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Molecule Parameter List for G-GDP | 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 | Osc_Ca_
IP3metabolism | 32 | Network |
MIPP, CaMKII, CaM,
PKC, IP3-3K, Gq,
PLCbeta, 134_dephos, 145_dephos,
IP4-system, IHP-system, 1345_dephos,
CaRegulation, Othmer-Tang-model | | This network models an oscillatory calcium response to GPCR mediated PLCbeta activation, alongwith detailed InsP3 metabolism in the neuron. It is similar to the Osc_Ca_IP3metab model (accession 24) except that some enzymes in the InsP3 metabolism network have been modified to have reversible kinetics rather than Michaelis-Menten kinetics. The modified enzymes belong to the groups: IP4-system, IP3-3K, 145_dephos and 134_dephos. Mishra J, Bhalla US. Biophys J. 2002 Sep;83(3):1298-316. |
G-GDP acting as a Molecule in Osc_Ca_IP3metabolism Network
| Name | Accession Name | Pathway Name | Initial Conc.
(uM) | Volume
(fL) | Buffered | | G-GDP | Osc_Ca_
IP3metabolism
Accession No. : 32 | Gq
Pathway No. : 163 | 1 | 1000 | No | | This is the G-alpha-beta-gamma trimer in association with GDP. From Pang and Sternweis JBC 265:30 18707-12 1990 we get concentration estimate of 1.6 uM to 0.8 uM. I use 1 uM which is well within this range. |
G-GDP acting as a Substrate in a reaction in Osc_Ca_IP3metabolism 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 | Basal-Act-G | Osc_Ca_
IP3metabolism
Accession No. : 32 | Gq
Pathway No. : 163 | 0.0001
(s^-1) | 0
(uM^-1 s^-1) | - | - | Substrate
G-GDP
Product
BetaGamma
G*GTP
| | | This is the basal exchange of GTP for GDP. So slow as to be nearly negligible. | | 2 | Rec-Glu-bind-Gq | Osc_Ca_
IP3metabolism
Accession No. : 32 | Gq
Pathway No. : 163 | 0.006
(uM^-1 s^-1) | 0.0001
(s^-1) | Kd(bf) = 0.0167(uM) | - | Substrate
G-GDP
Rec-Glu
Product
Rec-Glu-Gq
| | | This is the k1-k2 equivalent for enzyme complex formation in the binding of Rec-Glu to Gq. See Fay et al Biochem 30 5066-5075 1991. Closer reading of Fay et al suggests that kb <= 0.0001, so kf = 1e-8 by detailed balance. This reaction appears to be neglible. | | 3 | Rec-bind-Gq | Osc_Ca_
IP3metabolism
Accession No. : 32 | Gq
Pathway No. : 163 | 0.6
(uM^-1 s^-1) | 1
(s^-1) | Kd(bf) = 1.6667(uM) | - | Substrate
G-GDP
mGluR
Product
Rec-Gq
| | | From Berstein et al 1992 JBC 267(12):8081-8088 we know that 15-40% of Gq binds, GTP_gamma_S. Also about 20-30% of Gq is bound to GTP. To get to these values the receptor-Gq amount should be similar. These rates are designed to give that steady state with a fast tau of 1 sec. |
G-GDP acting as a Product in a reaction in Osc_Ca_IP3metabolism 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-G | Osc_Ca_
IP3metabolism
Accession No. : 32 | Gq
Pathway No. : 163 | 6
(uM^-1 s^-1) | 0
(s^-1) | - | - | Substrate
BetaGamma
G*GDP
Product
G-GDP
| | kf == kg3 = 1e-5 /cell/sec. As usual, there is no back-reaction kb = 0 |
| Database compilation and code copyright (C) 2022, Upinder S. Bhalla and NCBS/TIFR
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