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Molecule Parameter List for GAP | 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_Tuning | 76 | Network |
PKC, Shared_Object_Ajay_Bhalla_2004_PKM_tuning, PLA2,
PLCbeta, Gq, MAPK,
Ras, EGFR, Sos,
PLC_g, CaMKII, CaM,
PP1, PP2B, PKA,
AC, PKM | | This model is taken from the Ajay SM, Bhalla US. Eur J Neurosci. 2004 Nov;20(10):2671-80. This is the reference feedforward model from Figure 8a. |
GAP acting as a Molecule in Ajay_Bhalla_2004_PKM_Tuning Network
| Name | Accession Name | Pathway Name | Initial Conc.
(uM) | Volume
(fL) | Buffered | | GAP | Ajay_Bhalla_
2004_PKM_Tuning
Accession No. : 76 | Ras
Pathway No. : 318 | 0.01 | 1.5 | No | | GTPase-activating proteins. See Boguski and McCormick. Turn off Ras by helping to hydrolyze bound GTP. This one is probably NF1, ie., Neurofibromin as it is inhibited by AA and lipids, and expressed in neural cells. p120-GAP is also a possible candidate, but is less regulated. Both may exist at similar levels. See Eccleston et al JBC 268(36) pp27012-19 Level=.002 16 May 2003: Increased level to 0.0036, in line with other concentration raises at the synapse. |
GAP acting as an Enzyme in Ajay_Bhalla_2004_PKM_Tuning Network
Enzyme Molecule /
Enzyme Activity | Accession Name | Pathway Name | Km (uM) | kcat (s^-1) | Ratio | Enzyme Type | Reagents | GAP /
GAP-inact-ras
| Ajay_Bhalla_
2004_PKM_Tuning
Accession No. : 76 | Ras
Pathway No. : 318 | 1.01039 | 10 | 4 | explicit E-S complex | Substrate
GTP-Ras
Product
GDP-Ras
| | From Eccleston et al JBC 268(36)pp27012-19 get Kd < 2uM, kcat - 10/sec From Martin et al Cell 63 843-849 1990 get Kd ~ 250 nM, kcat = 20/min I will go with the Eccleston figures as there are good error bars (10%). In general the values are reasonably close. k1 = 1.666e-3/sec, k2 = 1000/sec, k3 = 10/sec (note k3 is rate-limiting) 5 Nov 2002: Changed ratio term to 4 from 100. Now we have k1=8.25e-5; k2=40, k3=10. k3 is still rate-limiting. |
GAP acting as a Substrate for an Enzyme in Ajay_Bhalla_2004_PKM_Tuning Network
GAP acting as a Product in a reaction in Ajay_Bhalla_2004_PKM_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 | | dephosph-GAP | Ajay_Bhalla_
2004_PKM_Tuning
Accession No. : 76 | Ras
Pathway No. : 318 | 0.1
(s^-1) | 0
(s^-1) | - | - | Substrate
GAP*
Product
GAP
| | Assume a reasonably good rate for dephosphorylating it, 1/sec |
| Database compilation and code copyright (C) 2022, Upinder S. Bhalla and NCBS/TIFR
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