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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	2	2	1	0

Accession and Pathway Details

Accession Name	Accession No.	Accession Type	Pathway Link
MAPK_MKP1_ oscillation	9	Network	Shared_Object_MAPK_MKP1_oscillation, PKC, MAPK, PLA2, Ras
This model relates to figure 5 in Bhalla US, Iyengar R. Chaos (2001) 11(1):221-226. It includes the model used for figures 2-4 and also has MKP-1 induction by MAPK activity in the synapse. PP2A is set to 0.16 uM and MKP synthesis is varied from 5x to 40 x basal to get a range of interesting behaviours.

craf-1* acting as a Molecule in MAPK_MKP1_oscillation Network

Name	Accession Name	Pathway Name	Initial Conc. (uM)	Volume (fL)	Buffered
craf-1*	MAPK_MKP1_ oscillation Accession No. : 9	MAPK Pathway No. : 61	0	1000	No

craf-1* acting as a Substrate for an Enzyme in MAPK_MKP1_oscillation Network

	Enzyme Molecule / Enzyme Activity	Accession Name	Pathway Name	Km (uM)	kcat (s^-1)	Ratio	Enzyme Type	Reagents
1	MAPK* / MAPK*-feedback	MAPK_MKP1_ oscillation Accession No. : 9	Shared_Object_ MAPK_MKP1_ oscillation Pathway No. : 59	25.641	10	4	explicit E-S complex	Substrate craf-1* Product craf-1**
	Ueki et al JBC 269(22):15756-15761 show the presence of this step, but not the rate consts, which are derived from Sanghera et al JBC 265(1):52-57, 1990, see the deriv in the MAPK notes.*
2	PPhosphatase2A / craf-deph	MAPK_MKP1_ oscillation Accession No. : 9	Shared_Object_ MAPK_MKP1_ oscillation Pathway No. : 59	15.6566	6	4.16667	explicit E-S complex	Substrate craf-1* Product craf-1
	See parent PPhosphatase2A for parms

craf-1* acting as a Product of an Enzyme in MAPK_MKP1_oscillation Network

	Enzyme Molecule / Enzyme Activity	Accession Name	Pathway Name	Km (uM)	kcat (s^-1)	Ratio	Enzyme Type	Reagents
1	PKC-active / PKC-act-raf	MAPK_MKP1_ oscillation Accession No. : 9	Shared_Object_ MAPK_MKP1_ oscillation Pathway No. : 59	66.6667	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 Lower k1 to 1e-6 to balance 10X DAG sensitivity of PKC 11 May2K: Double Vmax. rates=1e-6, 32,8 29 May 2k: Vmax * 0.6. Rates=6e-7, 19.2, 4.8 30 May 2k: vmax=5. Rates=6.25e-7,20,5 3 Jun 2k: vmax=4. Rates=5e-7,16,4
2	PPhosphatase2A / craf**-deph	MAPK_MKP1_ oscillation Accession No. : 9	Shared_Object_ MAPK_MKP1_ oscillation Pathway No. : 59	15.6566	6	4.16667	explicit E-S complex	Substrate craf-1 Product** craf-1*
	Ueki et al JBC 269(22) pp 15756-15761 1994 show hyperphosphorylation of craf, so this is there to dephosphorylate it. Identity of phosphatase is not known to me, but it may be PP2A like the rest, so I have made it so.

craf-1* acting as a Substrate in a reaction in MAPK_MKP1_oscillation 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-craf	MAPK_MKP1_ oscillation Accession No. : 9	Shared_Object_ MAPK_MKP1_ oscillation Pathway No. : 59	24 (uM^-1 s^-1)	0.5 (s^-1)	Kd(bf) = 0.0208(uM)	-	Substrate GTP-Ras craf-1* Product Raf-GTP-Ras*
Assume binding is fast and limited only by available Ras. So kf = kb/[craf-1] If kb is 1/sec, then kf = 1/0.2 uM = 1/(0.2 6e5) = 8.3e-6 Later: Raise it by 10 X to 4e-5 From Hallberg et al JBC 269:6 3913-3916 1994, 3% of cellular Raf is complexed with Ras. So raise kb 4x to 4e-5 This step needed to memb-anchor and activate Raf: Leevers et al Nature 369 411-414.

Database compilation and code copyright (C) 2022, Upinder S. Bhalla and NCBS/TIFR
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