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Molecule Parameter List for craf-1

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

*craf-1* 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	1	1	1	0

Accession and Pathway Details

Accession Name	Accession No.	Accession Type	Pathway Link
Ajay_Bhalla_ 2007_PKM	80	Network	Shared_Object_Ajay_Bhalla_2007_PKM, PKC, MAPK, Ras, CaM, PKM
This is a non-bistable model of ERKII signaling that also incorporates PKM synthesis triggered by Ca influx. It is a simplified variant of the model of Ajay SM, Bhalla US. Eur J Neurosci. 2004 Nov;20(10):2671-80.

craf-1 acting as a Molecule in Ajay_Bhalla_2007_PKM Network

Name	Accession Name	Pathway Name	Initial Conc. (uM)	Volume (fL)	Buffered
craf-1	Ajay_Bhalla_ 2007_PKM Accession No. : 80	MAPK Pathway No. : 371	0.5	1.5	No
Couldn't find any ref to the actual conc of craf-1 but I should try Strom et al Oncogene 5 pp 345 In line with the other kinases in the cascade, I estimate the conc to be 0.2 uM. To init we use 0.15, which is close to equil 16 May 2003: Changing to synaptic levels. Increasing 2.5 fold to 0.5 uM. See Mihaly et al 1991 Brain Res 547(2):309-14 and Morice et al 1999 Eur J Neurosci 11(6):1995-2006

craf-1 acting as a Substrate for an Enzyme in Ajay_Bhalla_2007_PKM Network

Enzyme Molecule / Enzyme Activity	Accession Name	Pathway Name	Km (uM)	kcat (s^-1)	Ratio	Enzyme Type	Reagents
PKC-active / PKC-act-raf	Ajay_Bhalla_ 2007_PKM Accession No. : 80	Shared_Object_ Ajay_Bhalla_ 2007_PKM Pathway No. : 369	20.0001	4	4	explicit E-S complex	Substrate craf-1 Product craf-1*
Rate consts from Chen et al Biochem 32, 1032 (1993) k3 = k2 = 4 k1 = 9e-5 recalculated gives 1.666e-5, which is not very different. Looks like k3 is rate-limiting in this case: there is a huge amount of craf locked up in the enz complex. Let us assume a 10x higher Km, ie, lower affinity. k1 drops by 10x. Also changed k2 to 4x k3. Lowerd k1 to 1e-6 to balance 10X DAG sensitivity of PKC

craf-1 acting as a Product of an Enzyme in Ajay_Bhalla_2007_PKM Network

Enzyme Molecule / Enzyme Activity	Accession Name	Pathway Name	Km (uM)	kcat (s^-1)	Ratio	Enzyme Type	Reagents
PPhosphatase2A / craf-deph	Ajay_Bhalla_ 2007_PKM Accession No. : 80	Shared_Object_ Ajay_Bhalla_ 2007_PKM Pathway No. : 369	15.6566	6	4	explicit E-S complex	Substrate craf-1* Product craf-1
See parent PPhosphatase2A for parms

craf-1 acting as a Substrate in a reaction in Ajay_Bhalla_2007_PKM 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
Ras-act-unphosph -raf	Ajay_Bhalla_ 2007_PKM Accession No. : 80	Shared_Object_ Ajay_Bhalla_ 2007_PKM Pathway No. : 369	0 (uM^-1 s^-1)	0 (s^-1)	-	-	Substrate GTP-Ras craf-1 Product Raf-GTP-Ras
18 May 2003. This reaction is here to provide basal activity for MAPK as well as the potential for direct EGF stimulus without PKC activation. Based on model from FB/fb28c.g: the model used for MKP-1 turnover. The rates there were constrained by basal activity values.

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