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Molecule Parameter List for inact-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-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	1	1	0	1	1

Accession and Pathway Details

Accession Name	Accession No.	Accession Type	Pathway Link
mTOR_pathway	92	Network	Shared_Object_mTOR_pathway,  AKT_mod,  S6Kinase,   PI3K_mod,  TrKB_mod,  mTOR_model,   MAPK,  PKC,  4E-BP_mod,   Ras,  Sos,  43S_complex,   CaM
This model consists of various sub-modules. They are as follows: 1) BDNF receptor signaling 2) AKT signaling 3) 4E-BP model 4) S6 Kinase model 5) CaMKIII model 6) Protein synthesis model 7) CaM 8) PKC 9) MAPK model.

inact-GEF acting as a Molecule in  mTOR_pathway Network

Name	Accession Name	Pathway Name	Initial Conc. (uM)	Volume (fL)	Buffered
inact-GEF	mTOR_pathway Accession No. : 92	Ras Pathway No. : 1106	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-GEF acting as an Enzyme in  mTOR_pathway Network

Enzyme Molecule / Enzyme Activity	Accession Name	Pathway Name	Km (uM)	kcat (s^-1)	Ratio	Enzyme Type	Reagents
inact-GEF / basal_GEF_ activity	mTOR_pathway Accession No. : 92	Ras Pathway No. : 1106	10.101	0.02	4	explicit E-S complex	Substrate GDP-Ras Product GTP-Ras

inact-GEF acting as a Substrate for an Enzyme in  mTOR_pathway Network

Enzyme Molecule / Enzyme Activity	Accession Name	Pathway Name	Km (uM)	kcat (s^-1)	Ratio	Enzyme Type	Reagents
PKC-active  / PKC-act-GEF	mTOR_pathway Accession No. : 92	Shared_Object_ mTOR_pathway Pathway No. : 1097	3.33333	4	4	explicit E-S complex	Substrate inact-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

inact-GEF acting as a Substrate in a reaction in  mTOR_pathway 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
CaM-bind-GEF	mTOR_pathway Accession No. : 92	Ras Pathway No. : 1106	199.998 (uM^-1 s^-1)	1 (s^-1)	Kd(bf) = 0.005(uM)	-	Substrate CaM-Ca4 inact-GEF Product CaM-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-GEF acting as a Product in a reaction in  mTOR_pathway 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
dephosph-GEF	mTOR_pathway Accession No. : 92	Ras Pathway No. : 1106	1 (s^-1)	0 (s^-1)	-	-	Substrate GEF_star Product inact-GEF