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Molecule Parameter List for GDP.Gabc | 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 | | PKA_2003 | 47 | Network |
Shared_Object_PKA_2003, PKA, AC,
Gs | | This model consists of receptor-ligand interaction, G-protein activation, Adenylyl cyclase mediated formation of cAMP and activation of PKA in the neuron. Demonstration programs using this model described in Bhalla US. (2004) Biophys J. 87(2):733-44 to generate a dose-response curve using stochastic calculations are available here. |
GDP.Gabc acting as a Molecule in PKA_2003 Network
| Name | Accession Name | Pathway Name | Initial Conc.
(uM) | Volume
(fL) | Buffered | | GDP.Gabc | PKA_2003
Accession No. : 47 | Gs
Pathway No. : 198 | 1 | 1000 | No | | The resting state of Gs: GDP bound to trimer. From Pang and Sternweis JBC 265:30 18707-12 1990 we get conc est 1.6 uM to 0.8 uM. We'll use 1 uM. |
GDP.Gabc acting as a Substrate in a reaction in PKA_2003 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 | R-bind-Gabc | PKA_2003
Accession No. : 47 | Gs
Pathway No. : 198 | 0.2
(uM^-1 s^-1) | 0.1
(s^-1) | Kd(bf) = 0.5(uM) | - | Substrate
GDP.Gabc
R
Product
R.GDP.Gabc
| | | Receptor binding to Gs. Scale it to the same slow rates described by Fay et al for L.R to L.R.G. From detailed balance, Kd is 50. | | 2 | L.R-bind-Gabc | PKA_2003
Accession No. : 47 | Gs
Pathway No. : 198 | 10.0002
(uM^-1 s^-1) | 0.1
(s^-1) | Kd(bf) = 0.01(uM) | - | Substrate
GDP.Gabc
L.R
Product
L.R.GDP.Gabc
| | | See Fay et al Biochem 30 5066-5075 1991. kf is 0.01/sec but does not account for Gs levels. kb is 0.0001/sec. The fraction of RG is about 50%, so we can estimate Kd at about the same as for Gs basal levels. This rate has to be faster since it has to feed GTP.Ga into the system faster than the GTPase. Waldhoer et al Mol Pharmacol 53:808-818 1988 say affinity for A1adenosine/Gi is 10 nM. |
GDP.Gabc acting as a Product in a reaction in PKA_2003 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 | | Trimerize-Gs | PKA_2003
Accession No. : 47 | Gs
Pathway No. : 198 | 6
(uM^-1 s^-1) | 0
(s^-1) | - | - | Substrate
GDP.Ga
Gbg
Product
GDP.Gabc
| | Negligible back-reaction. |
| Database compilation and code copyright (C) 2022, Upinder S. Bhalla and NCBS/TIFR
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