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Accession Type:
Network
Ajay_Bhalla_
2004_PKM_MKP3_
Tuning
Shared_Object_
Ajay_Bhalla_
2004_PKM_MKP3_
Tuning
 Molecule
 Enzyme
 Reaction
PKC
PLA2
PLCbeta
Ras
Gq
MAPK
EGFR
Sos
PLC_g
CaMKII
CaM
PP1
PP2B
PKA
AC
MKP3
PKM

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Molecule List for pathway Shared_Object_Ajay_Bhalla_2004_PKM_MKP3_Tuning (Pathway Number 329)

 Name Initial Conc. (uM) Volume (fL) Buffered
1AA01.5No
2BetaGamma01.5No
    These exist in a nebulous sense in this model, basically only to balance the conservation equations. The details of their reassociation with G-GDP are not modeled Resting level =0.0094, stim level =.0236 from all42.g ish.
3Ca0.081.5No
4CaM(Ca)n-CaNAB01.5No
5CaM-Ca301.5No
6CaM-Ca401.5No
7CaM-TR2-Ca201.5No
    This is the intermediate where the TR2 end (the high-affinity end) has bound the Ca but the TR1 end has not.
8cAMP01.5No
    The conc of this has been a problem. Schaecter and Benowitz use 50 uM, but Shinomura et al have < 5. So I have altered the cAMP-dependent rates in the PKA model to reflect this.
9CaNAB-Ca401.5No
10Ca_input0.081.5No
11DAG01.5No
12G*GDP01.5No
13G*GTP01.5No
    Activated G protein. Berstein et al indicate that about 20-40% of the total Gq alpha should bind GTP at steady stim. This sim gives more like 65%.
14Glu01.5Yes
    Varying the amount of (steady state) glu between .01 uM and up, the final amount of G*GTP complex does not change much. This means that the system should be reasonably robust wr to the amount of glu in the synaptic cleft. It would be nice to know how fast it is removed.
15Gs-alpha01.5No
16IP30.731.5No
    Peak IP3 is perhaps 15 uM, basal <= 0.2 uM.
17MAPK*01.5No
18PIP2101.5Yes
19PKA-active01.5No
20PKC-active0.09341.5No
21PP1-active1.81.5No
    Cohen et al Meth Enz 159 390-408 is main source of info conc = 1.8 uM
22PP2A0.121.5No
23PPhosphatase2A11.5No
    Refs: Pato et al Biochem J 293:35-41(93); Takai&Mieskes Biochem J 275:233-239 k1=1.46e-4, k2=1000,k3=250. these use kcat values for calponin. Also, units of kcat may be in min! revert to Vmax base: k3=6, k2=25,k1=3.3e-6 or 6,6,1e-6 CoInit assumed 0.1 uM. See NOTES for MAPK_Ras50.g. CoInit now 0.08 Sep 17 1997: Raise CoInt 1.4x to 0.224, see parm searches from jun 96 on.
24Shc*.Sos.Grb201.5No
25temp-PIP22.51.5Yes
    This isn't explicitly present in the M&L model, but is obviously needed. I assume its conc is fixed at 1uM for now, which is a bit high. PLA2 is stim 7x by PIP2 @ 0.5 uM (Leslie and Channon BBA 1045:261(1990) Leslie and Channon say PIP2 is present at 0.1 - 0.2mol% range in membs, which comes to 50 nM. Ref is Majerus et al Cell 37 pp 701-703 1984 Lets use a lower level of 30 nM, same ref....

Summed Molecule List

  Target Inputs
1 CaM(Ca)n-CaNABCaMCa4-CaNAB
CaMCa3-CaNAB
CaMCa2-CANAB
2 PKC-activePKC-Ca-memb*
PKC-DAG-memb*
PKM-zeta


Pathway Details  Molecule List   Enzyme List   Reaction List  


Database compilation and code copyright (C) 2022, Upinder S. Bhalla and NCBS/TIFR
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