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Molecule Parameter List for nuc_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. |
nuc_MAPK* acting as a Molecule in mkp1_feedback_effects Network
| Name | Accession Name | Pathway Name | Initial Conc.
(uM) | Volume
(fL) | Buffered | | nuc_MAPK* | mkp1_feedback_
effects
Accession No. : 4 | MAPK
Pathway No. : 35 | 0 | 200 | No | | Cytoplasmic MAPK declines 20%, nuclear MAPK rises 100%. Furuno et al J Immunol 166:4416 (2001) Assume nuc vol 1/5 that of cytoplasm so nuc vol = 2e-16 Note therefore that the concentrations here will be higher for the same number of molecules. |
nuc_MAPK* acting as a Summed Molecule in mkp1_feedback_effects Network
nuc_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 | nuc_MAPK* /
act_
transcription
| mkp1_feedback_
effects
Accession No. : 4 | MAPK
Pathway No. : 35 | 4.00002 | 0.0008 | 4 | explicit E-S complex | Substrate
Nucleotides
Product
MKP1-RNA
| | This is a 'black box' representation of a lot of steps. Constraint provided by determining rate of formation of MKP-1. |
nuc_MAPK* acting as a Product 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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