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Molecule List for pathway Shared_Object_mTOR_pathway (Pathway Number 1097)
| Name | Initial Conc. (uM) | Volume (fL) | Buffered | ||
| 1 | 40S | 0 | 1000 | No | |
| Activated form of S6 | |||||
| 2 | 40S_basal | 0.0001 | 1000 | No | |
| 3 | 43Scomplex | 0 | 1000 | No | |
| 40S_complex consist of Quaternary complex, mRNA complex, 40S Ribosomes. | |||||
| 4 | 4E-BP_t37_46 | 0 | 1000 | No | |
| 5 | 60S_R | 0.068 | 1000 | Yes | |
| 6 | 80S_ribos_clx | 0 | 1000 | No | |
| 7 | AA | 0.1 | 1000 | Yes | |
| 8 | Arachidonic_Acid | 5 | 1000 | Yes | |
| 9 | Basal_Translation | 0.0002 | 1000 | No | |
| It will contribute to mTOR independent translation. | |||||
| 10 | BDNF | 0.0001 | 1000 | Yes | |
| 11 | Ca | 0.08 | 1000 | No | |
| 12 | CaM-Ca4 | 0 | 1000 | No | |
| 13 | CaMKIII | 0.06 | 1000 | No | |
| 14 | CaMKIII_basal | 0 | 1000 | No | |
| 15 | CaMKIII_CaM-Ca4 | 0 | 1000 | No | |
| 16 | CaMKIII_star | 0 | 1000 | No | |
| 17 | DAG | 11 | 1000 | Yes | |
| 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 DAG-dependent rates in the PKC model to reflect this. | |||||
| 18 | degraded_protein | 0 | 1000 | No | |
| 19 | eEF2 | 0.5 | 1000 | No | |
| 20 | eEFthr-56 | 0 | 1000 | No | |
| 21 | eIF4A | 0.2 | 1000 | No | |
| 22 | eIF4E | 0 | 1000 | No | |
| 23 | eIF4F | 0 | 1000 | No | |
| 24 | eIF4F-mRNA_clx | 0 | 1000 | No | |
| 25 | eIF4G | 0.04 | 1000 | No | |
| 26 | eIF4G-A_clx | 0 | 1000 | No | |
| 27 | Grb2 | 1 | 1000 | No | |
| There is probably a lot of it in the cell: it is also known as Ash (abundant src homology protein I think). Also Waters et al JBC 271:30 18224 1996 say that only a small fraction of cellular Grb is precipitated out when SoS is precipitated. As most of the Sos seems to be associated with Grb2, it would seem like there is a lot of the latter. Say 1 uM. I haven't been able to find a decent.... | |||||
| 28 | MAPK_star | 0 | 1000 | No | |
| 29 | MKP-1 | 0.02 | 1000 | No | |
| MKP-1 dephosphoryates and inactivates MAPK in vivo: Sun et al Cell 75 487-493 1993. Levels of MKP-1 are regulated, and rise in 1 hour. Kinetics from Charles et al PNAS 90:5292-5296 1993. They refer to Charles et al Oncogene 7 187-190 who show that half-life of MKP1/3CH134 is 40 min. 80% deph of MAPK in 20 min Sep 17 1997: CoInit now 0.4x to 0.0032. See parm searches from jun96 on. | |||||
| 30 | mRNA | 0.08 | 1000 | No | |
| 31 | PDK1 | 1 | 1000 | No | |
| 32 | peptide | 0 | 1000 | No | |
| 33 | PIP3 | 0 | 1000 | No | |
| 34 | PKC-active | 0 | 1000 | No | |
| Conc of PKC in brain is about 1 uM (?) | |||||
| 35 | PLCg_basal | 0.0007 | 1000 | No | |
| 36 | PLC_g | 0.1 | 1000 | No | |
| 37 | PLC_g_star | 0 | 1000 | No | |
| 38 | PP2A | 0.15 | 1000 | No | |
| Protein Phosphatase | |||||
| 39 | PPhosphatase2A | 1 | 1000 | No | |
| 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. | |||||
| 40 | protein | 0 | 1000 | No | |
| 41 | PTEN | 0.27 | 1000 | No | |
| 42 | rad_AA | 0 | 1000 | No | |
| 43 | rad_deg_pro | 0 | 1000 | No | |
| 44 | rad_peptide | 0 | 1000 | No | |
| 45 | rad_protein | 0 | 1000 | No | |
| 46 | Ras-GTP_PI3K | 0 | 1000 | No | |
| 47 | Rheb-GDP | 0 | 1000 | No | |
| 48 | Rheb-GTP | 1 | 1000 | No | |
| 49 | S6K_basal | 0.001 | 1000 | No | |
| 50 | S6K_thr-252 | 0 | 1000 | No | |
| 51 | Shc_star | 0 | 1000 | No | |
| 52 | Shc_star.Sos.Grb2 | 0 | 1000 | No | |
| 53 | TOR_Rheb-GTP_clx | 0 | 1000 | No | |
| 54 | Translation_clx | 0 | 1000 | No | |
| 55 | TSC1-TSC2 | 1 | 1000 | No | |
Summed Molecule List
| Target | Inputs | |
| 1 | PKC-active | PKC-DAG-AA_star star PKC-Ca-AA_star star PKC-basal_star PKC-AA_star | Conc of PKC in brain is about 1 uM (?) |
| Pathway Detail | Molecule List | Enzyme List | Reaction List |