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Molecule Parameter List for MAPK* | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 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. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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| MAPK* 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 | 1 | 4 | 3 | 1 | 1 | 0 |
Accession and Pathway Details |
| Accession Name | Accession No. | Accession Type | Pathway Link |
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. | |||
MAPK* acting as a Molecule in mkp1_feedback_effects Network
| Name | Accession Name | Pathway Name | Initial Conc. (uM) | Volume (fL) | Buffered | |
| MAPK* | effects Accession No. : 4 | mkp1_feedback_ effects Pathway No. : 32 | 0 | 1000 | No | |
| This molecule is phosphorylated on both the tyr and thr residues and is active: Seger R, Ahn NG, Posada J, Munar ES, Jensen AM, Cooper JA, Cobb MH, Krebs EG. (1992) J Biol Chem. 267(20):14373-81. The rate constants are from two sources - combine Sanghera JS, Paddon HB, Bader SA, Pelech SL. (1990) J Biol Chem. 265(1):52-57 with Nemenoff RA, Winitz S, Qian NX, Van Putten V, Johnson GL, Heasley LE. (1993) J Biol Chem. 268(3):1960-1964 to get k3 = 10, k2 = 40, k1 = 3.25e-6 | ||||||
MAPK* acting as a Summed Molecule in mkp1_feedback_effects Network
| Accession Name | Pathway Name | Target | Input |
effects Accession No. : 4 | mkp1_feedback_ effects Pathway No. : 32 | tot_MAPK | MAPK* nuc_MAPK* |
| Total available active MAPK. This sums the levels of the cytosolic and nuclear localized forms. | |||
MAPK* 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 | MAPK* / MAPK*-feedback | effects Accession No. : 4 | mkp1_feedback_ effects Pathway No. : 32 | 25.641 | 10 | 4 | explicit E-S complex | Substrate craf-1* Product craf-1** |
| Ueki K, Matsuda S, Tobe K, Gotoh Y, Tamemoto H, Yachi M, Akanuma Y, Yazaki Y, Nishida E, Kadowaki T. (1994) J Biol Chem. 269(22):15756-15761 show the presence of this step, but not the rate constants, which are derived from Sanghera JS, Paddon HB, Bader SA, Pelech SL. (1990) J Biol Chem. 265(1):52-57; follow the derivation in the MAPK* notes. | ||||||||
| 2 | MAPK* / MAPK* | effects Accession No. : 4 | mkp1_feedback_ effects Pathway No. : 32 | 25.641 | 20 | 4 | explicit E-S complex | Substrate PLA2-cytosolic Product PLA2* |
| Km for MBP = 25 uM at 50 uM ATP, Km for ATP = 58 uM at 1mg/ml MBP (huge excess of substrate), Vmax = 4124 pmol/min/ml at a concentartion of 125 pmol/ml of enzyme. Numbers are from pp. 54 Sanghera JS, Paddon HB, Bader SA, Pelech SL. (1990) J Biol Chem. 265(1):52-7. From Nemenoff RA, Winitz S, Qian NX, Van Putten V, Johnson GL, Heasley LE. (1993) J Biol Chem. 268(3):1960-1964 - using Sanghera's 1e-4 ratio of MAPK to protein, we get k3 = 7/sec from 1000 pmol/min/mg total protein in fig 5 I take the Vmax to be higher for PLA2 given the fold activation of PLA2 by MAPK. This is actually a balance term between MAPK and the dephosphorylation step. | ||||||||
| 3 | MAPK* / MKP-1-phosph | effects Accession No. : 4 | mkp1_feedback_ effects Pathway No. : 32 | 25.641 | 1 | 4 | explicit E-S complex | Substrate MKP-1 Product MKP-1-ser359* |
| 3 Feb 2000. MAPK rates based on Sanghera JS, Paddon HB, Bader SA, Pelech SL. (1990) 265(1):52-57. The Vmax is scaled down 10 fold to match the time-course of phosph by MAPK, from Brondello JM, Pouyssegur J, McKenzie FR. (1999) Science 286(5449):2514-2517. | ||||||||
| 4 | MAPK* / MKP-1-phosph2 | effects Accession No. : 4 | mkp1_feedback_ effects Pathway No. : 32 | 25.641 | 1 | 4 | explicit E-S complex | Substrate MKP-1-ser359* Product MKP-1** |
| 3 Feb 2000. MAPK rates based on Sanghera JS, Paddon HB, Bader SA, Pelech SL. (1990) 265(1):52-57. The Vmax is scaled down 10 fold to match the time-course of phosph by MAPK, from Brondello JM, Pouyssegur J, McKenzie FR. (1999) Science 286(5449):2514-2517. | ||||||||
MAPK* acting as a Substrate for 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 | MKP-1** / MKP1*-thr-deph | effects Accession No. : 4 | MAPK Pathway No. : 35 | 0.0666667 | 1 | 4 | Classical Michaelis-Menten V = Etot.S.Kcat/Km+S | Substrate MAPK* Product MAPK-tyr |
| 3 Feb 2000. Same rates as MKP1 | ||||||||
| 2 | MKP-1 / MKP1-thr-deph | effects Accession No. : 4 | mkp1_feedback_ effects Pathway No. : 32 | 0.0666667 | 1 | 4 | Classical Michaelis-Menten V = Etot.S.Kcat/Km+S | Substrate MAPK* Product MAPK-tyr |
| See MKP1-tyr-deph | ||||||||
| 3 | MKP-2 / MKP2-thr-deph | effects Accession No. : 4 | mkp1_feedback_ effects Pathway No. : 32 | 0.0666667 | 1 | 4 | explicit E-S complex | Substrate MAPK* Product MAPK-tyr |
| See MKP2-tyr-deph | ||||||||
MAPK* acting as a Product of an Enzyme in mkp1_feedback_effects Network
| Enzyme Molecule / Enzyme Activity | Accession Name | Pathway Name | Km (uM) | kcat (s^-1) | Ratio | Enzyme Type | Reagents |
| MAPKK* / MAPKKthr | effects Accession No. : 4 | MAPK Pathway No. : 35 | 0.0462963 | 0.15 | 4 | explicit E-S complex | Substrate MAPK-tyr Product MAPK* |
| Rate consts same as for MAPKKtyr. | |||||||
MAPK* acting as a Substrate 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 |
| translocation | effects Accession No. : 4 | MAPK Pathway No. : 35 | 0.01 (#^-1 s^-1) | 0.005 (s^-1) | Not applicable** | - | Substrate MAPK* MAPK* Product nuc_MAPK* |
| A nuclear translocation step. This lumps in all sorts of processes into a single set of rates constrained by time courses. Furuno et al J Immunol 166:4416-4421 (2001): In within 6 min, out within 7. The outgoing path is dephosphorylated MAPK so this reac will be one-way. Kf=0.01, Kb=0.005. The reaction is 2nd order in MAPK*, to represent dimerization of transcription factors. | |||||||