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Molecule Parameter List for inact_dash_GEF

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

inact_dash_GEF 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	2	0	2	2

Accession and Pathway Details

Accession Name	Accession No.	Accession Type	Pathway Link
mRNA synthesis	94	Network	kinetics,  compartment_1,  compartment_2
The model consists of three major pathways: Calcium-calmodulin dependent protein kinase IV (CaMKIV), Mitogen-activated protein kinase (MAPK) and Protein Phosphatase 1 (PP1). Each of these converged on CREB activation. We also modeled further interactions with Transducer of regulated CREB activity 1 (TORC1) and the protein kinase A (PKA) pathway.

inact_dash_GEF acting as a Molecule in  mRNA synthesis Network

Name	Accession Name	Pathway Name	Initial Conc. (uM)	Volume (fL)	Buffered
inact_dash_GEF	mRNA synthesis Accession No. : 94	kinetics Pathway No. : 1112	0.1	1000	No
Assume that SoS is present only at 50 nM. Revised to 100 nM to get equil to experimentally known levels.

inact_dash_GEF acting as a Substrate for an Enzyme in  mRNA synthesis Network

	Enzyme Molecule / Enzyme Activity	Accession Name	Pathway Name	Km (uM)	kcat (s^-1)	Ratio	Enzyme Type	Reagents
1	PKC_dash_active  / PKC_dash_act_ dash_GEF	mRNA synthesis Accession No. : 94	kinetics Pathway No. : 1112	3.3333	4	4	explicit E-S complex	Substrate inact_dash_GEF Product GEF_star
	Rate consts from PKC-act-raf. This reaction activates GEF. It can lead to at least 2X stim of ras, and a 2X stim of MAPK over and above that obtained via direct phosph of c-raf. Note that it is a push-pull reaction, and there is also a contribution through the phosphorylation and inactivation of GAPs. The original PKC-act-raf rate consts are too fast. We lower K1 by 10 X
2	PKA_dash_active  / PKA_dash_ phosph_dash_GEF	mRNA synthesis Accession No. : 94	kinetics Pathway No. : 1112	7.5	9	4	explicit E-S complex	Substrate inact_dash_GEF Product inact_dash_GEF_ star
	This pathway inhibits Ras when cAMP is elevated. See: Hordijk et al JBC 269:5 3534-3538 1994 Burgering et al EMBO J 12:11 4211-4220 1993 The rates are the same as used in PKA-phosph-I1

inact_dash_GEF acting as a Substrate in a reaction in  mRNA synthesis 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	bg_dash_act_ dash_GEF	mRNA synthesis Accession No. : 94	kinetics Pathway No. : 1112	6 (uM^-1 s^-1)	1 (s^-1)	Kd(bf) = 0.1667(uM)	-	Substrate BetaGamma inact_dash_GEF Product GEF_dash_Gprot_ dash_bg
	SoS/GEF is present at 50 nM ie 3e4/cell. BetaGamma maxes out at 9e4. Assume we have 1/3 of the GEF active when the BetaGamma is 1.5e4. so 1e4 * kb = 2e4 * 1.5e4 * kf, so kf/kb = 3e-5. The rate of this equil should be reasonably fast, say 1/sec
2	CaM_dash_bind_ dash_GEF	mRNA synthesis Accession No. : 94	kinetics Pathway No. : 1112	60 (uM^-1 s^-1)	1 (s^-1)	Kd(bf) = 0.0167(uM)	-	Substrate CaM_dash_Ca4 inact_dash_GEF Product CaM_dash_GEF
	We have no numbers for this. It is probably between the two extremes represented by the CaMKII phosph states, and I have used guesses based on this. kf=1e-4 kb=1 The reaction is based on Farnsworth et al Nature 376 524-527 1995

inact_dash_GEF acting as a Product in a reaction in  mRNA synthesis 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	dephosph_dash_ GEF	mRNA synthesis Accession No. : 94	kinetics Pathway No. : 1112	1 (s^-1)	0 (s^-1)	-	-	Substrate GEF_star Product inact_dash_GEF
2	dephosph_dash_ inact_dash_GEF_ star	mRNA synthesis Accession No. : 94	kinetics Pathway No. : 1112	1 (s^-1)	0 (s^-1)	-	-	Substrate inact_dash_GEF_ star Product inact_dash_GEF