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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 as | Molecule | Sum total of | Enzyme | Substrate of an enzyme | Product of an enzyme | Substrate in Reaction | Product in Reaction | No. of occurrences | 1 | 0 | 0 | 0 | 0 | 0 | 1 |
Accession and Pathway Details | |
Accession Name | Accession No. | Accession Type | Pathway Link | mkp1_feedback_ effects | 4 | Network | Shared_Object_mkp1_feedback_effects, Sos, PKC, MAPK, PLA2, Ras, PDGFR | This is a network involving the MAPK-PKC feedback loop with input from the PDGFR in the synapse. The distinctive feature of this model is that it includes MKP-1 induction by MAPK, and the consequent inhibitory regulation of MAPK and the feedback loop. Lots of interesting dynamics arise from this. This link provides supplementary material for the paper Bhalla US et al. Science (2002) 297(5583):1018-23. In the form of several example simulations and demos for the figures in the paper. |
Internal_L.PDGFR acting as a Molecule in mkp1_feedback_effects Network
Name | Accession Name | Pathway Name | Initial Conc. (uM) | Volume (fL) | Buffered | Internal_L.PDGFR | mkp1_feedback_ effects Accession No. : 4 | PDGFR Pathway No. : 38 | 0 | 1000 | No | 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 mkp1_feedback_effects 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. |
Name | Accession Name | Pathway Name | Kf | Kb | Kd | tau | Reagents | Internalize | mkp1_feedback_ effects Accession No. : 4 | PDGFR Pathway No. : 38 | 0.001 (s^-1) | 0.0007 (s^-1) | Keq = 0.66(uM) | 588.235sec | Substrate 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. |
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