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Molecule Parameter List for RGR | 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 |
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. |
RGR acting as a Molecule in mkp1_feedback_effects Network
| Name | Accession Name | Pathway Name | Initial Conc.
(uM) | Volume
(fL) | Buffered | | RGR | mkp1_feedback_
effects
Accession No. : 4 | MAPK
Pathway No. : 35 | 0 | 1000 | No | | Shorthand name for Raf.GTP.Ras. This refers to the complex between GTP.Ras and the unphosphorylated Raf. I treat this as having the same enzyme activity as the Raf*.GTP.Ras form. |
RGR acting as an Enzyme in mkp1_feedback_effects Network
| | Enzyme Molecule /
Enzyme Activity | Accession Name | Pathway Name | Km (uM) | kcat (s^-1) | Ratio | Enzyme Type | Reagents | | 1 | RGR /
RGR.1
| mkp1_feedback_
effects
Accession No. : 4 | MAPK
Pathway No. : 35 | 0.159091 | 0.105 | 4 | explicit E-S complex | Substrate
MAPKK
Product
MAPKK-ser
| | | Kinetics are the same as for the craf-1* activity, ie., k1=5.5e-6, k2=.42, k3 =0.105 These are based on Force et al PNAS USA 91 1270-1274 1994. | | 2 | RGR /
RGR.2
| mkp1_feedback_
effects
Accession No. : 4 | MAPK
Pathway No. : 35 | 0.159091 | 0.105 | 4 | explicit E-S complex | Substrate
MAPKK-ser
Product
MAPKK*
| | | Same kinetics as other c-raf activated forms. See Force et al PNAS 91 1270-1274 1994. k1 = 5.5e-6, k2 = .42, k3 = 0.105 |
RGR 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 | Ras-act-unphosph
-raf | mkp1_feedback_
effects
Accession No. : 4 | Shared_Object_
mkp1_feedback_
effects
Pathway No. : 32 | 6
(uM^-1 s^-1) | 1
(s^-1) | Kd(bf) = 0.1667(uM) | - | Substrate
GTP-Ras
craf-1
Product
RGR
| | Based on rates of Ras-act-craf which has Kf=60, Kb= 0.5. This reaction was introduced to account for the PKC-independent activation of MAPK. This reac should have less affinity but similar tau as compared to the Ras-cat-craf, since the phosphorylated Raf form has a greater effect on MAPK. |
| Database compilation and code copyright (C) 2022, Upinder S. Bhalla and NCBS/TIFR
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