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Molecule Parameter List for GAP

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

GAP 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	0	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.

GAP acting as a Molecule in  mTOR_pathway Network

Name	Accession Name	Pathway Name	Initial Conc. (uM)	Volume (fL)	Buffered
GAP	mTOR_pathway Accession No. : 92	Ras Pathway No. : 1106	0.01	1000	No
GTPase-activating proteins. See Boguski and McCormick. Turn off Ras by helping to hydrolyze bound GTP. This one is probably NF1, ie., Neurofibromin as it is inhibited by AA and lipids, and expressed in neural cells. p120-GAP is also a possible candidate, but is less regulated. Both may exist at similar levels. See Eccleston et al JBC 268(36) pp27012-19 Level=.002 16 May 2003: Increased level to 0.0036, in line with other concentration raises at the synapse.

GAP 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
GAP / GAP-inact-ras	mTOR_pathway Accession No. : 92	Ras Pathway No. : 1106	1.01039	10	4	explicit E-S complex	Substrate GTP-Ras Product GDP-Ras
From Eccleston et al JBC 268(36)pp27012-19 get Kd < 2uM, kcat - 10/sec From Martin et al Cell 63 843-849 1990 get Kd ~ 250 nM, kcat = 20/min I will go with the Eccleston figures as there are good error bars (10%). In general the values are reasonably close. k1 = 1.666e-3/sec, k2 = 1000/sec, k3 = 10/sec (note k3 is rate-limiting) 5 Nov 2002: Changed ratio term to 4 from 100. Now we have k1=8.25e-5; k2=40, k3=10. k3 is still rate-limiting.

GAP 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-inact-GAP	mTOR_pathway Accession No. : 92	Shared_Object_ mTOR_pathway Pathway No. : 1097	3.33333	4	4	explicit E-S complex	Substrate GAP Product GAP_star
Rate consts copied from PCK-act-raf This reaction inactivates GAP. The idea is from the Boguski and McCormick review.

GAP 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-GAP	mTOR_pathway Accession No. : 92	Ras Pathway No. : 1106	0.1 (s^-1)	0 (s^-1)	-	-	Substrate GAP_star Product GAP
Assume a reasonably good rate for dephosphorylating it, 1/sec