| |
Reaction
Name | Pathway Name /
Pathway No. | Kf | Kb | Kd | tau | Reagents |
| 1 | translocation | MAPK
Pathway No. 35 | 0.01
(#^-1 s^-1) | 0.005
(s^-1) | Not applicable** | - | Substrate:
MAPK*
MAPK*
Products:
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. | | 2 | turnover_MKP1 | MAPK
Pathway No. 35 | 0.0004
(s^-1) | 0
(s^-1) | - | - | Substrate:
MKP-1
Products:
Ubiquitination
|
| Rate of turnover of non-phosph form of MKP1 is from Brondello et al Science 286:2514 1999. Tau is about 45 min. | | 3 | turnover_MKP1** | MAPK
Pathway No. 35 | 0.0001
(s^-1) | 0
(s^-1) | - | - | Substrate:
MKP-1**
Products:
Ubiquitination
|
| Rate of turnover of phosph form of MKP1 is from Brondello et al Science 286:2514 1999. Tau is about 150 min though it is not a clean exponential falloff. | | 4 | turnover_MKP1* | MAPK
Pathway No. 35 | 0.0001
(s^-1) | 0
(s^-1) | - | - | Substrate:
MKP-1-ser359*
Products:
Ubiquitination
|
| Rate of turnover of phosph form of MKP1 is from Brondello et al Science 286:2514 1999. Tau is about 150 min though it is not a clean exponential falloff. | | 5 | MKP-1*dephosph | MAPK
Pathway No. 35 | 0.0001
(s^-1) | 0
(s^-1) | - | - | Substrate:
MKP-1-ser359*
Products:
MKP-1
|
| 24 Apr 2K: Based on 12 Feb 2K: Scaled up 10x so kf=0.01, kb=0 13 Apr 2001: MKP1* Goes down too fast, equil amount too small. Note that tau for turnover is 150 min. Doesn't make sense to have this tau be so much less. Go for 1e-4 | | 6 | MKP-1**dephosph | MAPK
Pathway No. 35 | 0.0001
(s^-1) | 0
(s^-1) | - | - | Substrate:
MKP-1**
Products:
MKP-1-ser359*
|
| 24 Apr 2K, based on 12 Feb 2K: Scaled up 10x to kf=0.01, kb=0 13 Apr 2001. Slowing down to 0.0001 to match turnover rates. | | 7 | MKP1_synth | MAPK
Pathway No. 35 | 0.002
(s^-1) | 0
(s^-1) | Not applicable** | - | Substrate:
MKP1-RNA
Products:
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. | | 8 | Basal_
transcription | MAPK
Pathway No. 35 | 0
(s^-1) | 0
(s^-1) | - | - | Substrate:
Nucleotides
Products:
MKP1-RNA
|
| This is just a basal rate of MKP-1 transcription scaled to give reasonable basal levels of the MKP-1. |
and 
color.
