys J. 2002 Aug;83(2):740-52
    Bhalla US J Comput Neurosci. 2002 Jul-Aug;13(1):49-62

    G-GDP acting as a Molecule in  
    Synaptic_Network Network
    NameAccession NamePathway NameInitial Conc.
    (uM)
    Volume
    (fL)
    Buffered
    G-GDP
  • Synaptic_
    Network

    Accession No. : 16
  • Gq
    Pathway No. : 74
    11000No
    This is the G-alpha-beta-gamma trimer in association with GDP. From Pang and Sternweis JBC 265:30 18707-12 1990 we get concentration estimate of 1.6 uM to 0.8 uM. I use 1 uM which is well within this range.

    G-GDP acting as a Substrate in a reaction in  
    Synaptic_Network 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
    1Basal-Act-G
  • Synaptic_
    Network

    Accession No. : 16
  • Gq
    Pathway No. : 74
    0.0001
    (s^-1)
    0
    (uM^-1 s^-1)
    --Substrate
    G-GDP

    Product
    BetaGamma
    G*GTP
      This is the basal exchange of GTP for GDP. So slow as to be nearly negligible.
    2Rec-Glu-bind-Gq
  • Synaptic_
    Network

    Accession No. : 16
  • Gq
    Pathway No. : 74
    0.006
    (uM^-1 s^-1)
    0.0001
    (s^-1)
    Kd(bf) = 0.0167(uM)-Substrate
    G-GDP
    Rec-Glu

    Product
    Rec-Glu-Gq
      This is the k1-k2 equivalent for enzyme complex formation in the binding of Rec-Glu to Gq. See Fay et al Biochem 30 5066-5075 1991. Closer reading of Fay et al suggests that kb <= 0.0001, so kf = 1e-8 by detailed balance. This reaction appears to be neglible.
    3Rec-bind-Gq
  • Synaptic_
    Network

    Accession No. : 16
  • Gq
    Pathway No. : 74
    0.6
    (uM^-1 s^-1)
    1
    (s^-1)
    Kd(bf) = 1.6667(uM)-Substrate
    G-GDP
    mGluR

    Product
    Rec-Gq
      From Berstein et al 1992 JBC 267(12):8081-8088 we know that 15-40% of Gq binds, GTP_gamma_S. Also about 20-30% of Gq is bound to GTP. To get to these values the receptor-Gq amount should be similar. These rates are designed to give that steady state with a fast tau of 1 sec.

    G-GDP acting as a Product in a reaction in  
    Synaptic_Network 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
    Trimerize-G
  • Synaptic_
    Network

    Accession No. : 16
  • Gq
    Pathway No. : 74
    6
    (uM^-1 s^-1)
    0
    (s^-1)
    --Substrate
    BetaGamma
    G*GDP

    Product
    G-GDP
    kf == kg3 = 1e-5 /cell/sec. As usual, there is no back-reaction kb = 0



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