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Molecule Parameter List for PDGF | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| PDGF 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 | 1 | 0 |
Accession and Pathway Details |
| Accession Name | Accession No. | Accession Type | Pathway Link |
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. | |||
PDGF acting as a Molecule in mkp1_feedback_effects Network
| Name | Accession Name | Pathway Name | Initial Conc. (uM) | Volume (fL) | Buffered | |
| PDGF | effects Accession No. : 4 | PDGFR Pathway No. : 38 | 0 | 1000 | Yes | |
| Platelet-derived growth factor. Heterodimer Mol wt. is approx 30 KDa Deuel et al 1985 Cancer Surv. 4(4):633-53 Conc of 50 ng/ml is close to saturating, and is used by P. Ram (personal communication). Other refs use 65 ng/ml Weise RJ et al 1995 JBC 270(7):3442-3446 A stimulus of 5 min is commonly used. Conversion factor: 1ng/ml = (1e-9/30K)* 1000 Moles/litre = 3e-11M = 3e-5 uM So 50 ng/ml ~ 1.5 nM. | ||||||
PDGF acting as a Substrate 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 |
| act_PDGFR | effects Accession No. : 4 | PDGFR Pathway No. : 38 | 199.998 (uM^-1 s^-1) | 0.1 (s^-1) | Kd(bf) = 0.0005(uM) | - | Substrate PDGF PDGFR Product L.PDGFR |
| From Heidaran et al JBC268(13):9287 Fig 5. Kd is ~0.5 nM | |||||||