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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 | Synaptic_
Network | 16 | Network |
Shared_Object_Synaptic_Network, PKC, PLA2,
PLCbeta, Gq, MAPK,
Ras, EGFR, Sos,
PLC_g, CaMKII, CaM,
PP1, PP2B, PKA,
AC, CaRegulation | This model is an annotated version of the synaptic signaling network.
The primary reference is Bhalla US and Iyengar R. Science (1999) 283(5400):381-7 but several of the model pathways have been updated.
Bhalla US Biophys J. 2002 Aug;83(2):740-52
Bhalla US J Comput Neurosci. 2002 Jul-Aug;13(1):49-62 |
inact-GEF acting as a Molecule in Synaptic_Network Network
| Name | Accession Name | Pathway Name | Initial Conc.
(uM) | Volume
(fL) | Buffered | | inact-GEF | Synaptic_
Network
Accession No. : 16 | Ras
Pathway No. : 76 | 0.1 | 1000 | No | | This is the amount of inactive GEF available to the system. The value is the same as the estimated amount of SoS, though I treat it here as a different pool. Probably several molecules can function as GEFs and this is a simplification. Orita et al JBC 268(34):25542-25546 Gulbins et al 1994 Mol Cell Biol 14(2):906-913 |
inact-GEF acting as a Substrate for an Enzyme in Synaptic_Network Network
| | Enzyme Molecule /
Enzyme Activity | Accession Name | Pathway Name | Km (uM) | kcat (s^-1) | Ratio | Enzyme Type | Reagents | | 1 | PKC-active /
PKC-act-GEF | Synaptic_
Network
Accession No. : 16 | Shared_Object_
Synaptic_
Network
Pathway No. : 70 | 3.33333 | 4 | 4 | explicit E-S complex | Substrate
inact-GEF
Product
GEF*
| | | Rate constants are generic PKC rates. See Chen et al 1993 Biochem 32:1032 This reaction activates GEF. Gives >= 2X stim of ras, and a 2X stim of MAPK over amount from direct phosph of c-raf. Note that it is a push-pull reaction, and also get effect through phosph and inact of GAPs. | | 2 | PKA-active /
PKA-phosph-GEF | Synaptic_
Network
Accession No. : 16 | Shared_Object_
Synaptic_
Network
Pathway No. : 70 | 7.5 | 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 |
inact-GEF acting as a Substrate in a reaction in Synaptic_Network 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 | Synaptic_
Network
Accession No. : 16 | Ras
Pathway No. : 76 | 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 | Synaptic_
Network
Accession No. : 16 | Ras
Pathway No. : 76 | 60
(uM^-1 s^-1) | 1
(s^-1) | Kd(bf) = 0.0167(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 |
inact-GEF acting as a Product in a reaction in Synaptic_Network 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 | dephosph-GEF | Synaptic_
Network
Accession No. : 16 | Ras
Pathway No. : 76 | 1
(s^-1) | 0
(s^-1) | - | - | Substrate
GEF*
Product
inact-GEF
| | | This rate is based on the known ratio of GDP-Ras to GTP-Ras. Basal: Ras.GTP = 7% Stimulated 15% Time course is within 10 min, probably much faster as not all early data points are there. See Gibbs et al JBC 265(33):20437-20422 | | 2 | dephosph-inact-G
EF* | Synaptic_
Network
Accession No. : 16 | Ras
Pathway No. : 76 | 1
(s^-1) | 0
(s^-1) | - | - | Substrate
inact-GEF*
Product
inact-GEF
|
| Database compilation and code copyright (C) 2022, Upinder S. Bhalla and NCBS/TIFR
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