| |
Name | Pathway Name /
Pathway No. | Accession
Type | Initial
Conc.
(uM) | Volume
(fL) | Buffered | Sum Total Of |
| 1 | IP5(12456) | MIPP
Pathway No. 120 | Network | 2.4 | 1000 | Yes | - |
| | Inositol(12456)pentakisphosphate Conc = 4% of total InsP5 |
| 2 | total-CaMKII | CaMKII
Pathway No. 121 | Network | 70 | 1000 | Yes | - |
| | This pool is purely here to provide a single, fixed number, which is the total amount of CaMKII. This is used by the autophosphorylation steps to scale down the rates so that the autophosphorylation reactions are independent of CaMKII levels. |
| 3 | AA | PKC
Pathway No. 123 | Network | 50 | 1000 | Yes | - |
| | Arachidonic Acid. This messenger diffuses through membranes as well as cytosolically, has been suggested as a possible retrograde messenger at synapses. |
| 4 | mGluRAntag | Gq
Pathway No. 125 | Network | 0 | 1000 | Yes | - |
| | I implement this as acting only on the Rec-Gq complex, based on a more complete model PLC_Gq48.g which showed that the binding to the receptor alone contributed only a small amount. |
| 5 | Glu | Gq
Pathway No. 125 | Network | 0 | 1000 | Yes | - |
| | 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. Schoepp et al 1990 TIPS 11:508-515 give a range of Glu EC50 from rat brain in the range 120 to 1000 uM. Nicoletti 1986 PNAS 83:1931-1935 and Schoepp and Johnson 1989 J Neurochem 53:1865-1870 give an off time of at least 30 sec. |
| 6 | PC | PLCbeta
Pathway No. 126 | Network | 0 | 1000 | Yes | - |
| | Phosphatidylcholine is the main (around 55%) metabolic product of DAG, follwed by PE (around 25%). Ref is Welsh and Cabot, JCB35:231-245(1987) |
| 7 | PIP2 | PLCbeta
Pathway No. 126 | Network | 150 | 1000 | Yes | - |
| | PIP2 conc: Willars et al; JBC 273 (9) 27.2.98; pp 5037-5046 |
| 8 | inositol | 145_dephos
Pathway No. 128 | Network | 500 | 1000 | Yes | - |
| 9 | bisPP-IP3 | IHP-system
Pathway No. 130 | Network | 0 | 1000 | Yes | - |
| | Bis(diphospho)inositol trisphosphate from Saiardi et al, JBC 275(32); 2000: 24686-92 |
| 10 | ATP | IHP-system
Pathway No. 130 | Network | 2700.05 | 1000 | Yes | - |
| | Conc for mammalian brain from Huang et al, Biochem 37; 1998 |
| 11 | ADP | IHP-system
Pathway No. 130 | Network | 699.995 | 1000 | Yes | - |
| | Conc for mammaliam brain from Huang et al, Biochem 37; 1998 |
| 12 | Ca-ext | CaRegulation
Pathway No. 132 | Network | 4000 | 100000 | Yes | - |
| | Extracell Ca conc = 4 mM Extracell vol assumed 100 X cell vol. It is anyway kept buffered for the purposes of the model, so the concentration won't change. |
| 13 | IP6_ER | MIPP
Pathway No. 120 | Network | 0 | 160 | No | - |
| 14 | IP5(12456)_ER | MIPP
Pathway No. 120 | Network | 0 | 160 | No | - |
| 15 | IP5(13456)_ER | MIPP
Pathway No. 120 | Network | 0 | 160 | No | - |
| 16 | IP4(1456)_ER | MIPP
Pathway No. 120 | Network | 0 | 160 | No | - |
| 17 | IP3(145)_ER | MIPP
Pathway No. 120 | Network | 0 | 160 | No | - |
| 18 | IP4(1345)_ER | MIPP
Pathway No. 120 | Network | 0 | 160 | No | - |
| 19 | MIPP | MIPP
Pathway No. 120 | Network | 0.398 | 160 | No | - |
| | Multiple Inositol Polyphosphate Phosphatase from Nogimori et al, JBC 266(25); 1991: 16499-506 MIPP clustered in ER. Distinct transporters present for cytosolic substrates. Accounts for 30-45% of total 3-phosphatase activity against substrates, hence cytosolic counterparts of this enzyme must be present (as per Chi et al, MCB 20; 2000: 6496-507) |
| 20 | CaMKII | CaMKII
Pathway No. 121 | Network | 70 | 1000 | No | - |
| | Huge concentration of CaMKII. In PSD it is 20-40% of protein, so we assume it is around 2.5% of protein in spine as a whole. This level is so high it is unlikely to matter much if we are off a bit. This comes to about 70 uM. Seen the review: Hanson and Schulman 1992 Ann. Rev. Biuochem 60:559-601 |
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