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Molecule Parameter List for MKP1-RNA | 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. |
MKP1-RNA acting as a Molecule in mkp1_feedback_effects Network
| Name | Accession Name | Pathway Name | Initial Conc.
(uM) | Volume
(fL) | Buffered | | MKP1-RNA | mkp1_feedback_
effects
Accession No. : 4 | MAPK
Pathway No. : 35 | 0.0001 | 200 | No | | The MKP-1 RNA is treated as the rate-limiting quantity for synthesis of MKP-1. |
MKP1-RNA 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 | 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. |
MKP1-RNA 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 | | MKP1_synth | mkp1_feedback_
effects
Accession No. : 4 | MAPK
Pathway No. : 35 | 0.002
(s^-1) | 0
(s^-1) | Not applicable** | - | Substrate
MKP1-RNA
Product
MKP-1
| | This is a 'black box' approximation to the process of translation. I assume that there is unity stoichiometry, that is, a single RNA gives a single protein. This is obviously wrong, but since the RNA level itself is just a ratio against baseline, the conversion factor is absorbed there. |
** 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
MKP1-RNA 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 | Basal_
transcription | mkp1_feedback_
effects
Accession No. : 4 | MAPK
Pathway No. : 35 | 0
(s^-1) | 0
(s^-1) | - | - | Substrate
Nucleotides
Product
MKP1-RNA
| | This is just a basal rate of MKP-1 transcription scaled to give reasonable basal levels of the MKP-1. |
| Database compilation and code copyright (C) 2022, Upinder S. Bhalla and NCBS/TIFR
This Copyright is applied to ensure that the contents of this database remain freely available. Please see FAQ for details. |
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