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Molecule Parameter List for inact-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 | Ajay_Bhalla_
2004_PKM_MKP3_
Tuning | 77 | Network |
Shared_Object_Ajay_Bhalla_2004_PKM_MKP3_Tuning, PKC, PLA2,
PLCbeta, Ras, Gq,
MAPK, EGFR, Sos,
PLC_g, CaMKII, CaM,
PP1, PP2B, PKA,
AC, MKP3, PKM | | This model is based on Ajay SM, Bhalla US. Eur J Neurosci. 2004 Nov;20(10):2671-80. This is the feedforward model with MPK3 from figure 8a. |
inact-GEF acting as a Molecule in Ajay_Bhalla_2004_PKM_MKP3_Tuning Network
| Name | Accession Name | Pathway Name | Initial Conc.
(uM) | Volume
(fL) | Buffered | | inact-GEF | Ajay_Bhalla_
2004_PKM_MKP3_
Tuning
Accession No. : 77 | Ras
Pathway No. : 333 | 0.1 | 1.5 | No | | Assume that SoS is present only at 50 nM. Revised to 100 nM to get equil to experimentally known levels. |
inact-GEF acting as a Substrate for an Enzyme in Ajay_Bhalla_2004_PKM_MKP3_Tuning Network
| | Enzyme Molecule /
Enzyme Activity | Accession Name | Pathway Name | Km (uM) | kcat (s^-1) | Ratio | Enzyme Type | Reagents | | 1 | PKA-active /
PKA-phosph-GEF | Ajay_Bhalla_
2004_PKM_MKP3_
Tuning
Accession No. : 77 | Shared_Object_
Ajay_Bhalla_
2004_PKM_MKP3_
Tuning
Pathway No. : 329 | 7.49996 | 9 | 4 | explicit E-S complex | Substrate
inact-GEF
Product
inact-GEF*
| | | 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 | | 2 | PKC-active /
PKC-act-GEF | Ajay_Bhalla_
2004_PKM_MKP3_
Tuning
Accession No. : 77 | Shared_Object_
Ajay_Bhalla_
2004_PKM_MKP3_
Tuning
Pathway No. : 329 | 3.33332 | 4 | 4 | explicit E-S complex | Substrate
inact-GEF
Product
GEF*
| | | 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 |
inact-GEF acting as a Substrate in a reaction in Ajay_Bhalla_2004_PKM_MKP3_Tuning 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-act-GEF | Ajay_Bhalla_
2004_PKM_MKP3_
Tuning
Accession No. : 77 | Ras
Pathway No. : 333 | 6
(uM^-1 s^-1) | 1
(s^-1) | Kd(bf) = 0.1667(uM) | - | Substrate
BetaGamma
inact-GEF
Product
GEF-Gprot-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-bind-GEF | Ajay_Bhalla_
2004_PKM_MKP3_
Tuning
Accession No. : 77 | Ras
Pathway No. : 333 | 199.998
(uM^-1 s^-1) | 1
(s^-1) | Kd(bf) = 0.005(uM) | - | Substrate
CaM-Ca4
inact-GEF
Product
CaM-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 2 Aug 2004 Raised Kf from 60 to 200 to achieve higher MAPK activation following Ca stimulus for PKM models. 3 Aug 2004. Lowered Kf to 100. |
inact-GEF acting as a Product in a reaction in Ajay_Bhalla_2004_PKM_MKP3_Tuning 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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