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Molecule Parameter List for Raf-GTP-Ras*

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

Raf-GTP-Ras* 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	2	0	0	0	1

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.

Raf-GTP-Ras* acting as a Molecule in MAPK_MKP1_oscillation Network

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

Raf-GTP-Ras* acting as 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	Raf-GTP-Ras* / Raf-GTP-Ras*.1	MAPK_MKP1_ oscillation Accession No. : 9	MAPK Pathway No. : 61	0.159091	0.105	4	explicit E-S complex	Substrate MAPKK Product MAPKK-ser
	Kinetics are the same as for the craf-1* activity, ie., k1=1.1e-6, k2=.42, k3 =0.105 These are based on Force et al PNAS USA 91 1270-1274 1994. These parms cannot reach the observed 4X stim of MAPK. So lets increase the affinity, ie, raise k1 10X to 1.1e-5 Lets take it back down to where it was. Back up to 5X: 5.5e-6
2	Raf-GTP-Ras* / Raf-GTP-Ras*.2	MAPK_MKP1_ oscillation Accession No. : 9	MAPK Pathway No. : 61	0.159091	0.105	4	explicit E-S complex	Substrate MAPKK-ser Product MAPKK*
	Same kinetics as other c-raf activated forms. See Force et al PNAS 91 1270-1274 1994. k1 = 1.1e-6, k2 = .42, k3 = 1.05 raise k1 to 5.5e-6

Raf-GTP-Ras* acting as a Product 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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