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Molecule Parameter List for inact_dash_GEF | 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 | | mRNA synthesis | 94 | Network |
kinetics, compartment_1, compartment_2 | | The model consists of three major pathways: Calcium-calmodulin dependent protein kinase IV (CaMKIV), Mitogen-activated protein kinase (MAPK) and Protein Phosphatase 1 (PP1). Each of these converged on CREB activation. We also modeled further interactions with Transducer of regulated CREB activity 1 (TORC1) and the protein kinase A (PKA) pathway. |
inact_dash_GEF acting as a Molecule in mRNA synthesis Network
| Name | Accession Name | Pathway Name | Initial Conc.
(uM) | Volume
(fL) | Buffered | | inact_dash_GEF | mRNA synthesis
Accession No. : 94 | kinetics
Pathway No. : 1112 | 0.1 | 1000 | No | | Assume that SoS is present only at 50 nM. Revised to 100 nM to get equil to experimentally known levels. |
inact_dash_GEF acting as a Substrate for an Enzyme in mRNA synthesis Network
| | Enzyme Molecule /
Enzyme Activity | Accession Name | Pathway Name | Km (uM) | kcat (s^-1) | Ratio | Enzyme Type | Reagents | | 1 | PKC_dash_active /
PKC_dash_act_
dash_GEF
| mRNA synthesis
Accession No. : 94 | kinetics
Pathway No. : 1112 | 3.3333 | 4 | 4 | explicit E-S complex | Substrate
inact_dash_GEF
Product
GEF_star
| | | Rate consts from PKC-act-raf. This reaction activates GEF. It can lead to at least 2X stim of ras, and a 2X stim of MAPK over and above that obtained via direct phosph of c-raf. Note that it is a push-pull reaction, and there is also a contribution through the phosphorylation and inactivation of GAPs. The original PKC-act-raf rate consts are too fast. We lower K1 by 10 X | | 2 | PKA_dash_active /
PKA_dash_
phosph_dash_GEF
| mRNA synthesis
Accession No. : 94 | kinetics
Pathway No. : 1112 | 7.5 | 9 | 4 | explicit E-S complex | Substrate
inact_dash_GEF
Product
inact_dash_GEF_
star
| | | This pathway inhibits Ras when cAMP is elevated. See: Hordijk et al JBC 269:5 3534-3538 1994 Burgering et al EMBO J 12:11 4211-4220 1993 The rates are the same as used in PKA-phosph-I1 |
inact_dash_GEF acting as a Substrate in a reaction in mRNA synthesis 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 | | 1 | bg_dash_act_
dash_GEF | mRNA synthesis
Accession No. : 94 | kinetics
Pathway No. : 1112 | 6
(uM^-1 s^-1) | 1
(s^-1) | Kd(bf) = 0.1667(uM) | - | Substrate
BetaGamma
inact_dash_GEF
Product
GEF_dash_Gprot_
dash_bg
| | | SoS/GEF is present at 50 nM ie 3e4/cell. BetaGamma maxes out at 9e4. Assume we have 1/3 of the GEF active when the BetaGamma is 1.5e4. so 1e4 * kb = 2e4 * 1.5e4 * kf, so kf/kb = 3e-5. The rate of this equil should be reasonably fast, say 1/sec | | 2 | CaM_dash_bind_
dash_GEF | mRNA synthesis
Accession No. : 94 | kinetics
Pathway No. : 1112 | 60
(uM^-1 s^-1) | 1
(s^-1) | Kd(bf) = 0.0167(uM) | - | Substrate
CaM_dash_Ca4
inact_dash_GEF
Product
CaM_dash_GEF
| | | We have no numbers for this. It is probably between the two extremes represented by the CaMKII phosph states, and I have used guesses based on this. kf=1e-4 kb=1 The reaction is based on Farnsworth et al Nature 376 524-527 1995 |
inact_dash_GEF acting as a Product in a reaction in mRNA synthesis 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. |
| Database compilation and code copyright (C) 2022, Upinder S. Bhalla and NCBS/TIFR
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