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Molecule Parameter List for Internal_L.PDGFR

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
Internal_L.PDGFR participated asMoleculeSum total ofEnzymeSubstrate of an enzymeProduct of an enzymeSubstrate in ReactionProduct in Reaction
No. of occurrences1000001

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.

    Internal_L.PDGFR acting as a Molecule in      MAPK-bistability-fig1c Network
    NameAccession NamePathway NameInitial Conc.
    (uM)    		Volume
    (fL)    		Buffered
    Internal_L.PDGFR
  • MAPK-bistability
    -fig1c
    Accession No. : 35
    		• PDGFR
    Pathway No. : 185    		01000No
    The internalized PDGFR is treated as a generic pool in equilibrium with the surface receptor. This simplifies the turnover processes but fits reasonably well with data.

    Internal_L.PDGFR 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
    Internalize
  • MAPK-bistability
    -fig1c
    Accession No. : 35
    		• PDGFR
    Pathway No. : 185    		0.001
    (s^-1)    		0.0007
    (s^-1)    		Keq = 0.66(uM)588.235secSubstrate
    L.PDGFR

    Product
  • Internal_
    L.PDGFR
    • Original model derived from EGFR model. See Helin and Beguinot JBC 266:13 1991 pg 8363-8368. In Fig 3 they have internalization tau about 10 min, equil at about 20% EGF available. So kf = 4x kb, and 1/(kf + kb) = 600 sec so kb = 1/3K = 3.3e-4, and kf = 1.33e-3. This doesn't take into account the unbound receptor, so we need to push the kf up a bit, to 0.002 26 apr 2001: Keq too low for the PDGF model. Now Kf=0.001,Kb=0.00066 The previously calculated internalization equilibrium led to very high internalization which shifted the effective dependence of the receptor on PDGF so it looked like the receptor binding was higher affinity than experimentally determined. Used two constraining factors: 1. Time course of SHC phosphorylation/dephosphorylation which is fast on, but 10-20 minutes off. 2. Conc dependence of MAPK on PDGF has a halfmax around 3ng/ml. See Brondello et al 1997 JBC 272(2):1368-1376 and Brondello et al 1999 Science 286:2514-1517.


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