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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
Synaptic_ Network	16	Network	Shared_Object_Synaptic_Network,  PKC,  PLA2,   PLCbeta,  Gq,  MAPK,   Ras,  EGFR,  Sos,   PLC_g,  CaMKII,  CaM,   PP1,  PP2B,  PKA,   AC,  CaRegulation
This model is an annotated version of the synaptic signaling network. The primary reference is Bhalla US and Iyengar R. Science (1999) 283(5400):381-7 but several of the model pathways have been updated. Bhalla US Biophys J. 2002 Aug;83(2):740-52 Bhalla US J Comput Neurosci. 2002 Jul-Aug;13(1):49-62

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

Name	Accession Name	Pathway Name	Initial Conc. (uM)	Volume (fL)	Buffered
Raf-GTP-Ras*	Synaptic_ Network Accession No. : 16	MAPK Pathway No. : 75	0	1000	No
This is the main activated form of craf. It really refers to the complex of GTP-Ras with phosphorylated Raf. See Leevers 1994 Nature 369:411-414 and Hallberg et al 1994 JBC 269(6):3913-3916. The naming is a bit awkward but kept in this model for consistency with previous models (Bhalla and Iyengar 1999 Science 283:381-387)

Raf-GTP-Ras* acting as an Enzyme in  Synaptic_Network 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	Synaptic_ Network Accession No. : 16	MAPK Pathway No. : 75	0.159091	0.105	4	explicit E-S complex	Substrate MAPKK Product MAPKK-ser
	This enzyme activity refers to the complex of phosphorylated Raf and activated Ras. Starting point for 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 who report a Km of 0.8 uM and Vmax of ~500 fm/min/ug for MAPKK. These parms cannot reach the observed 4X stim of MAPK. So we increase the affinity, ie, raise k1 5X to 5.5e-6 which is equivalent to a 5x reduction in Km to about 0.16.
2	Raf-GTP-Ras* / Raf-GTP-Ras*.2	Synaptic_ Network Accession No. : 16	MAPK Pathway No. : 75	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.

Raf-GTP-Ras* acting as a Product in a reaction in  Synaptic_Network 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	Synaptic_ Network Accession No. : 16	Shared_Object_ Synaptic_ Network Pathway No. : 70	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 about 1e-4, giving a Kf of 60 for Kb of 0.5 and a tau of approx 2 sec. Based on: Hallberg et al JBC 269:6 3913-3916 1994, 3% of cellular Raf is complexed with Ras. This step needed to memb-anchor and activate Raf: Leevers et al Nature 369 411-414. Also see Koide et al 1993 PNAS USA 90(18):8683-8686