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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. | | Statistics |
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. |
MAPK* acting as a Molecule in mkp1_feedback_effects Network
| Name | Accession Name | Pathway Name | Initial Conc.
(uM) | Volume
(fL) | Buffered | | MAPK* | mkp1_feedback_
effects
Accession No. : 4 | Shared_Object_
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
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
| mkp1_feedback_
effects
Accession No. : 4 | Shared_Object_
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*
| mkp1_feedback_
effects
Accession No. : 4 | Shared_Object_
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
| mkp1_feedback_
effects
Accession No. : 4 | Shared_Object_
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
| mkp1_feedback_
effects
Accession No. : 4 | Shared_Object_
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
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 | mkp1_feedback_
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 | mkp1_feedback_
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. |
** This is a trasport reation between compartments of different volumes. Therefore Kd is not applicable. Please Note Kf, Kb units are in number of molecules instead of concentration
| Database compilation and code copyright (C) 2022, Upinder S. Bhalla and NCBS/TIFR
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