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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 | MAPK
Pathway No. : 35 | 0.36 | 1000 | No | | Mol wt is 42 KDa. conc is from Sanghera et al JBC 265 pp 52 (1990) They estimate MAPK is 1e-4x total protein, and protein is 15% of cell wt, so MAPK is 1.5e-5g/ml = 0.36uM. Lets use this. Note though that Huang and Ferrell 1996 PNAS 93(19):10078 report 1.2 uM in oocytes. Also note that brain concs may be high. Ortiz et al 1995 J. Neurosci 15(2):1285-1297 report 0.3 ng/ug protein in Cingulate Gyrus and 1.2 ng/ug protein in nucleus accumbens. In hippocampus 270 ng/mg protein for ERK1 and 820 ng/mg protein for ERK 2. If 15% of cell weight is protein, that means that about 300 * 0.15 ng/ul is ERK 1. ie, 45e-9g/1e-6 litre = 45 mg/litre or about 1 uM. For non-neuronal tissues a lower value may be better. |
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 | MAPKK* /
MAPKKtyr | mkp1_feedback_
effects
Accession No. : 4 | MAPK
Pathway No. : 35 | 0.0462963 | 0.15 | 4 | explicit E-S complex | Substrate
MAPK
Product
MAPK-tyr
| | The actual MAPKK is 2 forms from Seger et al JBC 267:20 14373(1992) Vmax = 150nmol/min/mg From Haystead et al FEBS 306(1):17-22 we get Km=46.6nM for at least one of the phosphs. Putting these together: k3=0.15/sec, ratio of 4 to get k2=0.6. k1=0.75/46.6nM=2.7e-5 In terms of Michaelis-Menten rates, Km = 0.046, Vmax = 0.15, ratio = 4. |
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 | | 1 | MKP-1** /
MKP1*-tyr-deph | mkp1_feedback_
effects
Accession No. : 4 | MAPK
Pathway No. : 35 | 0.0666667 | 1 | 4 | Classical Michaelis-Menten
V = Etot.S.Kcat/Km+S | Substrate
MAPK-tyr
Product
MAPK
| | | 3 Feb 2000. Same rates as MKP-1. | | 2 | MKP-1 /
MKP1-tyr-deph | mkp1_feedback_
effects
Accession No. : 4 | Shared_Object_
mkp1_feedback_
effects
Pathway No. : 32 | 0.0666667 | 1 | 4 | Classical Michaelis-Menten
V = Etot.S.Kcat/Km+S | Substrate
MAPK-tyr
Product
MAPK
| | | The original kinetics from Bhalla US and Iyengar R. (1999) Science 283(5400):381-387 have now been modified to obey the k2 = 4 * k3 rule, while keeping kcat and Km fixed. The main constraining data point is the time course of MAPK dephosphorylation, which this model satisfies. See Charles CH, Sun H, Lau LF, Tonks NK. (1993) Proc Natl Acad Sci U S A. 90(11):5292-5296 and Charles CH, Abler AS, Lau LF. (1992) Oncogene 7(1):187-190. Effective Km : 67 nM kcat = 1.43 umol/min/mg. | | 3 | MKP-2 /
MKP2-tyr-deph | mkp1_feedback_
effects
Accession No. : 4 | Shared_Object_
mkp1_feedback_
effects
Pathway No. : 32 | 0.0666667 | 1 | 4 | explicit E-S complex | Substrate
MAPK-tyr
Product
MAPK
| | | 22 Apr 2001: Based on MKP1 parameters. The original kinetics have been modified to obey the k2 = 4 * k3 rule, while keeping kcat and Km fixed. The only constraining data point is the time course of MAPK dephosphorylation, which this model satisfies. The rates are treated as the same as for MKP-1, based on Chu Y, Solski PA, Khosravi-Far R, Der CJ, Kelly K. (1996) J Biol Chem. 271(11):6497-6501. |
| Database compilation and code copyright (C) 2022, Upinder S. Bhalla and NCBS/TIFR
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