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Molecule Parameter List for RGR

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

RGR 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
mkp1_feedback_ effects	4	Network	Shared_Object_mkp1_feedback_effects,  Sos,  PKC,   MAPK,  PLA2,  Ras,   PDGFR
This is a network involving the MAPK-PKC feedback loop with input from the PDGFR in the synapse. The distinctive feature of this model is that it includes MKP-1 induction by MAPK, and the consequent inhibitory regulation of MAPK and the feedback loop. Lots of interesting dynamics arise from this. This link provides supplementary material for the paper Bhalla US et al. Science (2002) 297(5583):1018-23. In the form of several example simulations and demos for the figures in the paper.

RGR acting as a Molecule in  mkp1_feedback_effects Network

Name	Accession Name	Pathway Name	Initial Conc. (uM)	Volume (fL)	Buffered
RGR	mkp1_feedback_ effects Accession No. : 4	MAPK Pathway No. : 35	0	1000	No
Shorthand name for Raf.GTP.Ras. This refers to the complex between GTP.Ras and the unphosphorylated Raf. I treat this as having the same enzyme activity as the Raf*.GTP.Ras form.

RGR acting as an Enzyme in  mkp1_feedback_effects Network

	Enzyme Molecule / Enzyme Activity	Accession Name	Pathway Name	Km (uM)	kcat (s^-1)	Ratio	Enzyme Type	Reagents
1	RGR / RGR.1	mkp1_feedback_ effects Accession No. : 4	MAPK Pathway No. : 35	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=5.5e-6, k2=.42, k3 =0.105 These are based on Force et al PNAS USA 91 1270-1274 1994.
2	RGR / RGR.2	mkp1_feedback_ effects Accession No. : 4	MAPK Pathway No. : 35	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 = 5.5e-6, k2 = .42, k3 = 0.105

RGR acting as a Product in a reaction in  mkp1_feedback_effects 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	mkp1_feedback_ effects Accession No. : 4	Shared_Object_ mkp1_feedback_ effects Pathway No. : 32	6 (uM^-1 s^-1)	1 (s^-1)	Kd(bf) = 0.1667(uM)	-	Substrate GTP-Ras craf-1 Product RGR
Based on rates of Ras-act-craf which has Kf=60, Kb= 0.5. This reaction was introduced to account for the PKC-independent activation of MAPK. This reac should have less affinity but similar tau as compared to the Ras-cat-craf, since the phosphorylated Raf form has a greater effect on MAPK.