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Reaction List for pathway MAPK (Pathway Number 35)

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 reactions is not considered.
  Name KfKbKdtauSubstrateProduct
1 Basal_
transcription		0
(s^-1)		0
(s^-1)		--Nucleotides
MKP1-RNA
  This is just a basal rate of MKP-1 transcription scaled to give reasonable basal levels of the MKP-1.
2 MKP-1**dephosph0.0001
(s^-1)		0
(s^-1)		--MKP-1**
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.
3 MKP-1*dephosph0.0001
(s^-1)		0
(s^-1)		--MKP-1-ser359*
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
4 MKP1_synth0.002
(s^-1)		0
(s^-1)		Not applicable**-MKP1-RNA
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.
5 translocation0.01
(#^-1 s^-1)		0.005
(s^-1)		Not applicable**-MAPK*
MAPK*
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.
6 turnover_MKP10.0004
(s^-1)		0
(s^-1)		--MKP-1
Ubiquitination
  Rate of turnover of non-phosph form of MKP1 is from Brondello et al Science 286:2514 1999. Tau is about 45 min.
7 turnover_MKP1*0.0001
(s^-1)		0
(s^-1)		--MKP-1-ser359*
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.
8 turnover_MKP1**0.0001
(s^-1)		0
(s^-1)		--MKP-1**
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.
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