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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
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

G-GDP acting as a Molecule in  Synaptic_Network Network

Name	Accession Name	Pathway Name	Initial Conc. (uM)	Volume (fL)	Buffered
G-GDP	Synaptic_ Network Accession No. : 16	Gq Pathway No. : 74	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  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	Basal-Act-G	Synaptic_ Network Accession No. : 16	Gq Pathway No. : 74	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	Synaptic_ Network Accession No. : 16	Gq Pathway No. : 74	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	Synaptic_ Network Accession No. : 16	Gq Pathway No. : 74	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  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
Trimerize-G	Synaptic_ Network Accession No. : 16	Gq Pathway No. : 74	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