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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 |
| 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. | |||||||