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Molecule Parameter List for Ras-MKKKK

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

*Ras-MKKKK* 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	1	0	0	1	0

Accession and Pathway Details

Accession Name	Accession No.	Accession Type	Pathway Link
MAPK_osc	27	Pathway	MAPK
This MAPK model is based on Boris N. Kholodenko Eur J Biochem. (2000) 267(6):1583-8 for data from Xenopus oocytes extracts.

Ras-MKKKK acting as a Molecule in MAPK_osc Network

Name	Accession Name	Pathway Name	Initial Conc. (uM)	Volume (fL)	Buffered
Ras-MKKKK	MAPK_osc Accession No. : 27	MAPK Pathway No. : 139	0.001	0.0016667	No
The concn. of Ras-MKKKK is set to 1 nM implicitly from Kholodenko, 2000*

Ras-MKKKK acting as an Enzyme in MAPK_osc Network

Enzyme Molecule / Enzyme Activity	Accession Name	Pathway Name	Km (uM)	kcat (s^-1)	Ratio	Enzyme Type	Reagents
Ras-MKKKK / 1	MAPK_osc Accession No. : 27	MAPK Pathway No. : 139	0.01	2.5	4	Classical Michaelis-Menten V = Etot.S.Kcat/Km+S	Substrate MKKK Product MKKK-P
The Km is 10nM and Vmax is 2.5nM sec^-1. We assume that there is 1 nM of the Ras-MKKKK. From Kholodenko, 2000. If the enzymes are not flagged as Available, then this Km should be set to 0.1 to obtain oscillations.

Ras-MKKKK acting as a Substrate in a reaction in MAPK_osc 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
Neg_feedback	MAPK_osc Accession No. : 27	MAPK Pathway No. : 139	1 (uM^-1 s^-1)	0.009 (s^-1)	Kd(bf) = 0.009(uM)	-	Substrate MAPK-PP Ras-MKKKK Product inactiveRas-MKKK
From Kholodenko, 2000 Eur J Biochem 267 the Kd is 9 nM. We use a rather fast Kf of 1/sec/uM so that equilibrium is maintained.

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