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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

G-GDP participated as	Molecule	Sum total of	Enzyme	Substrate of an enzyme	Product of an enzyme	Substrate in Reaction	Product in Reaction
No. of occurrences	1	0	0	0	0	3	1

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.

G-GDP acting as a Molecule in  Ajay_Bhalla_2004_PKM_Tuning Network

Name	Accession Name	Pathway Name	Initial Conc. (uM)	Volume (fL)	Buffered
G-GDP	Ajay_Bhalla_ 2004_PKM_Tuning Accession No. : 76	Gq Pathway No. : 316	1	1.5	No
From M&L, total Gprot = 1e5molecules/cell At equil, 92340 are here, 400 are in G*GTP, and another 600 are assoc with the PLC and 6475 are as G*GDP. This is OK. From Pang and Sternweis JBC 265:30 18707-12 1990 we get conc est 1.6 uM to 0.8 uM. A number of other factors are involved too.

G-GDP acting as a Substrate 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
1	Basal-Act-G	Ajay_Bhalla_ 2004_PKM_Tuning Accession No. : 76	Gq Pathway No. : 316	0.0001 (s^-1)	0 (uM^-1 s^-1)	-	-	Substrate G-GDP Product BetaGamma G*GTP
	kf = kg1 = 0.01/sec, kb = 0. This is the basal exchange of GTP for GDP.
2	Rec-Glu-bind-Gq	Ajay_Bhalla_ 2004_PKM_Tuning Accession No. : 76	Gq Pathway No. : 316	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. kf = 5e-5 which is nearly the same as calculated by Fay et al. (4.67e-5) kb = .04 June 1996: 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	Ajay_Bhalla_ 2004_PKM_Tuning Accession No. : 76	Gq Pathway No. : 316	0.6 (uM^-1 s^-1)	1 (s^-1)	Kd(bf) = 1.6667(uM)	-	Substrate G-GDP mGluR Product Rec-Gq
	Lets try out the same kinetics as the Rec-Glu-bind-Gq This is much too forward. We know that the steady-state amount of Rec-Gq should be 40% of the total amount of receptor. This is for a different receptor, still we can try to match the value. kf = 1e-6 and kb = 1 give 0.333:0.8 which is pretty close.

G-GDP 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
Trimerize-G	Ajay_Bhalla_ 2004_PKM_Tuning Accession No. : 76	Gq Pathway No. : 316	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